matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

abcrf

Version: 1.9
GitHub: NA
Source code: https://github.com/cran/abcrf
Date/Publication: 2022-08-09 15:30:19 UTC
Number of recursive dependencies: 39

Run revdepcheck::revdep_details(, "abcrf") for more info

checking installed package size ... NOTE installed size is 8.7Mb sub-directories of 1Mb or more: data 2.6Mb libs 5.9Mb

airpart

Version: 1.14.0
GitHub: https://github.com/Wancen/airpart
Source code: https://github.com/cran/airpart
Date/Publication: 2024-10-29
Number of recursive dependencies: 175

Run revdepcheck::revdep_details(, "airpart") for more info

checking Rd files ... NOTE checkRd: (-1) cellQC.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) cellQC.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) cellQC.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) cellQC.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) cellQC.Rd:50-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) cellQC.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) featureQC.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) featureQC.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) featureQC.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) featureQC.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) makeSimulatedData.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) makeSimulatedData.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) makeSimulatedData.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summaryAllelicRatio.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summaryAllelicRatio.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summaryAllelicRatio.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly

AlpsNMR

Version: 4.8.0
GitHub: https://github.com/sipss/AlpsNMR
Source code: https://github.com/cran/AlpsNMR
Date/Publication: 2024-10-29
Number of recursive dependencies: 189

Run revdepcheck::revdep_details(, "AlpsNMR") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown Error: processing vignette 'Vig01-introduction-to-alpsnmr.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01-introduction-to-alpsnmr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. --- failed re-building ‘Vig01-introduction-to-alpsnmr.Rmd’

--- re-building ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using rmarkdown Error: processing vignette 'Vig01b-introduction-to-alpsnmr-old-api.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01b-introduction-to-alpsnmr-old-api.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. ... LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’

SUMMARY: processing the following files failed: ‘Vig01-introduction-to-alpsnmr.Rmd’ ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ ‘Vig02-handling-metadata-and-annotations.Rmd’

Error: Vignette re-building failed. Execution halted ```

AMARETTO

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/AMARETTO
Date/Publication: 2024-10-29
Number of recursive dependencies: 154

Run revdepcheck::revdep_details(, "AMARETTO") for more info

checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'get_firehoseData.Rd': get_firehoseData Code: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "https://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "http://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Mismatches in argument default values: Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 1.5Mb doc 2.4Mb
checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Apache License (== 2.0) + file LICENSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘knitr’ A package should be listed in only one of these fields. 'LinkingTo' field is unused: package has no 'src' directory
checking R code for possible problems ... NOTE AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’ AMARETTO_HTMLreport: no visible binding for global variable ‘RegulatorIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’ AMARETTO_HTMLreport: no visible binding for global variable ‘padj’ AMARETTO_HTMLreport: no visible binding for global variable ‘n_Overlapping’ ... GmtFromModules: no visible binding for global variable ‘GeneNames’ HyperGTestGeneEnrichment: no visible binding for global variable ‘i’ HyperGTestGeneEnrichment: no visible binding for global variable ‘j’ read_gct: no visible binding for global variable ‘Description’ Undefined global functions or variables: Color Description GeneNames Genes Geneset Geneset_length ModuleNr Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr n_Overlapping overlap_perc p.value p_value padj q.value value variable
checking data for non-ASCII characters ... NOTE Note: found 152 marked UTF-8 strings

amplican

Version: 1.28.0
GitHub: https://github.com/valenlab/amplican
Source code: https://github.com/cran/amplican
Date/Publication: 2024-10-29
Number of recursive dependencies: 133

Run revdepcheck::revdep_details(, "amplican") for more info

checking installed package size ... NOTE installed size is 17.6Mb sub-directories of 1Mb or more: doc 15.1Mb libs 1.6Mb
checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘get_seq’
checking Rd files ... NOTE checkRd: (-1) amplicanAlign.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:60-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:107-110: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) amplicanPipelineConservative.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:77-78: Lost braces in \itemize; meant \describe ?
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘CrispRVariants’
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'getEventInfo.Rd': ‘ampl_len’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

apollo

Version: 0.3.4
GitHub: NA
Source code: https://github.com/cran/apollo
Date/Publication: 2024-10-01 21:30:08 UTC
Number of recursive dependencies: 78

Run revdepcheck::revdep_details(, "apollo") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 1.3Mb libs 3.3Mb

aroma.affymetrix

Version: 3.2.2
GitHub: https://github.com/HenrikBengtsson/aroma.affymetrix
Source code: https://github.com/cran/aroma.affymetrix
Date/Publication: 2024-02-18 20:40:03 UTC
Number of recursive dependencies: 85

Run revdepcheck::revdep_details(, "aroma.affymetrix") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: R 2.3Mb help 1.1Mb testScripts 1.1Mb

aroma.core

Version: 3.3.1
GitHub: https://github.com/HenrikBengtsson/aroma.core
Source code: https://github.com/cran/aroma.core
Date/Publication: 2024-02-19 08:40:02 UTC
Number of recursive dependencies: 67

Run revdepcheck::revdep_details(, "aroma.core") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

aroma.light

Version: 3.36.0
GitHub: https://github.com/HenrikBengtsson/aroma.light
Source code: https://github.com/cran/aroma.light
Date/Publication: 2024-10-29
Number of recursive dependencies: 6

Run revdepcheck::revdep_details(, "aroma.light") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/rsp/.rspPlugins These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

autonomics

Version: 1.14.6
GitHub: NA
Source code: https://github.com/cran/autonomics
Date/Publication: 2024-11-15
Number of recursive dependencies: 278

Run revdepcheck::revdep_details(, "autonomics") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: doc 3.1Mb

bage

Version: 0.7.4
GitHub: https://github.com/bayesiandemography/bage
Source code: https://github.com/cran/bage
Date/Publication: 2024-08-28 08:10:20 UTC
Number of recursive dependencies: 77

Run revdepcheck::revdep_details(, "bage") for more info

checking installed package size ... NOTE installed size is 91.7Mb sub-directories of 1Mb or more: libs 89.6Mb

bahc

Version: 0.3.0
GitHub: NA
Source code: https://github.com/cran/bahc
Date/Publication: 2020-09-21 16:40:02 UTC
Number of recursive dependencies: 2

Run revdepcheck::revdep_details(, "bahc") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

Banksy

Version: 1.2.0
GitHub: https://github.com/prabhakarlab/Banksy
Source code: https://github.com/cran/Banksy
Date/Publication: 2024-10-29
Number of recursive dependencies: 265

Run revdepcheck::revdep_details(, "Banksy") for more info

checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: doc 3.7Mb help 1.4Mb
checking Rd files ... NOTE checkRd: (-1) computeBanksy.Rd:81: Lost braces in \itemize; meant \describe ?

BASiCS

Version: 2.18.0
GitHub: https://github.com/catavallejos/BASiCS
Source code: https://github.com/cran/BASiCS
Date/Publication: 2024-10-29
Number of recursive dependencies: 198

Run revdepcheck::revdep_details(, "BASiCS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 14.7Mb sub-directories of 1Mb or more: data 2.0Mb doc 1.6Mb libs 10.1Mb

BatchQC

Version: 2.2.0
GitHub: https://github.com/wejlab/BatchQC
Source code: https://github.com/cran/BatchQC
Date/Publication: 2024-10-29
Number of recursive dependencies: 235

Run revdepcheck::revdep_details(, "BatchQC") for more info

checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: data 1.0Mb doc 6.4Mb

BayesfMRI

Version: 0.3.11
GitHub: https://github.com/mandymejia/BayesfMRI
Source code: https://github.com/cran/BayesfMRI
Date/Publication: 2023-12-18 08:50:21 UTC
Number of recursive dependencies: 120

Run revdepcheck::revdep_details(, "BayesfMRI") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE installed size is 23.1Mb sub-directories of 1Mb or more: libs 22.7Mb

BayesianPlatformDesignTimeTrend

Version: 1.2.3
GitHub: https://github.com/ZXW834/BayesianPlatformDesignTimeTrend
Source code: https://github.com/cran/BayesianPlatformDesignTimeTrend
Date/Publication: 2023-12-07 11:00:02 UTC
Number of recursive dependencies: 120

Run revdepcheck::revdep_details(, "BayesianPlatformDesignTimeTrend") for more info

checking installed package size ... NOTE installed size is 126.6Mb sub-directories of 1Mb or more: data 1.3Mb help 1.9Mb libs 122.3Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

bcf

Version: 2.0.2
GitHub: NA
Source code: https://github.com/cran/bcf
Date/Publication: 2024-02-27 17:30:05 UTC
Number of recursive dependencies: 98

Run revdepcheck::revdep_details(, "bcf") for more info

checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: libs 8.8Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

bingat

Version: 1.3
GitHub: NA
Source code: https://github.com/cran/bingat
Date/Publication: 2017-07-05 18:30:37 UTC
Number of recursive dependencies: 32

Run revdepcheck::revdep_details(, "bingat") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘genalg’

BioNERO

Version: 1.14.0
GitHub: https://github.com/almeidasilvaf/BioNERO
Source code: https://github.com/cran/BioNERO
Date/Publication: 2024-10-29
Number of recursive dependencies: 175

Run revdepcheck::revdep_details(, "BioNERO") for more info

checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: data 2.2Mb doc 4.6Mb
checking Rd files ... NOTE checkRd: (-1) SFT_fit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SFT_fit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) exp2grn.Rd:28: Lost braces 28 | say (ij), is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.} | ^ checkRd: (-1) grn_combined.Rd:27: Lost braces 27 | is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.1.} | ^ checkRd: (-1) grn_infer.Rd:39: Lost braces 39 | is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.1.} | ^

biscuiteer

Version: 1.20.0
GitHub: https://github.com/trichelab/biscuiteer
Source code: https://github.com/cran/biscuiteer
Date/Publication: 2024-10-29
Number of recursive dependencies: 221

Run revdepcheck::revdep_details(, "biscuiteer") for more info

checking whether package ‘biscuiteer’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.4Mb
checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found.
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’ See the note in ?`:::` about the use of this operator.

blackbox

Version: 1.1.46
GitHub: NA
Source code: https://github.com/cran/blackbox
Date/Publication: 2023-12-08 03:20:11 UTC
Number of recursive dependencies: 60

Run revdepcheck::revdep_details(, "blackbox") for more info

checking installed package size ... NOTE installed size is 14.3Mb sub-directories of 1Mb or more: libs 13.7Mb

BloodGen3Module

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/BloodGen3Module
Date/Publication: 2024-10-29
Number of recursive dependencies: 170

Run revdepcheck::revdep_details(, "BloodGen3Module") for more info

checking whether package ‘BloodGen3Module’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘SummarizedExperiment::rowRanges’ by ‘matrixStats::rowRanges’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘SummarizedExperiment::start’ by ‘stats::start’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘SummarizedExperiment::end’ by ‘stats::end’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘matrixStats::rowRanges’ by ‘SummarizedExperiment::rowRanges’ when loading ‘BloodGen3Module’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BloodGen3Module/new/BloodGen3Module.Rcheck/00install.out’ for details.
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.

bmm

Version: 1.0.1
GitHub: https://github.com/venpopov/bmm
Source code: https://github.com/cran/bmm
Date/Publication: 2024-05-27 18:10:05 UTC
Number of recursive dependencies: 131

Run revdepcheck::revdep_details(, "bmm") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’

bnbc

Version: 1.28.0
GitHub: https://github.com/hansenlab/bnbc
Source code: https://github.com/cran/bnbc
Date/Publication: 2024-10-29
Number of recursive dependencies: 145

Run revdepcheck::revdep_details(, "bnbc") for more info

checking installed package size ... NOTE installed size is 8.4Mb sub-directories of 1Mb or more: cooler 2.9Mb data 2.4Mb libs 1.6Mb

bnclassify

Version: 0.4.8
GitHub: https://github.com/bmihaljevic/bnclassify
Source code: https://github.com/cran/bnclassify
Date/Publication: 2024-03-13 12:20:02 UTC
Number of recursive dependencies: 101

Run revdepcheck::revdep_details(, "bnclassify") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘methods.Rmd’ using rmarkdown --- finished re-building ‘methods.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown --- finished re-building ‘overview.Rmd’

--- re-building ‘usage.rmd’ using rmarkdown ! Undefined control sequence. ...

Error: processing vignette 'usage.rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/bnclassify/new/bnclassify.Rcheck/vign_test/bnclassify/vignettes/usage.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See usage.log for more info. --- failed re-building ‘usage.rmd’

SUMMARY: processing the following file failed: ‘usage.rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: libs 10.7Mb

bnem

Version: 1.14.0
GitHub: https://github.com/MartinFXP/bnem
Source code: https://github.com/cran/bnem
Date/Publication: 2024-10-29
Number of recursive dependencies: 172

Run revdepcheck::revdep_details(, "bnem") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rmarkdown’ All declared Imports should be used.

brms

Version: 2.22.0
GitHub: https://github.com/paul-buerkner/brms
Source code: https://github.com/cran/brms
Date/Publication: 2024-09-23 13:00:29 UTC
Number of recursive dependencies: 203

Run revdepcheck::revdep_details(, "brms") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 8.8Mb sub-directories of 1Mb or more: R 3.8Mb doc 3.6Mb

BSgenome

Version: 1.74.0
GitHub: https://github.com/Bioconductor/BSgenome
Source code: https://github.com/cran/BSgenome
Date/Publication: 2024-10-29
Number of recursive dependencies: 83

Run revdepcheck::revdep_details(, "BSgenome") for more info

checking examples ... ERROR ``` Running examples in ‘BSgenome-Ex.R’ failed The error most likely occurred in:

Name: SNPlocs-class

Title: SNPlocs objects

Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs

ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs

OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method

providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName

releaseName,SNPlocs-method referenceGenome

... [1] "UCSC" seqlevelsStyle(snps) # NCBI [1] "NCBI" seqlevelsStyle(my_cds) <- seqlevelsStyle(snps) Warning in download.file(url, destfile, method, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/': FTP status was '400 Unknown Error' Error in download.file(url, destfile, method, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/' Calls: seqlevelsStyle<- ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted ```
checking for missing documentation entries ... WARNING Undocumented code objects: ‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’ ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’ ‘getBatchesByOverlapsFromOnDiskLongTable’ ‘getBatchesBySeqnameFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’ ‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’ ‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’ ‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’ ... generic 'seqinfo' and siglist 'TwobitNamedSequences' generic 'seqnames' and siglist 'OnDiskNamedSequences' generic 'show' and siglist 'OnDiskLongTable' generic 'show' and siglist 'OnDiskLongTable_old' generic 'show' and siglist 'OnDiskNamedSequences' generic 'spatialIndex' and siglist 'OnDiskLongTable' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: R 1.6Mb extdata 5.2Mb
checking dependencies in R code ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’ See the note in ?`:::` about the use of this operator.

BSW

Version: 0.1.1
GitHub: https://github.com/adam-bec/BSW
Source code: https://github.com/cran/BSW
Date/Publication: 2021-03-22 16:20:09 UTC
Number of recursive dependencies: 45

Run revdepcheck::revdep_details(, "BSW") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

bulkAnalyseR

Version: 1.1.0
GitHub: https://github.com/Core-Bioinformatics/bulkAnalyseR
Source code: https://github.com/cran/bulkAnalyseR
Date/Publication: 2022-12-15 12:20:02 UTC
Number of recursive dependencies: 195

Run revdepcheck::revdep_details(, "bulkAnalyseR") for more info

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 2.3Mb extdata 3.4Mb

bumphunter

Version: 1.48.0
GitHub: https://github.com/rafalab/bumphunter
Source code: https://github.com/cran/bumphunter
Date/Publication: 2024-10-29
Number of recursive dependencies: 118

Run revdepcheck::revdep_details(, "bumphunter") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach', 'iterators', 'parallel', 'locfit' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘doParallel:::.options’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE bumphunterEngine: no visible binding for global variable ‘bootstraps’ Undefined global functions or variables: bootstraps

CARBayesST

Version: 4.0
GitHub: https://github.com/duncanplee/CARBayesST
Source code: https://github.com/cran/CARBayesST
Date/Publication: 2023-10-30 16:40:02 UTC
Number of recursive dependencies: 106

Run revdepcheck::revdep_details(, "CARBayesST") for more info

checking installed package size ... NOTE installed size is 12.2Mb sub-directories of 1Mb or more: R 1.0Mb libs 10.0Mb

cardelino

Version: 1.8.0
GitHub: https://github.com/single-cell-genetics/cardelino
Source code: https://github.com/cran/cardelino
Date/Publication: 2024-10-29
Number of recursive dependencies: 152

Run revdepcheck::revdep_details(, "cardelino") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’

CATALYST

Version: 1.30.2
GitHub: https://github.com/HelenaLC/CATALYST
Source code: https://github.com/cran/CATALYST
Date/Publication: 2024-12-02
Number of recursive dependencies: 223

Run revdepcheck::revdep_details(, "CATALYST") for more info

checking installed package size ... NOTE installed size is 15.7Mb sub-directories of 1Mb or more: data 3.1Mb doc 11.2Mb
checking Rd files ... NOTE checkRd: (-1) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotDiffHeatmap.Rd:88: Lost braces in \itemize; meant \describe ?

causalOT

Version: 1.0.2
GitHub: NA
Source code: https://github.com/cran/causalOT
Date/Publication: 2024-02-18 22:50:08 UTC
Number of recursive dependencies: 105

Run revdepcheck::revdep_details(, "causalOT") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rkeops’
checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: R 1.6Mb libs 6.7Mb

CDI

Version: 1.4.0
GitHub: https://github.com/jichunxie/CDI
Source code: https://github.com/cran/CDI
Date/Publication: 2024-10-29
Number of recursive dependencies: 174

Run revdepcheck::revdep_details(, "CDI") for more info

checking Rd files ... NOTE checkRd: (-1) one_batch_matrix_label_df.Rd:18: Lost braces; missing escapes or markup? 18 | be {2,3,..., 7}. | ^ checkRd: (-1) two_batch_matrix_label_df.Rd:20: Lost braces; missing escapes or markup? 20 | The number of clusters are set to be {2,3,..., 10}. | ^

celda

Version: 1.22.0
GitHub: https://github.com/campbio/celda
Source code: https://github.com/cran/celda
Date/Publication: 2024-10-29
Number of recursive dependencies: 391

Run revdepcheck::revdep_details(, "celda") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘singleCellTK’
checking installed package size ... NOTE installed size is 15.5Mb sub-directories of 1Mb or more: R 1.0Mb doc 3.5Mb libs 10.2Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking Rd files ... NOTE checkRd: (-1) semiPheatmap.Rd:319-323: Lost braces 319 | callback = function(hc, mat) { | ^

CelliD

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/CelliD
Date/Publication: 2024-10-29
Number of recursive dependencies: 282

Run revdepcheck::revdep_details(, "CelliD") for more info

checking whether package ‘CelliD’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘data.table::shift’ by ‘tictoc::shift’ when loading ‘CelliD’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/CelliD/new/CelliD.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: doc 3.4Mb libs 3.6Mb

cellmigRation

Version: 1.14.0
GitHub: https://github.com/ocbe-uio/cellmigRation
Source code: https://github.com/cran/cellmigRation
Date/Publication: 2024-10-29
Number of recursive dependencies: 137

Run revdepcheck::revdep_details(, "cellmigRation") for more info

checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'fixDA.Rd': ‘object’

Documented arguments not in \usage in Rd file 'fixFM1.Rd': ‘object’

Documented arguments not in \usage in Rd file 'fixFM2.Rd': ‘object’

Documented arguments not in \usage in Rd file 'fixFM3.Rd': ... ‘x’

Documented arguments not in \usage in Rd file 'innerBondRaster.Rd': ‘i’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

cellWise

Version: 2.5.3
GitHub: NA
Source code: https://github.com/cran/cellWise
Date/Publication: 2023-10-25 13:00:02 UTC
Number of recursive dependencies: 66

Run revdepcheck::revdep_details(, "cellWise") for more info

checking installed package size ... NOTE installed size is 20.2Mb sub-directories of 1Mb or more: data 3.2Mb doc 2.0Mb libs 14.5Mb

CEMiTool

Version: 1.30.0
GitHub: NA
Source code: https://github.com/cran/CEMiTool
Date/Publication: 2024-10-29
Number of recursive dependencies: 196

Run revdepcheck::revdep_details(, "CEMiTool") for more info

checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: data 3.1Mb doc 2.4Mb extdata 2.8Mb
checking R code for possible problems ... NOTE flip_vector: no visible global function definition for ‘setNames’ select_genes: no visible global function definition for ‘var’ get_hubs,CEMiTool : <anonymous>: no visible global function definition for ‘head’ get_merged_mods,CEMiTool: no visible global function definition for ‘as.dist’ get_mods,CEMiTool: no visible global function definition for ‘as.dist’ get_phi,CEMiTool: no visible global function definition for ‘tail’ get_phi,CEMiTool: no visible global function definition for ‘head’ mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’ ... save_plots,CEMiTool: no visible global function definition for ‘dev.off’ Undefined global functions or variables: ..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist head modules num_genes setNames tail var Consider adding importFrom("grDevices", "dev.off") importFrom("stats", "as.dist", "dist", "setNames", "var") importFrom("utils", "data", "head", "tail") to your NAMESPACE file.

ChAMP

Version: 2.36.0
GitHub: NA
Source code: https://github.com/cran/ChAMP
Date/Publication: 2024-10-29
Number of recursive dependencies: 253

Run revdepcheck::revdep_details(, "ChAMP") for more info

checking whether package ‘ChAMP’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ChAMP/new/ChAMP.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.
checking Rd \usage sections ... WARNING ``` Duplicated \argument entries in Rd file 'champ.SVD.Rd': ‘Rplot’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db', 'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 1.9Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rmarkdown’ A package should be listed in only one of these fields.
checking whether startup messages can be suppressed ... NOTE ``` No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'prettydoc' All declared Imports should be used. Package in Depends field not imported from: 'DT' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE champ.DMR: possible error in dmrcate(myannotation, min.cpgs = minProbes, lambda = lambda, C = C, mc.cores = cores): unused argument (mc.cores = cores) champ.ebGSEA : gseaWTfn: no visible global function definition for 'wilcox.test' champ.ebGSEA: no visible global function definition for 'stopCluster' champ.norm: no visible global function definition for 'stopCluster' champ.process: no visible global function definition for 'champ.EpiMod' Undefined global functions or variables: champ.EpiMod stopCluster wilcox.test Consider adding importFrom("stats", "wilcox.test") to your NAMESPACE file.

ChemoSpec2D

Version: 0.5.0
GitHub: https://github.com/bryanhanson/ChemoSpec2D
Source code: https://github.com/cran/ChemoSpec2D
Date/Publication: 2021-10-11 07:40:38 UTC
Number of recursive dependencies: 100

Run revdepcheck::revdep_details(, "ChemoSpec2D") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘ChemoSpec2D.Rmd’ using rmarkdown ! Undefined control sequence. l.66 \NewDocumentCommand \citeproctext{}{}

Error: processing vignette 'ChemoSpec2D.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/ChemoSpec2D/new/ChemoSpec2D.Rcheck/vign_test/ChemoSpec2D/vignettes/ChemoSpec2D.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ChemoSpec2D.log for more info. --- failed re-building ‘ChemoSpec2D.Rmd’

SUMMARY: processing the following file failed: ‘ChemoSpec2D.Rmd’

Error: Vignette re-building failed. Execution halted ```

ChIPpeakAnno

Version: 3.40.0
GitHub: NA
Source code: https://github.com/cran/ChIPpeakAnno
Date/Publication: 2024-10-29
Number of recursive dependencies: 230

Run revdepcheck::revdep_details(, "ChIPpeakAnno") for more info

checking examples ... ERROR ``` Running examples in ‘ChIPpeakAnno-Ex.R’ failed The error most likely occurred in:

Name: findEnhancers

Title: Find possible enhancers depend on DNA interaction data

Aliases: findEnhancers

Keywords: misc

** Examples

...

Try to keep the seqname style consistent.

Try to keep the seqname style consistent.

data("myPeakList") findEnhancers(myPeakList[500:1000], annoData, DNAinteractiveData) Error in findEnhancers(myPeakList[500:1000], annoData, DNAinteractiveData) : length(intersect(seqlevelsStyle(peaks), seqlevelsStyle(annoData))) > .... is not TRUE Calls: findEnhancers -> stopifnot Execution halted ```
checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 50 lines of output: INFO [2024-12-29 10:56:45] [1] "serif" INFO [2024-12-29 10:56:45] INFO [2024-12-29 10:56:45] $x INFO [2024-12-29 10:56:45] $x$TF1 INFO [2024-12-29 10:56:45] [1] 3 4 5 INFO [2024-12-29 10:56:45] ... 6. └─BSgenome (local) .local(x, ...) 7. └─BSgenome:::.extractFromBSgenomeMultipleSequences(...) 8. ├─BiocGenerics::lapply(...) 9. └─base::lapply(...)
1. └─BSgenome (local) FUN(X[[i]], ...)
2. └─BSgenome:::.getOneSeqFromBSgenomeMultipleSequences(...)
[ FAIL 1 | WARN 3 | SKIP 6 | PASS 316 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-2.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-3.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-11-1.png" but not available. Warning: call dbDisconnect() when finished working with a connection The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-18-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-19-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/ChIPpeakAnno/new/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-20-1.png" but not available. ... Quitting from lines 1380-1385 [unnamed-chunk-76] (ChIPpeakAnno.Rmd) Error: processing vignette 'ChIPpeakAnno.Rmd' failed with diagnostics: length(intersect(seqlevelsStyle(peaks), seqlevelsStyle(annoData))) > .... is not TRUE --- failed re-building ‘ChIPpeakAnno.Rmd’

SUMMARY: processing the following file failed: ‘ChIPpeakAnno.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 27.9Mb sub-directories of 1Mb or more: R 1.0Mb data 12.6Mb doc 6.8Mb extdata 7.2Mb

cifti

Version: 0.4.5
GitHub: NA
Source code: https://github.com/cran/cifti
Date/Publication: 2018-02-01 23:25:24 UTC
Number of recursive dependencies: 50

Run revdepcheck::revdep_details(, "cifti") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cliqueMS

Version: 1.20.0
GitHub: https://github.com/osenan/cliqueMS
Source code: https://github.com/cran/cliqueMS
Date/Publication: 2024-10-29
Number of recursive dependencies: 166

Run revdepcheck::revdep_details(, "cliqueMS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: libs 7.8Mb

clusterExperiment

Version: 2.26.0
GitHub: https://github.com/epurdom/clusterExperiment
Source code: https://github.com/cran/clusterExperiment
Date/Publication: 2024-10-29
Number of recursive dependencies: 178

Run revdepcheck::revdep_details(, "clusterExperiment") for more info

checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'renameClusters.Rd' ‘object’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking contents of ‘data’ directory ... WARNING Output for data("rsecFluidigm", package = "clusterExperiment"): Search path was changed
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 19.9Mb sub-directories of 1Mb or more: R 1.4Mb data 3.6Mb doc 12.0Mb libs 2.4Mb
checking foreign function calls ... NOTE Foreign function calls to a different package: .C(ape::node_depth, ...) .C(ape::node_depth_edgelength, ...) .C(ape::node_height, ...) .C(ape::node_height_clado, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking Rd files ... NOTE checkRd: (-1) ClusterExperiment-class.Rd:177-180: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterExperiment-class.Rd:181-182: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:71-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:78-84: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:85-94: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:95-97: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:98-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:104-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterFunction-class.Rd:106: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) plottingFunctions.Rd:155-161: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plottingFunctions.Rd:162-167: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plottingFunctions.Rd:173-174: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plottingFunctions.Rd:175-176: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plottingFunctions.Rd:177-178: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceFunctions.Rd:191-192: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceFunctions.Rd:193-194: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) seqCluster.Rd:80-83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) seqCluster.Rd:85-88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) seqCluster.Rd:90-91: Lost braces in \itemize; \value handles \item{}{} directly
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘scRNAseq’, ‘ConsensusClusterPlus’

clustifyr

Version: 1.18.0
GitHub: https://github.com/rnabioco/clustifyr
Source code: https://github.com/cran/clustifyr
Date/Publication: 2024-10-29
Number of recursive dependencies: 156

Run revdepcheck::revdep_details(, "clustifyr") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 1.8Mb doc 1.7Mb help 1.0Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

cmapR

Version: 1.18.0
GitHub: https://github.com/cmap/cmapR
Source code: https://github.com/cran/cmapR
Date/Publication: 2024-10-29
Number of recursive dependencies: 78

Run revdepcheck::revdep_details(, "cmapR") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .dockerignore docs/build/html/.buildinfo These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: data 2.3Mb extdata 4.1Mb
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocManager’ 'library' or 'require' call not declared from: ‘BiocManager’

cna

Version: 3.6.2
GitHub: NA
Source code: https://github.com/cran/cna
Date/Publication: 2024-07-05 09:30:02 UTC
Number of recursive dependencies: 110

Run revdepcheck::revdep_details(, "cna") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘cna.Rnw’ using Sweave Registered S3 method overwritten by 'cna': method from some.data.frame car Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'cna.Rnw' failed with diagnostics: unable to run pdflatex on 'cna.tex' LaTeX errors: ... l.12 \usepackage {float}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'cna.Rnw'

SUMMARY: processing the following file failed: 'cna.Rnw'

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: libs 8.4Mb

CNVScope

Version: 3.7.2
GitHub: https://github.com/jamesdalg/CNVScope
Source code: https://github.com/cran/CNVScope
Date/Publication: 2022-03-30 23:40:08 UTC
Number of recursive dependencies: 206

Run revdepcheck::revdep_details(, "CNVScope") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘HiCseg’
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: doc 3.2Mb extdata 1.7Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'Hmisc' All declared Imports should be used.

coin

Version: 1.4-3
GitHub: NA
Source code: https://github.com/cran/coin
Date/Publication: 2023-09-27 16:10:02 UTC
Number of recursive dependencies: 20

Run revdepcheck::revdep_details(, "coin") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘Implementation.Rnw’ using Sweave Loading required package: survival Loading required package: grid Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation --- finished re-building ‘Implementation.Rnw’

--- re-building ‘LegoCondInf.Rnw’ using Sweave Loading required package: coin ... of the subset pivotality condition Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation --- finished re-building ‘coin.Rnw’

SUMMARY: processing the following file failed: ‘LegoCondInf.Rnw’

Error: Vignette re-building failed. Execution halted ```

cola

Version: 2.12.0
GitHub: https://github.com/jokergoo/cola
Source code: https://github.com/cran/cola
Date/Publication: 2024-10-29
Number of recursive dependencies: 241

Run revdepcheck::revdep_details(, "cola") for more info

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: data 3.2Mb extdata 1.0Mb libs 2.5Mb

compcodeR

Version: 1.42.0
GitHub: https://github.com/csoneson/compcodeR
Source code: https://github.com/cran/compcodeR
Date/Publication: 2024-10-29
Number of recursive dependencies: 203

Run revdepcheck::revdep_details(, "compcodeR") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'rpanel', 'DSS'
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'generateLengthsPhylo.Rd': ‘lengths.lambda’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

ComplexHeatmap

Version: 2.22.0
GitHub: https://github.com/jokergoo/ComplexHeatmap
Source code: https://github.com/cran/ComplexHeatmap
Date/Publication: 2024-10-29
Number of recursive dependencies: 117

Run revdepcheck::revdep_details(, "ComplexHeatmap") for more info

checking package vignettes ... NOTE Package vignettes with \VignetteEngine{} not specifying an engine package: ‘complex_heatmap.rmd’ ‘most_probably_asked_questions.Rmd’ Engines should be specified as \VignetteEngine{PKG::ENG}.

condiments

Version: 1.14.0
GitHub: https://github.com/HectorRDB/condiments
Source code: https://github.com/cran/condiments
Date/Publication: 2024-10-29
Number of recursive dependencies: 209

Run revdepcheck::revdep_details(, "condiments") for more info

checking R code for possible problems ... NOTE .condition_sling: no visible binding for global variable ‘.’ .condition_sling : <anonymous>: no visible binding for global variable ‘.’ .distinct_inputs: no visible binding for global variable ‘Samples’ .distinct_inputs: no visible binding for global variable ‘.’ .fateSelectionTest: no visible binding for global variable ‘pair’ .fateSelectionTest: no visible binding for global variable ‘statistic’ .fateSelectionTest: no visible binding for global variable ‘p.value’ .multiple_samples: no visible binding for global variable ‘p.value’ .progressionTest: no visible binding for global variable ‘lineage’ ... .progressionTest: no visible binding for global variable ‘statistic’ .progressionTest: no visible binding for global variable ‘p.value’ .topologyTest_multipleSamples: no visible binding for global variable ‘p.value’ fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ progressionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ Undefined global functions or variables: . Samples condition lineage p.value pair statistic

conquer

Version: 1.3.3
GitHub: https://github.com/XiaoouPan/conquer
Source code: https://github.com/cran/conquer
Date/Publication: 2023-03-06 08:40:02 UTC
Number of recursive dependencies: 5

Run revdepcheck::revdep_details(, "conquer") for more info

checking installed package size ... NOTE installed size is 24.9Mb sub-directories of 1Mb or more: libs 24.6Mb

consensus

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/consensus
Date/Publication: 2024-10-29
Number of recursive dependencies: 35

Run revdepcheck::revdep_details(, "consensus") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

cophescan

Version: 1.4.1
GitHub: https://github.com/ichcha-m/cophescan
Source code: https://github.com/cran/cophescan
Date/Publication: 2024-06-11 15:20:20 UTC
Number of recursive dependencies: 113

Run revdepcheck::revdep_details(, "cophescan") for more info

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: data 3.5Mb libs 3.1Mb

corrcoverage

Version: 1.2.1
GitHub: https://github.com/annahutch/corrcoverage
Source code: https://github.com/cran/corrcoverage
Date/Publication: 2019-12-06 23:20:12 UTC
Number of recursive dependencies: 73

Run revdepcheck::revdep_details(, "corrcoverage") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.8Mb sub-directories of 1Mb or more: extdata 7.9Mb libs 3.5Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

CRISPRball

Version: 1.2.0
GitHub: https://github.com/j-andrews7/CRISPRball
Source code: https://github.com/cran/CRISPRball
Date/Publication: 2024-10-29
Number of recursive dependencies: 248

Run revdepcheck::revdep_details(, "CRISPRball") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

crlmm

Version: 1.64.0
GitHub: NA
Source code: https://github.com/cran/crlmm
Date/Publication: 2024-10-29
Number of recursive dependencies: 68

Run revdepcheck::revdep_details(, "crlmm") for more info

checking Rd files ... WARNING checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:127: Lost braces 127 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readGenCallOutput.Rd:39: Lost braces 39 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) readIdatFiles.Rd:68: Lost braces 68 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: R 1.2Mb data 2.7Mb
checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
checking whether startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘splines’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .test: no visible global function definition for ‘defineTestSuite’ .test: no visible global function definition for ‘runTestSuite’ .test: no visible global function definition for ‘printTextProtocol’ calculateRBafCNSet : processByChromosome: no visible global function definition for ‘position’ genotypeInf: no visible binding for global variable ‘anno’ krlmm: no visible binding for global variable ‘VGLMparameters’ Undefined global functions or variables: VGLMparameters anno defineTestSuite position printTextProtocol runTestSuite

cSEM

Version: 0.5.0
GitHub: https://github.com/M-E-Rademaker/cSEM
Source code: https://github.com/cran/cSEM
Date/Publication: 2022-11-24 17:50:05 UTC
Number of recursive dependencies: 127

Run revdepcheck::revdep_details(, "cSEM") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rdpack’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup? 24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between | ^

cytofQC

Version: 1.6.0
GitHub: https://github.com/jillbo1000/cytofQC
Source code: https://github.com/cran/cytofQC
Date/Publication: 2024-10-29
Number of recursive dependencies: 230

Run revdepcheck::revdep_details(, "cytofQC") for more info

checking Rd files ... NOTE checkRd: (-1) initialGuess.Rd:20-22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) initialGuess.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) initialGuess.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) initialGuess.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly

cytomapper

Version: 1.18.0
GitHub: https://github.com/BodenmillerGroup/cytomapper
Source code: https://github.com/cran/cytomapper
Date/Publication: 2024-10-29
Number of recursive dependencies: 161

Run revdepcheck::revdep_details(, "cytomapper") for more info

checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: R 1.3Mb doc 5.1Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘CATALYST’

DCATS

Version: 1.4.0
GitHub: NA
Source code: https://github.com/cran/DCATS
Date/Publication: 2024-10-29
Number of recursive dependencies: 211

Run revdepcheck::revdep_details(, "DCATS") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking package subdirectories ... NOTE Found the following CITATION file in a non-standard place: CITATION.cff Most likely ‘inst/CITATION’ should be used instead.
checking R code for possible problems ... NOTE svm_simMat: no visible binding for global variable ‘clusterRes’ Undefined global functions or variables: clusterRes
checking Rd files ... NOTE checkRd: (-1) multinom_EM.Rd:26: Lost braces 26 | \code{simMM}, the input of simMM, code{X}, the input of X, \code{X_prop}, | ^

ddtlcm

Version: 0.2.1
GitHub: https://github.com/limengbinggz/ddtlcm
Source code: https://github.com/cran/ddtlcm
Date/Publication: 2024-04-04 02:32:57 UTC
Number of recursive dependencies: 154

Run revdepcheck::revdep_details(, "ddtlcm") for more info

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: data 7.0Mb

dearseq

Version: 1.18.0
GitHub: https://github.com/borishejblum/dearseq
Source code: https://github.com/cran/dearseq
Date/Publication: 2024-10-29
Number of recursive dependencies: 158

Run revdepcheck::revdep_details(, "dearseq") for more info

checking Rd files ... NOTE checkRd: (-1) plot.dearseq.Rd:12: Lost braces; missing escapes or markup? 12 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^ checkRd: (-1) plot_ord_pvals.Rd:13: Lost braces; missing escapes or markup? 13 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^ checkRd: (-1) summary.dearseq.Rd:15: Lost braces; missing escapes or markup? 15 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^

DelayedMatrixStats

Version: 1.28.0
GitHub: https://github.com/PeteHaitch/DelayedMatrixStats
Source code: https://github.com/cran/DelayedMatrixStats
Date/Publication: 2024-10-29
Number of recursive dependencies: 65

Run revdepcheck::revdep_details(, "DelayedMatrixStats") for more info

checking dependencies in R code ... NOTE Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’ Unexported objects imported by ':::' calls: ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’ ‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’ ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’ ‘DelayedArray:::to_linear_index’ See the note in ?`:::` about the use of this operator.

DELocal

Version: 1.6.0
GitHub: https://github.com/dasroy/DELocal
Source code: https://github.com/cran/DELocal
Date/Publication: 2024-10-29
Number of recursive dependencies: 118

Run revdepcheck::revdep_details(, "DELocal") for more info

checking installed package size ... NOTE installed size is 9.4Mb sub-directories of 1Mb or more: extdata 8.5Mb

DeMixT

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/DeMixT
Date/Publication: 2024-10-29
Number of recursive dependencies: 138

Run revdepcheck::revdep_details(, "DeMixT") for more info

checking whether package ‘DeMixT’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeMixT/new/DeMixT.Rcheck/00install.out’ for details.
checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'DeMixT_preprocessing.Rd': DeMixT_preprocessing Code: function(count.matrix, normal.id, tumor.id, selected.genes = 9000, cutoff_normal_range = c(0.1, 1), cutoff_tumor_range = c(0, 2.5), cutoff_step = 0.2) Docs: function(count.matrix, normal.id, tumor.id, cutoff_normal_range = c(0.1, 1), cutoff_tumor_range = c(0, 2.5), cutoff_step = 0.2) Argument names in code not in docs: selected.genes Mismatches in argument names: Position: 4 Code: selected.genes Docs: cutoff_normal_range Position: 5 Code: cutoff_normal_range Docs: cutoff_tumor_range Position: 6 Code: cutoff_tumor_range Docs: cutoff_step
checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'detect_suspicious_sample_by_hierarchical_clustering_2comp.Rd' ‘labels’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth', 'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 8.8Mb sub-directories of 1Mb or more: data 1.9Mb doc 2.6Mb libs 4.0Mb
checking R code for possible problems ... NOTE DeMixT_GS: no visible global function definition for ‘qchisq’ detect_suspicious_sample_by_hierarchical_clustering_2comp : <anonymous>: no visible global function definition for ‘wilcox.test’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘prcomp’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘dist’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘hclust’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible ... simulate_3comp: no visible global function definition for ‘DataFrame’ Undefined global functions or variables: DataFrame SimpleList abline as.dendrogram dist hclust legend median par points prcomp qchisq rainbow segments wilcox.test Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "legend", "par", "points", "segments") importFrom("stats", "as.dendrogram", "dist", "hclust", "median", "prcomp", "qchisq", "wilcox.test") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘calibrate’

DepecheR

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/DepecheR
Date/Publication: 2024-10-30
Number of recursive dependencies: 124

Run revdepcheck::revdep_details(, "DepecheR") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking compiled code ... NOTE ``` File ‘DepecheR/libs/DepecheR.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘Clusterer.o’ Found ‘srand’, possibly from ‘srand’ (C) Objects: ‘Clusterer.o’, ‘InterfaceUtils.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

DEqMS

Version: 1.24.0
GitHub: https://github.com/yafeng/DEqMS
Source code: https://github.com/cran/DEqMS
Date/Publication: 2024-10-29
Number of recursive dependencies: 101

Run revdepcheck::revdep_details(, "DEqMS") for more info

checking examples ... ERROR ``` Running examples in ‘DEqMS-Ex.R’ failed The error most likely occurred in:

Name: Residualplot

Title: plot the residuals against the number of quantified

peptides/PSMs.

Aliases: Residualplot

** Examples

... eh = ExperimentHub(localHub=TRUE) Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use query(eh, "DEqMS") ExperimentHub with 0 records

snapshotDate(): 2024-12-19

dat.psm = eh[["EH1663"]] Error: File not previously downloaded. Run with 'localHub=FALSE' Execution halted ```

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘matrixStats’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

DESeq2

Version: 1.46.0
GitHub: https://github.com/thelovelab/DESeq2
Source code: https://github.com/cran/DESeq2
Date/Publication: 2024-10-29
Number of recursive dependencies: 192

Run revdepcheck::revdep_details(, "DESeq2") for more info

checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: doc 3.0Mb libs 4.3Mb

detrendr

Version: 0.6.15
GitHub: https://github.com/rorynolan/detrendr
Source code: https://github.com/cran/detrendr
Date/Publication: 2023-03-04 21:20:02 UTC
Number of recursive dependencies: 115

Run revdepcheck::revdep_details(, "detrendr") for more info

checking installed package size ... NOTE installed size is 11.2Mb sub-directories of 1Mb or more: libs 10.0Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DHS.rates

Version: 0.9.2
GitHub: NA
Source code: https://github.com/cran/DHS.rates
Date/Publication: 2024-01-11 15:00:02 UTC
Number of recursive dependencies: 63

Run revdepcheck::revdep_details(, "DHS.rates") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rlang’ All declared Imports should be used.

diffUTR

Version: 1.14.0
GitHub: https://github.com/ETHZ-INS/diffUTR
Source code: https://github.com/cran/diffUTR
Date/Publication: 2024-10-29
Number of recursive dependencies: 151

Run revdepcheck::revdep_details(, "diffUTR") for more info

checking R code for possible problems ... NOTE deuBinPlot: no visible binding for global variable 'x_start' deuBinPlot: no visible binding for global variable 'x_end' deuBinPlot: no visible binding for global variable 'y_start' deuBinPlot: no visible binding for global variable 'y_end' plotTopGenes: no visible binding for global variable 'sizeScore' plotTopGenes: no visible binding for global variable 'q.value' plotTopGenes: no visible binding for global variable 'density.ratio' plotTopGenes: no visible binding for global variable 'geneMeanDensity' plotTopGenes: no visible binding for global variable 'w.abs.coef' plotTopGenes: no visible binding for global variable 'tmp' plotTopGenes: no visible binding for global variable 'name' Undefined global functions or variables: density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef x_end x_start y_end y_start
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘ggbio’

Dino

Version: 1.12.0
GitHub: https://github.com/JBrownBiostat/Dino
Source code: https://github.com/cran/Dino
Date/Publication: 2024-10-29
Number of recursive dependencies: 252

Run revdepcheck::revdep_details(, "Dino") for more info

checking R code for possible problems ... NOTE checkCounts: no visible global function definition for ‘as’ Undefined global functions or variables: as Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

disbayes

Version: 1.1.0
GitHub: https://github.com/chjackson/disbayes
Source code: https://github.com/cran/disbayes
Date/Publication: 2023-09-09 20:10:02 UTC
Number of recursive dependencies: 168

Run revdepcheck::revdep_details(, "disbayes") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘disbayes.Rmd’ using rmarkdown

Quitting from lines 254-259 [unnamed-chunk-6] (disbayes.Rmd) Error: processing vignette 'disbayes.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘disbayes.Rmd’

SUMMARY: processing the following file failed: ‘disbayes.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 118.1Mb sub-directories of 1Mb or more: libs 117.2Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DiscoRhythm

Version: 1.22.0
GitHub: https://github.com/matthewcarlucci/DiscoRhythm
Source code: https://github.com/cran/DiscoRhythm
Date/Publication: 2024-10-29
Number of recursive dependencies: 158

Run revdepcheck::revdep_details(, "DiscoRhythm") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.
checking R code for possible problems ... NOTE discoApp: no visible binding for global variable ‘.discorhythm_ncores’ discoApp: no visible binding for global variable ‘.discorhythm_local’ discoBatch: no visible binding for global variable ‘discoODAres’ Undefined global functions or variables: .discorhythm_local .discorhythm_ncores discoODAres
checking Rd files ... NOTE checkRd: (-1) discoParseMeta.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) discoParseMeta.Rd:29: Escaped LaTeX specials: \_

dmrseq

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/dmrseq
Date/Publication: 2024-10-29
Number of recursive dependencies: 156

Run revdepcheck::revdep_details(, "dmrseq") for more info

checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: data 4.8Mb doc 1.3Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

Doscheda

Version: 1.28.0
GitHub: NA
Source code: https://github.com/cran/Doscheda
Date/Publication: 2024-11-01
Number of recursive dependencies: 157

Run revdepcheck::revdep_details(, "Doscheda") for more info

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 2.1Mb doc 1.8Mb shiny-examples 2.0Mb
checking Rd metadata ... NOTE Invalid package aliases in Rd file 'doscheda.Rd': ‘doscheda-package’

DSWE

Version: 1.8.2
GitHub: https://github.com/TAMU-AML/DSWE-Package
Source code: https://github.com/cran/DSWE
Date/Publication: 2024-02-17 15:40:02 UTC
Number of recursive dependencies: 83

Run revdepcheck::revdep_details(, "DSWE") for more info

checking installed package size ... NOTE installed size is 10.6Mb sub-directories of 1Mb or more: data 2.8Mb libs 7.5Mb

dwp

Version: 1.1
GitHub: NA
Source code: https://github.com/cran/dwp
Date/Publication: 2023-07-01 07:40:05 UTC
Number of recursive dependencies: 74

Run revdepcheck::revdep_details(, "dwp") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GenEst’ ‘expint’ ‘numDeriv’ All declared Imports should be used.

eaf

Version: 2.5.1
GitHub: https://github.com/MLopez-Ibanez/eaf
Source code: https://github.com/cran/eaf
Date/Publication: 2024-08-19 22:20:02 UTC
Number of recursive dependencies: 41

Run revdepcheck::revdep_details(, "eaf") for more info

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

easier

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/easier
Date/Publication: 2024-10-29
Number of recursive dependencies: 194

Run revdepcheck::revdep_details(, "easier") for more info

checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘reannotate_genes’
checking R code for possible problems ... NOTE compute_TF_activity: no visible binding for global variable ‘condition’ compute_TF_activity: no visible binding for global variable ‘score’ Undefined global functions or variables: condition score

EMDomics

Version: 2.36.0
GitHub: NA
Source code: https://github.com/cran/EMDomics
Date/Publication: 2024-10-29
Number of recursive dependencies: 46

Run revdepcheck::revdep_details(, "EMDomics") for more info

checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre] Daniel Schmolze <emd@schmolze.com> [aut, cre]
checking R code for possible problems ... NOTE .cvm_pairwise_q: no visible global function definition for ‘combn’ .cvm_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .emd_gene_pairwise: no visible global function definition for ‘hist’ .emd_pairwise_q: no visible global function definition for ‘combn’ .emd_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .ks_pairwise_table: no visible global function definition for ‘ks.test’ calculate_cvm: no visible global function definition for ‘combn’ calculate_cvm : <anonymous>: no visible global function definition for ... ‘median’ calculate_ks_gene: no visible global function definition for ‘combn’ calculate_ks_gene: no visible global function definition for ‘ks.test’ Undefined global functions or variables: combn hist ks.test median p.adjust Consider adding importFrom("graphics", "hist") importFrom("stats", "ks.test", "median", "p.adjust") importFrom("utils", "combn") to your NAMESPACE file.
checking Rd metadata ... NOTE Invalid package aliases in Rd file 'emdomics-package.Rd': ‘emdomics-package’

ENmix

Version: 1.42.0
GitHub: https://github.com/Bioconductor/ENmix
Source code: https://github.com/cran/ENmix
Date/Publication: 2024-10-29
Number of recursive dependencies: 172

Run revdepcheck::revdep_details(, "ENmix") for more info

checking installed package size ... NOTE installed size is 21.0Mb sub-directories of 1Mb or more: doc 2.3Mb

EnrichedHeatmap

Version: 1.36.0
GitHub: https://github.com/jokergoo/EnrichedHeatmap
Source code: https://github.com/cran/EnrichedHeatmap
Date/Publication: 2024-10-29
Number of recursive dependencies: 96

Run revdepcheck::revdep_details(, "EnrichedHeatmap") for more info

checking installed package size ... NOTE installed size is 16.8Mb sub-directories of 1Mb or more: doc 13.8Mb extdata 1.6Mb libs 1.2Mb

EpiDISH

Version: 2.22.0
GitHub: https://github.com/sjczheng/EpiDISH
Source code: https://github.com/cran/EpiDISH
Date/Publication: 2024-10-29
Number of recursive dependencies: 113

Run revdepcheck::revdep_details(, "EpiDISH") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘centCAB100i.m’ Undocumented data sets: ‘centCAB100i.m’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking data for ASCII and uncompressed saves ... WARNING Warning: large data file saved inefficiently: size ASCII compress centCAB100i.rda 317Kb FALSE none
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

epimutacions

Version: 1.10.0
GitHub: https://github.com/isglobal-brge/epimutacions
Source code: https://github.com/cran/epimutacions
Date/Publication: 2024-10-29
Number of recursive dependencies: 241

Run revdepcheck::revdep_details(, "epimutacions") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘epimutacions.Rmd’ using rmarkdown

Quitting from lines 227-230 [unnamed-chunk-5] (epimutacions.Rmd) Error: processing vignette 'epimutacions.Rmd' failed with diagnostics: Corrupt Cache: sqlite file See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache cache: /c4/home/henrik/.cache/R/ExperimentHub filename: experimenthub.sqlite3 --- failed re-building ‘epimutacions.Rmd’

SUMMARY: processing the following file failed: ‘epimutacions.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking Rd files ... NOTE checkRd: (-1) add_ensemble_regulatory.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_ensemble_regulatory.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_ensemble_regulatory.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) add_ensemble_regulatory.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘CompQuadForm’, ‘car’

epistasisGA

Version: 1.8.0
GitHub: https://github.com/mnodzenski/epistasisGA
Source code: https://github.com/cran/epistasisGA
Date/Publication: 2024-10-29
Number of recursive dependencies: 126

Run revdepcheck::revdep_details(, "epistasisGA") for more info

checking installed package size ... NOTE installed size is 14.6Mb sub-directories of 1Mb or more: doc 4.1Mb libs 9.9Mb
checking Rd files ... NOTE checkRd: (-1) GADGETS.Rd:158: Lost braces 158 | the cluster. See code{run.gadgets} for additional details.} | ^

eseis

Version: 0.8.0
GitHub: NA
Source code: https://github.com/cran/eseis
Date/Publication: 2024-11-24 13:40:02 UTC
Number of recursive dependencies: 61

Run revdepcheck::revdep_details(, "eseis") for more info

checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: libs 3.7Mb
checking whether startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```

EstimationTools

Version: 4.0.0
GitHub: https://github.com/Jaimemosg/EstimationTools
Source code: https://github.com/cran/EstimationTools
Date/Publication: 2022-12-10 07:20:02 UTC
Number of recursive dependencies: 123

Run revdepcheck::revdep_details(, "EstimationTools") for more info

checking Rd files ... NOTE checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup? 138 | $j^{th}$ for all the observations. | ^

evaluomeR

Version: 1.22.0
GitHub: https://github.com/neobernad/evaluomeR
Source code: https://github.com/cran/evaluomeR
Date/Publication: 2024-10-29
Number of recursive dependencies: 117

Run revdepcheck::revdep_details(, "evaluomeR") for more info

checking Rd metadata ... WARNING Rd files with duplicated alias 'getMetricRangeByCluster': ‘getMetricRangeByCluster.Rd’ ‘getMetricsRelevancy.Rd’
checking for missing documentation entries ... WARNING Undocumented code objects: ‘clusterbootWrapper’ ‘standardizeQualityData’ ‘standardizeStabilityData’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'quality.Rd' ‘...’

Undocumented arguments in Rd file 'qualityRange.Rd' ‘...’

Undocumented arguments in Rd file 'qualitySet.Rd' ‘...’

Undocumented arguments in Rd file 'stability.Rd' ... ‘...’

Undocumented arguments in Rd file 'stabilitySet.Rd' ‘...’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc', 'randomForest', 'flexmix', 'RSKC', 'sparcl' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘kableExtra’ All declared Imports should be used. Packages in Depends field not imported from: ‘RSKC’ ‘sparcl’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

EventPointer

Version: 3.14.0
GitHub: https://github.com/jpromeror/EventPointer
Source code: https://github.com/cran/EventPointer
Date/Publication: 2024-10-29
Number of recursive dependencies: 164

Run revdepcheck::revdep_details(, "EventPointer") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’ ‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’ ‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’ ‘SGSeq:::splitCharacterList’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE EventDetection_transcriptome: no visible binding for global variable ‘jj’ SF_Prediction: no visible binding for global variable ‘valueRanking’ SF_Prediction: no visible binding for global variable ‘PSI_table’ annotate2: no visible global function definition for ‘addDummySpliceSites’ annotate2: no visible global function definition for ‘annotatePaths’ annotateFeatures2: no visible global function definition for ‘matchTxFeatures’ callGRseq_parallel: no visible global function definition for ... ‘stopCluster’ fitgl: no visible binding for global variable ‘hist’ myphyper: no visible global function definition for ‘dhyper’ Undefined global functions or variables: PSI_table addDummySpliceSites annotatePaths dhyper hist i ii jj makeCluster matchTxFeatures stopCluster valueRanking Consider adding importFrom("graphics", "hist") importFrom("stats", "dhyper") to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in Rd file 'InternalFunctions.Rd': ‘sort.exons’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

ExCluster

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/ExCluster
Date/Publication: 2024-10-29
Number of recursive dependencies: 50

Run revdepcheck::revdep_details(, "ExCluster") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

ExpHunterSuite

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/ExpHunterSuite
Date/Publication: 2024-11-01
Number of recursive dependencies: 304

Run revdepcheck::revdep_details(, "ExpHunterSuite") for more info

checking examples ... ERROR ``` Running examples in ‘ExpHunterSuite-Ex.R’ failed The error most likely occurred in:

Name: write_functional_report

Title: Write Main DEgenes Hunter functional report This function allows

you to report the Functional analysis.

Aliases: write_functional_report

** Examples

...

processing file: ./func_top_genes.Rmd Error in enrich_density(enrich_obj, attributes = attr_vector, showCategory = n_category) : object 'fortify.internal' not found Calls: write_functional_report ... withRestartList -> withOneRestart -> docall -> do.call -> fun

Quitting from lines 49-77 [ORA_analysis] (functional_report.Rmd) Calling clean_tmpfiles_mod() Execution halted ```
checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: example 2.0Mb extData 3.9Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘EnhancedVolcano’ ‘biomaRt’ ‘ggupset’ All declared Imports should be used. Missing object imported by a ':::' call: ‘enrichplot:::fortify.internal’ Unexported object imported by a ':::' call: ‘clusterProfiler:::enricher_internal’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ``` Found the following possibly unsafe calls: File ‘ExpHunterSuite/R/write_report.R’: assignInNamespace("clean_tmpfiles", clean_tmpfiles_mod, ns = "rmarkdown") assignInNamespace("clean_tmpfiles", clean_tmpfiles_mod, ns = "rmarkdown")

enrich_density: no visible binding for global variable ‘attribute’ enrich_density: no visible binding for global variable ‘Description’ enrich_density: no visible binding for global variable ‘p.adjust’ get_kegg_db_path: no visible binding for global variable ‘root_path’ get_miRNA_ct: no visible binding for global variable ‘sig_pairs’ ... get_sig_genes: no visible binding for global variable ‘genes_tag’ main_degenes_Hunter: no visible binding for global variable ‘Row.names’ write_global_cormit: no visible global function definition for ‘aggregate’ Undefined global functions or variables: Description Row.names aggregate attribute genes_tag p.adjust root_path sig_pairs Consider adding importFrom("stats", "aggregate", "p.adjust") to your NAMESPACE file. ```

ExpressionNormalizationWorkflow

Version: 1.32.0
GitHub: https://github.com/NA/NA
Source code: https://github.com/cran/ExpressionNormalizationWorkflow
Date/Publication: 2024-11-01
Number of recursive dependencies: 111

Run revdepcheck::revdep_details(, "ExpressionNormalizationWorkflow") for more info

checking whether package ‘ExpressionNormalizationWorkflow’ can be installed ... WARNING Found the following significant warnings: Warning: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section Warning: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section Warning: replacing previous import ‘Biobase::rowMedians’ by ‘matrixStats::rowMedians’ when loading ‘ExpressionNormalizationWorkflow’ Warning: replacing previous import ‘Biobase::anyMissing’ by ‘matrixStats::anyMissing’ when loading ‘ExpressionNormalizationWorkflow’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpressionNormalizationWorkflow/new/ExpressionNormalizationWorkflow.Rcheck/00install.out’ for details.
checking Rd files ... WARNING prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section
checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: doc 2.9Mb extdata 4.7Mb
checking R code for possible problems ... NOTE expSetobj: no visible global function definition for ‘new’ pvcAnaly: no visible global function definition for ‘barplot’ pvcAnaly: no visible global function definition for ‘axis’ pvcAnaly: no visible global function definition for ‘text’ pvcaBatchAssess: no visible global function definition for ‘cor’ pvcaBatchAssess: no visible binding for global variable ‘na.omit’ pvcaBatchAssess: no visible global function definition for ‘sigma’ snmAnaly: no visible global function definition for ‘model.matrix’ snmAnaly: no visible global function definition for ‘write.table’ surVarAnaly: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: axis barplot cor model.matrix na.omit new sigma text write.table Consider adding importFrom("graphics", "axis", "barplot", "text") importFrom("methods", "new") importFrom("stats", "cor", "model.matrix", "na.omit", "sigma") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd cross-references ... NOTE Unknown package ‘<pkg>’ in Rd xrefs
checking Rd contents ... NOTE Auto-generated content requiring editing in Rd file 'ExpressionNormalizationWorkflow-package.Rd': \references: ‘~~ Literature or other references for background information ~~’ \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocManager’

expss

Version: 0.11.6
GitHub: https://github.com/gdemin/expss
Source code: https://github.com/cran/expss
Date/Publication: 2023-07-15 21:40:02 UTC
Number of recursive dependencies: 91

Run revdepcheck::revdep_details(, "expss") for more info

checking Rd files ... NOTE checkRd: (-1) as.dichotomy.Rd:94-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.dichotomy.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.dichotomy.Rd:97-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute.Rd:51-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute.Rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute.Rd:57-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) count_if.Rd:121-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) count_if.Rd:124-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) criteria.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) criteria.Rd:164-165: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) write_labelled_csv.Rd:157-160: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:161-164: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:165-166: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:167-169: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:170-172: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:173-175: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:181-182: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:183: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:184-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) write_labelled_csv.Rd:186-191: Lost braces in \itemize; meant \describe ?

extraChIPs

Version: 1.10.0
GitHub: https://github.com/smped/extraChIPs
Source code: https://github.com/cran/extraChIPs
Date/Publication: 2024-10-29
Number of recursive dependencies: 265

Run revdepcheck::revdep_details(, "extraChIPs") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside', 'SummarizedExperiment', 'tibble' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

fastcpd

Version: 0.14.6
GitHub: https://github.com/doccstat/fastcpd
Source code: https://github.com/cran/fastcpd
Date/Publication: 2024-11-05 09:00:02 UTC
Number of recursive dependencies: 110

Run revdepcheck::revdep_details(, "fastcpd") for more info

checking installed package size ... NOTE installed size is 22.9Mb sub-directories of 1Mb or more: doc 2.5Mb help 1.8Mb libs 17.4Mb

FastPCS

Version: 0.1.4
GitHub: NA
Source code: https://github.com/cran/FastPCS
Date/Publication: 2024-03-06 14:40:07 UTC
Number of recursive dependencies: 4

Run revdepcheck::revdep_details(, "FastPCS") for more info

checking installed package size ... NOTE installed size is 13.8Mb sub-directories of 1Mb or more: libs 13.7Mb

FastRCS

Version: 0.0.9
GitHub: NA
Source code: https://github.com/cran/FastRCS
Date/Publication: 2024-03-06 15:30:06 UTC
Number of recursive dependencies: 4

Run revdepcheck::revdep_details(, "FastRCS") for more info

checking installed package size ... NOTE installed size is 30.1Mb sub-directories of 1Mb or more: libs 30.0Mb

FDb.FANTOM4.promoters.hg19

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/FDb.FANTOM4.promoters.hg19
Number of recursive dependencies: 70

Run revdepcheck::revdep_details(, "FDb.FANTOM4.promoters.hg19") for more info

checking package subdirectories ... WARNING Found the following non-empty subdirectories of ‘inst’ also used by R: inst/build It is recommended not to interfere with package subdirectories used by R.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘GenomicFeatures’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘BSgenome.Hsapiens.UCSC.hg19’ ‘matrixStats’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘Biostrings’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘matrixStats:::rowProds’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE oecg: no visible global function definition for ‘is’ oecg: no visible global function definition for ‘seqlengths’ oecg: no visible binding for global variable ‘Hsapiens’ oecg: no visible global function definition for ‘seqlevels’ oecg: no visible global function definition for ‘seqnames’ oecg: no visible global function definition for ‘resize’ oecg: no visible global function definition for ‘start’ oecg: no visible global function definition for ‘start<-’ oecg: no visible global function definition for ‘end’ oecg: no visible global function definition for ‘end<-’ ... oecg: no visible global function definition for ‘letterFrequency’ oecg: no visible global function definition for ‘dinucleotideFrequency’ Undefined global functions or variables: Hsapiens dinucleotideFrequency end end<- getSeq is letterFrequency resize seqlengths seqlevels seqnames start start<- width Consider adding importFrom("methods", "is") importFrom("stats", "end", "start") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

FEAST

Version: 1.14.0
GitHub: https://github.com/suke18/FEAST
Source code: https://github.com/cran/FEAST
Date/Publication: 2024-10-29
Number of recursive dependencies: 228

Run revdepcheck::revdep_details(, "FEAST") for more info

checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: data 3.9Mb doc 1.4Mb
checking R code for possible problems ... NOTE FEAST: multiple local function definitions for ‘bp_fun’ with different formal arguments SC3_Clust: no visible global function definition for ‘metadata’ Visual_Rslt: no visible global function definition for ‘ggbarplot’ Visual_Rslt: no visible global function definition for ‘theme’ Visual_Rslt: no visible global function definition for ‘element_text’ Visual_Rslt: no visible global function definition for ‘ggline’ Visual_Rslt: no visible global function definition for ‘get_palette’ Visual_Rslt: no visible global function definition for ‘scale_y_continuous’ Visual_Rslt: no visible global function definition for ‘guides’ Visual_Rslt: no visible global function definition for ‘guide_legend’ Visual_Rslt: no visible global function definition for ‘ggarrange’ aricode_NMI : entropy: no visible global function definition for ‘sortPairs’ Undefined global functions or variables: element_text get_palette ggarrange ggbarplot ggline guide_legend guides metadata scale_y_continuous sortPairs theme

fipp

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/fipp
Date/Publication: 2021-02-11 10:30:02 UTC
Number of recursive dependencies: 29

Run revdepcheck::revdep_details(, "fipp") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

fishpond

Version: 2.12.0
GitHub: NA
Source code: https://github.com/cran/fishpond
Date/Publication: 2024-10-29
Number of recursive dependencies: 202

Run revdepcheck::revdep_details(, "fishpond") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘allelic.Rmd’ using rmarkdown

Quitting from lines 306-308 [unnamed-chunk-12] (allelic.Rmd) Error: processing vignette 'allelic.Rmd' failed with diagnostics: cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/' --- failed re-building ‘allelic.Rmd’

--- re-building ‘swish.Rmd’ using rmarkdown --- finished re-building ‘swish.Rmd’

SUMMARY: processing the following file failed: ‘allelic.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 5.7Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'samr:::localfdr' 'samr:::predictlocalfdr' 'samr:::qvalue.func' 'samr:::samr.compute.delta.table.seq' See the note in ?`:::` about the use of this operator.

flowCore

Version: 2.18.0
GitHub: NA
Source code: https://github.com/cran/flowCore
Date/Publication: 2024-10-29
Number of recursive dependencies: 118

Run revdepcheck::revdep_details(, "flowCore") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘multiRangeGate’ Undocumented S4 classes: ‘multiRangeGate’ Undocumented S4 methods: generic '%in%' and siglist 'flowFrame,multiRangeGate' generic 'show' and siglist 'multiRangeGate' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CPPFLAGS': -w -Wfatal-errors
checking compiled code ... WARNING ``` File ‘flowCore/libs/flowCore.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Object: ‘fcsTextParse.o’ Found ‘sprintf’, possibly from ‘sprintf’ (C) Object: ‘Logicle.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘HowTo-flowCore.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'HowTo-flowCore.Rnw' failed with diagnostics: unable to run pdflatex on 'HowTo-flowCore.tex' LaTeX errors: ! LaTeX Error: Filecomment.sty' not found.

... l.65 \usepackage {graphicx}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘HowTo-flowCore.Rnw’

SUMMARY: processing the following file failed: ‘HowTo-flowCore.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 18.2Mb sub-directories of 1Mb or more: R 1.2Mb data 5.4Mb extdata 1.1Mb libs 9.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^ checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^ checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$

flowGraph

Version: 1.14.0
GitHub: https://github.com/aya49/flowGraph
Source code: https://github.com/cran/flowGraph
Date/Publication: 2024-10-29
Number of recursive dependencies: 92

Run revdepcheck::revdep_details(, "flowGraph") for more info

checking R code for possible problems ... NOTE get_child: no visible binding for global variable ‘no_cores’ get_paren: no visible binding for global variable ‘no_cores’ ms_psig: no visible binding for global variable ‘meta’ Undefined global functions or variables: meta no_cores
checking Rd files ... NOTE checkRd: (-1) fg_get_graph.Rd:13: Lost braces 13 | A list containing two data frames (\code{v} and ]code{e}) | ^ checkRd: (-1) ggdf.Rd:22: Lost braces 22 | code{ggdf} adds to the data frames \code{v} and \code{e} in slot | ^
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘doParallel’

flowWorkspace

Version: 4.18.0
GitHub: NA
Source code: https://github.com/cran/flowWorkspace
Date/Publication: 2024-10-29
Number of recursive dependencies: 107

Run revdepcheck::revdep_details(, "flowWorkspace") for more info

checking whether package ‘flowWorkspace’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/flowWorkspace/new/flowWorkspace.Rcheck/00install.out’ for details.

* installing *source* package ‘flowWorkspace’ ...
** package ‘flowWorkspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 13.3.1 20240611 (Red Hat 13.3.1-2)’
using C++17
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_API.cpp -o R_API.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
...
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c setCounts.cpp -o setCounts.o
g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -L/usr/local/lib64 -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/lib/libcytolib.a /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/lib/libhdf5_cpp.a /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lRlapack -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lRblas -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lR
/opt/rh/gcc-toolset-13/root/usr/libexec/gcc/x86_64-redhat-linux/13/ld: cannot find -lsz: No such file or directory
/opt/rh/gcc-toolset-13/root/usr/libexec/gcc/x86_64-redhat-linux/13/ld: cannot find -laec: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/share/make/shlib.mk:10: flowWorkspace.so] Error 1
ERROR: compilation failed for package ‘flowWorkspace’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/flowWorkspace/new/flowWorkspace.Rcheck/flowWorkspace’

* installing *source* package ‘flowWorkspace’ ...
** package ‘flowWorkspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 13.3.1 20240611 (Red Hat 13.3.1-2)’
using C++17
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_API.cpp -o R_API.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
...
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
g++ -std=gnu++17 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cpp11/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/RProtoBufLib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c setCounts.cpp -o setCounts.o
g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -L/usr/local/lib64 -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/cytolib/lib/libcytolib.a /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/lib/libhdf5_cpp.a /c4/home/henrik/repositories/matrixStats/revdep/library/flowWorkspace/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lRlapack -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lRblas -L/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/lib -lR
/opt/rh/gcc-toolset-13/root/usr/libexec/gcc/x86_64-redhat-linux/13/ld: cannot find -lsz: No such file or directory
/opt/rh/gcc-toolset-13/root/usr/libexec/gcc/x86_64-redhat-linux/13/ld: cannot find -laec: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/share/make/shlib.mk:10: flowWorkspace.so] Error 1
ERROR: compilation failed for package ‘flowWorkspace’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/flowWorkspace/old/flowWorkspace.Rcheck/flowWorkspace’

footBayes

Version: 0.2.0
GitHub: https://github.com/leoegidi/footbayes
Source code: https://github.com/cran/footBayes
Date/Publication: 2023-08-31 14:50:02 UTC
Number of recursive dependencies: 146

Run revdepcheck::revdep_details(, "footBayes") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyverse’ All declared Imports should be used.

FRASER

Version: 2.2.0
GitHub: https://github.com/gagneurlab/FRASER
Source code: https://github.com/cran/FRASER
Date/Publication: 2024-10-29
Number of recursive dependencies: 216

Run revdepcheck::revdep_details(, "FRASER") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘FRASER.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'FRASER.Rnw' failed with diagnostics: unable to run pdflatex on 'FRASER.tex' LaTeX errors: ! LaTeX Error: Filenowidow.sty' not found.

... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘FRASER.Rnw’

SUMMARY: processing the following file failed: ‘FRASER.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 10.6Mb sub-directories of 1Mb or more: R 1.4Mb doc 2.1Mb libs 6.1Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::selectSome' 'ggbio:::.buildFacetsFromArgs' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE annotateRangesWithTxDb: no visible binding for global variable ‘include’ calculatePadjValuesOnSubset : <anonymous>: no visible binding for global variable ‘gene_rowIdx’ plotVolcano.FRASER: no visible binding for global variable ‘aberrantLabel’ plotVolcano,FraserDataSet: no visible binding for global variable ‘aberrantLabel’ results,FraserDataSet: no visible binding for global variable ‘padjust’ results,FraserDataSet: no visible binding for global variable ‘pValueGene’ results,FraserDataSet: no visible binding for global variable ‘padjustGene’ Undefined global functions or variables: aberrantLabel gene_rowIdx include pValueGene padjust padjustGene

funcharts

Version: 1.6.0
GitHub: https://github.com/unina-sfere/funcharts
Source code: https://github.com/cran/funcharts
Date/Publication: 2024-12-11 15:50:02 UTC
Number of recursive dependencies: 129

Run revdepcheck::revdep_details(, "funcharts") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: libs 4.0Mb

funtooNorm

Version: 1.30.0
GitHub: NA
Source code: https://github.com/cran/funtooNorm
Date/Publication: 2024-10-29
Number of recursive dependencies: 153

Run revdepcheck::revdep_details(, "funtooNorm") for more info

checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in Rd file 'show-SampleSet-method.Rd': ‘...’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MyEndnoteLibrary.bib’ ‘funtooNorm.Rmd’ ‘funtooNorm.pdf’ ‘validationcurvesPCRlow.jpg’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/funtooNorm.Rmd’ (Is a VignetteBuilder field missing?)
checking Rd files ... NOTE checkRd: (-1) fromRGChannelSet.Rd:5: Lost braces; missing escapes or markup? 5 | \title{Creates an object of class SampleSet from a RGChannelSet {minfi}} | ^
checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file?

gap

Version: 1.6
GitHub: https://github.com/jinghuazhao/R
Source code: https://github.com/cran/gap
Date/Publication: 2024-08-27 04:40:06 UTC
Number of recursive dependencies: 199

Run revdepcheck::revdep_details(, "gap") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘shiny’
checking installed package size ... NOTE installed size is 9.1Mb sub-directories of 1Mb or more: doc 7.4Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘car’

gDNAx

Version: 1.4.0
GitHub: https://github.com/functionalgenomics/gDNAx
Source code: https://github.com/cran/gDNAx
Date/Publication: 2024-10-29
Number of recursive dependencies: 113

Run revdepcheck::revdep_details(, "gDNAx") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments’ ‘GenomicAlignments:::.normargParam’ ‘S4Vectors:::makePowersOfTwo’ See the note in ?`:::` about the use of this operator.

GenEst

Version: 1.4.9
GitHub: NA
Source code: https://github.com/cran/GenEst
Date/Publication: 2023-05-25 16:10:03 UTC
Number of recursive dependencies: 67

Run revdepcheck::revdep_details(, "GenEst") for more info

checking Rd files ... NOTE checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup? 70 | covariates included in \code{formula_l} or {formula_s} (required).} | ^

geneticae

Version: 0.4.0
GitHub: https://github.com/jangelini/geneticae
Source code: https://github.com/cran/geneticae
Date/Publication: 2022-07-20 15:40:06 UTC
Number of recursive dependencies: 159

Run revdepcheck::revdep_details(, "geneticae") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’ ‘reshape2’ All declared Imports should be used.

GeneTonic

Version: 3.0.0
GitHub: https://github.com/federicomarini/GeneTonic
Source code: https://github.com/cran/GeneTonic
Date/Publication: 2024-10-29
Number of recursive dependencies: 226

Run revdepcheck::revdep_details(, "GeneTonic") for more info

checking installed package size ... NOTE installed size is 18.3Mb sub-directories of 1Mb or more: data 1.2Mb doc 14.7Mb extdata 1.4Mb

genomation

Version: 1.38.0
GitHub: https://github.com/BIMSBbioinfo/genomation
Source code: https://github.com/cran/genomation
Date/Publication: 2024-10-29
Number of recursive dependencies: 116

Run revdepcheck::revdep_details(, "genomation") for more info

checking whether package ‘genomation’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/genomation/new/genomation.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: doc 3.7Mb extdata 1.2Mb libs 2.0Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ScoreMatrixBin,RleList-GRangesList: no visible binding for global variable ‘id’ ScoreMatrixBin,RleList-GRangesList: no visible global function definition for ‘:=’ Undefined global functions or variables: := id
checking Rd files ... NOTE checkRd: (-1) plotMeta.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:59-60: Lost braces in \itemize; meant \describe ?

GenomAutomorphism

Version: 1.8.0
GitHub: https://github.com/genomaths/GenomAutomorphism
Source code: https://github.com/cran/GenomAutomorphism
Date/Publication: 2024-10-29
Number of recursive dependencies: 88

Run revdepcheck::revdep_details(, "GenomAutomorphism") for more info

checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'AutomorphismList,ANY' generic '[' and siglist 'ListCodonMatrix,ANY' generic '[' and siglist 'MatrixSeq,ANY' generic '[[' and siglist 'AutomorphismList' generic '[[' and siglist 'ListCodonMatrix' generic 'names<-' and siglist 'AutomorphismList' generic 'names<-' and siglist 'MatrixSeq' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.

geocmeans

Version: 0.3.4
GitHub: https://github.com/JeremyGelb/geocmeans
Source code: https://github.com/cran/geocmeans
Date/Publication: 2023-09-12 03:10:02 UTC
Number of recursive dependencies: 199

Run revdepcheck::revdep_details(, "geocmeans") for more info

checking installed package size ... NOTE installed size is 14.3Mb sub-directories of 1Mb or more: extdata 3.0Mb libs 9.0Mb

geva

Version: 1.14.0
GitHub: https://github.com/sbcblab/geva
Source code: https://github.com/cran/geva
Date/Publication: 2024-10-29
Number of recursive dependencies: 125

Run revdepcheck::revdep_details(, "geva") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... --- re-building ‘geva.Rmd’ using rmarkdown Warning in Sys.setlocale("LC_TIME", "English_United States") : OS reports request to set locale to "English_United States" cannot be honored The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-summary-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-grouped-1.png" but not available. ...

Error: processing vignette 'geva.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See geva.log for more info. --- failed re-building ‘geva.Rmd’

SUMMARY: processing the following file failed: ‘geva.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: doc 4.5Mb

ggdmc

Version: 0.2.6.0
GitHub: https://github.com/yxlin/ggdmc
Source code: https://github.com/cran/ggdmc
Date/Publication: 2019-04-29 05:10:03 UTC
Number of recursive dependencies: 50

Run revdepcheck::revdep_details(, "ggdmc") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 10.1Mb sub-directories of 1Mb or more: libs 9.7Mb
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

GGPA

Version: 1.18.0
GitHub: https://github.com/dongjunchung/GGPA
Source code: https://github.com/cran/GGPA
Date/Publication: 2024-10-29
Number of recursive dependencies: 76

Run revdepcheck::revdep_details(, "GGPA") for more info

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 1.7Mb libs 4.9Mb
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘network’ ‘scales’ ‘sna’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking Rd files ... NOTE checkRd: (-1) GGPA-class.Rd:37: Lost braces; missing escapes or markup? 37 | Nodes i and j are connected if the posterior probability of E_{ij} > \code{pCutoff} and the posterior probability of beta_{ij} > \code{betaCI}. } | ^ checkRd: (-1) GGPA-class.Rd:37: Lost braces; missing escapes or markup? 37 | Nodes i and j are connected if the posterior probability of E_{ij} > \code{pCutoff} and the posterior probability of beta_{ij} > \code{betaCI}. } | ^
checking compiled code ... NOTE ``` File ‘GGPA/libs/GGPA.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘3_Param.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

GJRM

Version: 0.2-6.7
GitHub: NA
Source code: https://github.com/cran/GJRM
Date/Publication: 2024-10-25 09:10:13 UTC
Number of recursive dependencies: 62

Run revdepcheck::revdep_details(, "GJRM") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘sp’

glmGamPoi

Version: 1.18.0
GitHub: https://github.com/const-ae/glmGamPoi
Source code: https://github.com/cran/glmGamPoi
Date/Publication: 2024-10-29
Number of recursive dependencies: 153

Run revdepcheck::revdep_details(, "glmGamPoi") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 14.4Mb sub-directories of 1Mb or more: doc 2.5Mb libs 11.4Mb

GPGame

Version: 1.2.0
GitHub: https://github.com/vpicheny/GPGame
Source code: https://github.com/cran/GPGame
Date/Publication: 2022-01-23 16:22:45 UTC
Number of recursive dependencies: 72

Run revdepcheck::revdep_details(, "GPGame") for more info

checking Rd files ... NOTE checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) solve_game.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) solve_game.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) solve_game.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) solve_game.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly

GPUmatrix

Version: 1.0.2
GitHub: NA
Source code: https://github.com/cran/GPUmatrix
Date/Publication: 2024-03-01 09:02:36 UTC
Number of recursive dependencies: 58

Run revdepcheck::revdep_details(, "GPUmatrix") for more info

checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘speedglm’ Missing link or links in Rd file 'LR_GradientConjugate_gpumatrix.Rd': ‘Matrix-class’

Missing link or links in Rd file 'gpu.matrix-class.Rd': ‘Matrix-class’

Missing link or links in Rd file 'gpu.matrix.Rd': ‘Matrix-class’

Missing link or links in Rd file 'matrix-product.Rd': ‘%&%’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```

GRaNIE

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/GRaNIE
Date/Publication: 2024-10-29
Number of recursive dependencies: 306

Run revdepcheck::revdep_details(, "GRaNIE") for more info

checking installed package size ... NOTE installed size is 15.2Mb sub-directories of 1Mb or more: R 1.0Mb doc 13.9Mb
checking R code for possible problems ... NOTE .performIHW: no visible binding for global variable 'adj_pvalue' Undefined global functions or variables: adj_pvalue

graper

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/graper
Date/Publication: 2024-10-29
Number of recursive dependencies: 70

Run revdepcheck::revdep_details(, "graper") for more info

checking whether package ‘graper’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/graper/new/graper.Rcheck/00install.out’ for details.

* installing *source* package ‘graper’ ...
** package ‘graper’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 13.3.1 20240611 (Red Hat 13.3.1-2)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG  -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG  -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include' -I/usr/local/include    -fpic  -g -O2   -c fit_graper.cpp -o fit_graper.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/digamma.hpp:16,
                 from graper_linear_dense_ff.h:2,
...
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/beta.hpp:1638:4: note: candidate: ‘template<class RT1, class RT2, class RT3, class Policy> boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::beta(RT1, RT2, RT3, const Policy&)’
 1638 |    beta(RT1 a, RT2 b, RT3 x, const Policy&)
      |    ^~~~
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/beta.hpp:1638:4: note:   template argument deduction/substitution failed:
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/binomial.hpp:49:61: note:   candidate expects 4 arguments, 3 provided
   49 |          result = static_cast<T>((n - k) * boost::math::beta(static_cast<T>(k+1), static_cast<T>(n-k), pol));
      |                                            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/etc/Makeconf:204: fit_graper.o] Error 1
ERROR: compilation failed for package ‘graper’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/graper/new/graper.Rcheck/graper’

* installing *source* package ‘graper’ ...
** package ‘graper’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 13.3.1 20240611 (Red Hat 13.3.1-2)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG  -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/include" -DNDEBUG  -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include' -I/usr/local/include    -fpic  -g -O2   -c fit_graper.cpp -o fit_graper.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/digamma.hpp:16,
                 from graper_linear_dense_ff.h:2,
...
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/beta.hpp:1638:4: note: candidate: ‘template<class RT1, class RT2, class RT3, class Policy> boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::beta(RT1, RT2, RT3, const Policy&)’
 1638 |    beta(RT1 a, RT2 b, RT3 x, const Policy&)
      |    ^~~~
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/beta.hpp:1638:4: note:   template argument deduction/substitution failed:
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/BH/include/boost/math/special_functions/binomial.hpp:49:61: note:   candidate expects 4 arguments, 3 provided
   49 |          result = static_cast<T>((n - k) * boost::math::beta(static_cast<T>(k+1), static_cast<T>(n-k), pol));
      |                                            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/software/c4/cbi/software/_rocky8/R-4.4.2-gcc13/lib64/R/etc/Makeconf:204: fit_graper.o] Error 1
ERROR: compilation failed for package ‘graper’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/graper/old/graper.Rcheck/graper’

GUIDEseq

Version: 1.36.0
GitHub: NA
Source code: https://github.com/cran/GUIDEseq
Date/Publication: 2024-10-29
Number of recursive dependencies: 200

Run revdepcheck::revdep_details(, "GUIDEseq") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘GUIDEseq.Rnw’ using Sweave Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'GUIDEseq.Rnw'

SUMMARY: processing the following file failed: 'GUIDEseq.Rnw'

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 12.7Mb sub-directories of 1Mb or more: extdata 12.0Mb
checking R code for possible problems ... NOTE .maskSubSeq: no visible global function definition for '.getMatchedInd' .nucleotideSubstitutionMatrix: no visible binding for global variable 'IUPAC_CODE_MAP' .nucleotideSubstitutionMatrix: no visible binding for global variable 'DNA_BASES' GUIDEseqAnalysis: no visible binding for global variable 'offTarget' GUIDEseqAnalysis: no visible binding for global variable 'peak_score' GUIDEseqAnalysis: no visible binding for global variable 'predicted_cleavage_score' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.name' ... feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM geom_smooth guideAlignment2OffTarget guide_legend guides h mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget offTargetStrand offTarget_End offTarget_Start offTarget_sequence pa.f1 pa.r2 peak_score pos.deletion pos.insertion predicted_cleavage_score qwidth.first qwidth.last readName seqnames.first seqnames.last start.first start.last strand.first strand.last thePeak total.mismatch.bulge unit width.first width.last y
checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_

GUniFrac

Version: 1.8
GitHub: NA
Source code: https://github.com/cran/GUniFrac
Date/Publication: 2023-09-14 00:02:32 UTC
Number of recursive dependencies: 103

Run revdepcheck::revdep_details(, "GUniFrac") for more info

checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: doc 3.5Mb libs 2.5Mb

Gviz

Version: 1.50.0
GitHub: https://github.com/ivanek/Gviz
Source code: https://github.com/cran/Gviz
Date/Publication: 2024-10-29
Number of recursive dependencies: 162

Run revdepcheck::revdep_details(, "Gviz") for more info

checking installed package size ... NOTE installed size is 10.5Mb sub-directories of 1Mb or more: R 1.7Mb doc 5.4Mb extdata 2.5Mb

GWENA

Version: 1.16.0
GitHub: https://github.com/Kumquatum/GWENA
Source code: https://github.com/cran/GWENA
Date/Publication: 2024-10-29
Number of recursive dependencies: 148

Run revdepcheck::revdep_details(, "GWENA") for more info

checking whether package ‘GWENA’ can be installed ... WARNING Found the following significant warnings: Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/GWENA/new/GWENA.Rcheck/00install.out’ for details.
checking Rd files ... WARNING prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: data 2.3Mb doc 5.7Mb

HACSim

Version: 1.0.6-1
GitHub: NA
Source code: https://github.com/cran/HACSim
Date/Publication: 2022-06-13 06:50:16 UTC
Number of recursive dependencies: 37

Run revdepcheck::revdep_details(, "HACSim") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: libs 2.1Mb shiny 4.3Mb

Harman

Version: 1.34.0
GitHub: NA
Source code: https://github.com/cran/Harman
Date/Publication: 2024-10-29
Number of recursive dependencies: 212

Run revdepcheck::revdep_details(, "Harman") for more info

checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: doc 4.1Mb libs 4.0Mb

hbamr

Version: 2.3.2
GitHub: https://github.com/jbolstad/hbamr
Source code: https://github.com/cran/hbamr
Date/Publication: 2024-09-23 12:20:07 UTC
Number of recursive dependencies: 90

Run revdepcheck::revdep_details(, "hbamr") for more info

checking installed package size ... NOTE installed size is 340.4Mb sub-directories of 1Mb or more: libs 338.7Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

HDSpatialScan

Version: 1.0.4
GitHub: NA
Source code: https://github.com/cran/HDSpatialScan
Date/Publication: 2023-05-25 07:30:05 UTC
Number of recursive dependencies: 112

Run revdepcheck::revdep_details(, "HDSpatialScan") for more info

checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: libs 5.9Mb

hermes

Version: 1.10.0
GitHub: https://github.com/insightsengineering/hermes
Source code: https://github.com/cran/hermes
Date/Publication: 2024-10-29
Number of recursive dependencies: 161

Run revdepcheck::revdep_details(, "hermes") for more info

checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 2.0Mb doc 2.9Mb

hipathia

Version: 3.6.0
GitHub: NA
Source code: https://github.com/cran/hipathia
Date/Publication: 2024-10-29
Number of recursive dependencies: 165

Run revdepcheck::revdep_details(, "hipathia") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘hipathia-vignette.Rmd’ using rmarkdown ! LaTeX Error: Filetitling.sty' not found.

! Emergency stop.

Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/hipathia/new/hipathia.Rcheck/vign_test/hipathia/vignettes/hipathia-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See hipathia-vignette.log for more info. --- failed re-building ‘hipathia-vignette.Rmd’

SUMMARY: processing the following file failed: ‘hipathia-vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 10.8Mb sub-directories of 1Mb or more: data 4.1Mb doc 1.8Mb extdata 4.4Mb
checking R code for possible problems ... NOTE DAreport: no visible binding for global variable ‘ID’ DAreport: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘statistic’ DAtop : <anonymous>: no visible binding for global variable ‘p.value’ DAtop : <anonymous>: no visible binding for global variable ‘name’ DAtop : <anonymous>: no visible binding for global variable ‘logPV’ DAtop : <anonymous>: no visible binding for global variable ‘feature’ DAtop: no visible binding for global variable ‘name’ ... summary_plot: no visible binding for global variable ‘UP.nodes’ summary_plot: no visible binding for global variable ‘DOWN.nodes’ summary_plot: no visible binding for global variable ‘nodes’ summary_plot: no visible binding for global variable ‘ratio.sigs’ summary_plot: no visible binding for global variable ‘ratio.UPs’ summary_plot: no visible binding for global variable ‘ratio.DOWNs’ Undefined global functions or variables: DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction feature from functional logPV name nodes p.value ratio.DOWNs ratio.UPs ratio.sigs statistic status to total type value variable

Hmsc

Version: 3.0-13
GitHub: https://github.com/hmsc-r/HMSC
Source code: https://github.com/cran/Hmsc
Date/Publication: 2022-08-11 14:10:14 UTC
Number of recursive dependencies: 75

Run revdepcheck::revdep_details(, "Hmsc") for more info

checking Rd files ... NOTE checkRd: (-1) sampleMcmc.Rd:93: Lost braces; missing escapes or markup? 93 | disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of | ^

Holomics

Version: 1.1.1
GitHub: https://github.com/MolinLab/Holomics
Source code: https://github.com/cran/Holomics
Date/Publication: 2024-06-07 19:10:02 UTC
Number of recursive dependencies: 140

Run revdepcheck::revdep_details(, "Holomics") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: app 1.7Mb doc 3.3Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RSpectra’ ‘ggrepel’ ‘markdown’ ‘matrixStats’ ‘reshape2’ ‘tidyr’ ‘uuid’ All declared Imports should be used.

hubEnsembles

Version: 0.1.9
GitHub: https://github.com/hubverse-org/hubEnsembles
Source code: https://github.com/cran/hubEnsembles
Date/Publication: 2024-10-02 20:20:09 UTC
Number of recursive dependencies: 87

Run revdepcheck::revdep_details(, "hubEnsembles") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'hubExamples', 'hubVis'

ICBioMark

Version: 0.1.4
GitHub: NA
Source code: https://github.com/cran/ICBioMark
Date/Publication: 2021-11-15 12:00:02 UTC
Number of recursive dependencies: 63

Run revdepcheck::revdep_details(, "ICBioMark") for more info

checking Rd files ... NOTE checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup? 29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details). | ^ checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup? 29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details). | ^

immApex

Version: 1.0.4
GitHub: https://github.com/ncborcherding/immApex
Source code: https://github.com/cran/immApex
Date/Publication: 2024-11-06
Number of recursive dependencies: 162

Run revdepcheck::revdep_details(, "immApex") for more info

checking examples ... ERROR ``` Running examples in ‘immApex-Ex.R’ failed The error most likely occurred in:

Name: getIMGT

Title: Get IMGT Sequences for Specific Loci

Aliases: getIMGT

** Examples

TRBV_aa <- getIMGT(species = "human", ... + sequence.type = "aa", + max.retries = 3) Data from IMGT is under a CC BY-NC-ND 4.0 license. Attribution is required. Getting sequences from IMGT... Attempt 1 failed. Retrying... Attempt 2 failed. Retrying... Attempt 3 failed. Retrying... Error in getIMGT(species = "human", chain = "TRB", frame = "inframe", : Failed to retrieve data after 3 attempts. Execution halted ```
checking tests ... ``` Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: > > library(testthat) > library(immApex) > > test_check("immApex") ... ▆
1. └─immApex::sequenceDecoder(sequence.matrix) at test-sequenceDecoder.R:7:3
2. └─immApex:::.onehotDecoder(...)
3. └─reticulate::array_reshape(...)
4. └─reticulate::import("numpy", convert = !is_py_object(x))
5. └─reticulate:::py_module_import(module, convert = convert)
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 29 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘immApex.Rmd’ using rmarkdown

Quitting from lines 173-180 [unnamed-chunk-8] (immApex.Rmd) Error: processing vignette 'immApex.Rmd' failed with diagnostics: Failed to retrieve data after 3 attempts. --- failed re-building ‘immApex.Rmd’

SUMMARY: processing the following file failed: ‘immApex.Rmd’

Error: Vignette re-building failed. Execution halted ```

incidental

Version: 0.1
GitHub: NA
Source code: https://github.com/cran/incidental
Date/Publication: 2020-09-16 09:50:03 UTC
Number of recursive dependencies: 66

Run revdepcheck::revdep_details(, "incidental") for more info

checking Rd files ... NOTE checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup? 16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise. | ^

iNETgrate

Version: 1.4.0
GitHub: https://github.com/Bioconductor/BiocManager
Source code: https://github.com/cran/iNETgrate
Date/Publication: 2024-10-29
Number of recursive dependencies: 286

Run revdepcheck::revdep_details(, "iNETgrate") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘iNETgrate_inference.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'iNETgrate_inference.Rnw' failed with diagnostics: unable to run pdflatex on 'iNETgrate_inference.tex' LaTeX errors: ! LaTeX Error: Filecommath.sty' not found.

... l.48 ^^M

! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘iNETgrate_inference.Rnw’

SUMMARY: processing the following file failed: ‘iNETgrate_inference.Rnw’

Error: Vignette re-building failed. Execution halted ```

InfiniumPurify

Version: 1.3.1
GitHub: NA
Source code: https://github.com/cran/InfiniumPurify
Date/Publication: 2017-01-14 12:12:25
Number of recursive dependencies: 1

Run revdepcheck::revdep_details(, "InfiniumPurify") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘minfi’

iPath

Version: 1.12.0
GitHub: https://github.com/suke18/iPath
Source code: https://github.com/cran/iPath
Date/Publication: 2024-10-29
Number of recursive dependencies: 121

Run revdepcheck::revdep_details(, "iPath") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 2.5Mb doc 1.1Mb libs 1.3Mb
checking R code for possible problems ... NOTE water_fall: no visible binding for global variable ‘value’ water_fall: no visible binding for global variable ‘type’ Undefined global functions or variables: type value

irace

Version: 4.1
GitHub: https://github.com/MLopez-Ibanez/irace
Source code: https://github.com/cran/irace
Date/Publication: 2024-12-17 08:30:02 UTC
Number of recursive dependencies: 38

Run revdepcheck::revdep_details(, "irace") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘irace-package.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'irace-package.Rnw' failed with diagnostics: unable to run pdflatex on 'irace-package.tex' LaTeX errors: ! LaTeX Error: Filerelsize.sty' not found.

... l.78 \usepackage {fancyvrb}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘irace-package.Rnw’

SUMMARY: processing the following file failed: ‘irace-package.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘Rmpi’

JMbayes2

Version: 0.5-0
GitHub: https://github.com/drizopoulos/JMbayes2
Source code: https://github.com/cran/JMbayes2
Date/Publication: 2024-05-30 07:30:03 UTC
Number of recursive dependencies: 76

Run revdepcheck::revdep_details(, "JMbayes2") for more info

checking installed package size ... NOTE installed size is 12.6Mb sub-directories of 1Mb or more: libs 11.8Mb

kgschart

Version: 1.3.5
GitHub: https://github.com/kota7/kgschart
Source code: https://github.com/cran/kgschart
Date/Publication: 2017-07-02 22:16:15 UTC
Number of recursive dependencies: 73

Run revdepcheck::revdep_details(, "kgschart") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

kissDE

Version: 1.26.0
GitHub: https://github.com/lbbe-software/kissDE
Source code: https://github.com/cran/kissDE
Date/Publication: 2024-11-06
Number of recursive dependencies: 204

Run revdepcheck::revdep_details(, "kissDE") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘kissDE.rnw’ using Sweave Pre-processing the data... Trying to fit models on data... This can be a time-consuming step, so do not hesitate to have a look at the very well-written vignette ! Computing pvalues... Computing size of the effect and last cutoffs... Pre-processing the data... Trying to fit models on data... ... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘kissDE.rnw’

SUMMARY: processing the following file failed: ‘kissDE.rnw’

Error: Vignette re-building failed. Execution halted ```

kpmt

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/kpmt
Date/Publication: 2017-08-01 04:51:06 UTC
Number of recursive dependencies: 1

Run revdepcheck::revdep_details(, "kpmt") for more info

checking Rd files ... NOTE checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly

LDM

Version: 6.0.1
GitHub: https://github.com/yijuanhu/LDM
Source code: https://github.com/cran/LDM
Date/Publication: 2023-09-07 08:40:07 UTC
Number of recursive dependencies: 94

Run revdepcheck::revdep_details(, "LDM") for more info

checking examples ... ERROR ``` Running examples in ‘LDM-Ex.R’ failed The error most likely occurred in:

Name: ldm

Title: Testing hypotheses about the microbiome using a linear

decomposition model (LDM)

Aliases: ldm

Keywords: microbiome

** Examples

res.ldm <- ldm(formula=throat.otu.tab5 | (Sex+AntibioticUse) ~ SmokingStatus+PackYears, + data=throat.meta, seed=67817, fdr.nominal=0.1, n.perm.max=1000, n.cores=1, + verbose=FALSE) Error in tiesMethodMissing() : [matrixStats (>= 1.3.0)] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank(). See also ?matrixStats::matrixStats.options Calls: ldm -> array -> colRanks -> tiesMethodMissing -> action Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("LDM") Loading required package: LDM [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════ ... ▆ 1. └─LDM::ldm(...) at test-ldm.R:10:5 2. ├─base::array(colRanks(mat), c(n.var1, n.otu.smallp, n.perm.completed)) 3. └─matrixStats::colRanks(mat) 4. └─matrixStats:::tiesMethodMissing() 5. └─base (local) action(msg = msg, package = .packageName)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted ```

ldsep

Version: 2.1.5
GitHub: https://github.com/dcgerard/ldsep
Source code: https://github.com/cran/ldsep
Date/Publication: 2022-10-18 22:52:43 UTC
Number of recursive dependencies: 160

Run revdepcheck::revdep_details(, "ldsep") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: libs 8.7Mb

lemur

Version: 1.4.0
GitHub: https://github.com/const-ae/lemur
Source code: https://github.com/cran/lemur
Date/Publication: 2024-10-29
Number of recursive dependencies: 165

Run revdepcheck::revdep_details(, "lemur") for more info

checking dependencies in R code ... WARNING Missing or unexported object: ‘BiocNeighbors::findAnnoy’ Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator.
checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: data 2.6Mb doc 1.1Mb libs 2.8Mb
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'fold_left.Rd': ‘x’ ‘FUN’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

LFDREmpiricalBayes

Version: 1.0
GitHub: NA
Source code: https://github.com/cran/LFDREmpiricalBayes
Date/Publication: 2017-09-27 09:08:46 UTC
Number of recursive dependencies: 26

Run revdepcheck::revdep_details(, "LFDREmpiricalBayes") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics: unable to run pdflatex on 'LFDREmpiricalBayes.tex' LaTeX errors: ! LaTeX Error: Filechangepage.sty' not found.

... l.10 \usepackage {url}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘LFDREmpiricalBayes.Rnw’

SUMMARY: processing the following file failed: ‘LFDREmpiricalBayes.Rnw’

Error: Vignette re-building failed. Execution halted ```

Linnorm

Version: 2.30.0
GitHub: NA
Source code: https://github.com/cran/Linnorm
Date/Publication: 2024-10-29
Number of recursive dependencies: 103

Run revdepcheck::revdep_details(, "Linnorm") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘Linnorm_User_Manual.Rmd’ using rmarkdown ! LaTeX Error: Filetitling.sty' not found.

! Emergency stop.

Error: processing vignette 'Linnorm_User_Manual.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/Linnorm/new/Linnorm.Rcheck/vign_test/Linnorm/vignettes/Linnorm_User_Manual.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Linnorm_User_Manual.log for more info. --- failed re-building ‘Linnorm_User_Manual.Rmd’

SUMMARY: processing the following file failed: ‘Linnorm_User_Manual.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 2.3Mb doc 1.9Mb libs 1.5Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking Rd files ... NOTE checkRd: (-1) Linnorm.Cor.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.Cor.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly ... checkRd: (-1) Linnorm.limma.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.limma.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Linnorm.tSNE.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly

LSAmitR

Version: 1.0-3
GitHub: NA
Source code: https://github.com/cran/LSAmitR
Date/Publication: 2022-06-01 07:50:02 UTC
Number of recursive dependencies: 182

Run revdepcheck::revdep_details(, "LSAmitR") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘kerdiest’
checking data for non-ASCII characters ... NOTE Note: found 55 marked UTF-8 strings

lspartition

Version: 0.4
GitHub: NA
Source code: https://github.com/cran/lspartition
Date/Publication: 2019-08-08 22:40:06 UTC
Number of recursive dependencies: 34

Run revdepcheck::revdep_details(, "lspartition") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

Luminescence

Version: 0.9.26
GitHub: https://github.com/R-Lum/Luminescence
Source code: https://github.com/cran/Luminescence
Date/Publication: 2024-11-18 12:00:14 UTC
Number of recursive dependencies: 151

Run revdepcheck::revdep_details(, "Luminescence") for more info

checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: R 2.0Mb help 1.1Mb libs 3.8Mb

M3Drop

Version: 1.32.0
GitHub: https://github.com/tallulandrews/M3Drop
Source code: https://github.com/cran/M3Drop
Date/Publication: 2024-10-29
Number of recursive dependencies: 219

Run revdepcheck::revdep_details(, "M3Drop") for more info

checking installed package size ... NOTE installed size is 13.0Mb sub-directories of 1Mb or more: doc 12.7Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scater’ All declared Imports should be used.
checking R code for possible problems ... NOTE M3DropConvertData: no visible global function definition for ‘assays’ NBumiConvertData: no visible global function definition for ‘assays’ bg__filter_cells: no visible binding for global variable ‘x’ bg__get_extreme_residuals: no visible binding for global variable ‘x’ Undefined global functions or variables: assays x
checking Rd files ... NOTE prepare_Rd: NBumi_FSOther.Rd:8-10: Dropping empty section \usage prepare_Rd: NBumi_TradDE.Rd:7-8: Dropping empty section \usage

maEndToEnd

Version: 2.26.0
GitHub: NA
Source code: https://github.com/cran/maEndToEnd
Date/Publication: 2024-11-01
Number of recursive dependencies: 254

Run revdepcheck::revdep_details(, "maEndToEnd") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘MA-Workflow.Rmd’ using rmarkdown trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/164_II.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/183_II.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2114_I.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2209_A.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2255_I.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2400_I.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2424_A.CEL' trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/255_I.CEL' ... /c4/home/henrik/.cache/R/maEndToEnd/848_B.CEL /c4/home/henrik/.cache/R/maEndToEnd/888_I.CEL /c4/home/henrik/.cache/R/maEndToEnd/888_II.CEL --- failed re-building ‘MA-Workflow.Rmd’

SUMMARY: processing the following file failed: ‘MA-Workflow.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking DESCRIPTION meta-information ... WARNING Invalid license file pointers: LICENSE
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'oligoClasses', 'ArrayExpress', 'pd.hugene.1.0.st.v1', 'hugene10sttranscriptcluster.db', 'oligo', 'arrayQualityMetrics', 'limma', 'topGO', 'ReactomePA', 'clusterProfiler', 'gplots', 'ggplot2', 'geneplotter', 'pheatmap', 'RColorBrewer', 'dplyr', 'tidyr', 'stringr', 'matrixStats', 'genefilter', 'openxlsx', 'Rgraphviz', 'enrichplot' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: doc 6.7Mb
checking top-level files ... NOTE File LICENCE is not mentioned in the DESCRIPTION file.
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘AnnotationDbi’

magpie

Version: 1.6.0
GitHub: https://github.com/dxd429/magpie
Source code: https://github.com/cran/magpie
Date/Publication: 2024-10-29
Number of recursive dependencies: 125

Run revdepcheck::revdep_details(, "magpie") for more info

checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'powerEval.Rd': powerEval Code: function(Input.file, IP.file, BamDir, annoDir, variable, bam_factor, nsim = 10, N.reps = c(2, 3, 5), depth_factor = c(1, 2, 5), thres = c(0.01, 0.05, 0.1, 0.2), dmrProp = NULL, Test_method = "TRESS") Docs: function(Input.file, IP.file, BamDir, annoDir, variable, bam_factor, nsim = 10, N.reps = c(2, 3, 5), depth_factor = c(1, 2, 5), thres = c(0.01, 0.05, 0.1, 0.2), Test_method = "TRESS") Argument names in code not in docs: dmrProp Mismatches in argument names: Position: 11 Code: dmrProp Docs: Test_method
checking Rd files ... NOTE checkRd: (-1) QuickPower.Rd:28: Lost braces 28 | {GSE46705: }{Human HeLa cell line: Two replicates of wild type (WT) and two replicates of knockdown (KD) of complex METTL3.}\cr | ^ checkRd: (-1) QuickPower.Rd:29: Lost braces; missing escapes or markup? 29 | {GSE55575: }{Mouse embryonic fibroblasts: Two replicates of wild type (WT) and four replicates of knockdown (KD) of WTAP.}\cr | ^ checkRd: (-1) QuickPower.Rd:29: Lost braces 29 | {GSE55575: }{Mouse embryonic fibroblasts: Two replicates of wild type (WT) and four replicates of knockdown (KD) of WTAP.}\cr | ^ checkRd: (-1) QuickPower.Rd:30: Lost braces; missing escapes or markup? ... | ^ checkRd: (-1) QuickPower.Rd:30: Lost braces 30 | {GSE115105: }{Two sample types from WT and YTHDF1 KO mice. Each type has two replicates.}\cr | ^ checkRd: (-1) QuickPower.Rd:31: Lost braces; missing escapes or markup? 31 | {GSE94613: }{Human leukemia cell line: Four replicates of wild type (WT) and eight replicates of knockdown (KD) of complex METTL3.} | ^ checkRd: (-1) QuickPower.Rd:31: Lost braces 31 | {GSE94613: }{Human leukemia cell line: Four replicates of wild type (WT) and eight replicates of knockdown (KD) of complex METTL3.} | ^
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘htmltools’

MatrixGenerics

Version: 1.18.0
GitHub: https://github.com/Bioconductor/MatrixGenerics
Source code: https://github.com/cran/MatrixGenerics
Date/Publication: 2024-10-29
Number of recursive dependencies: 51

Run revdepcheck::revdep_details(, "MatrixGenerics") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MatrixGenerics) Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

... Error in tiesMethodMissing(): [matrixStats (>= 1.3.0)] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank(). See also ?matrixStats::matrixStats.options Backtrace: ▆ 1. └─matrixStats::colRanks(x = mat) at test-api_compatibility.R:513:9 2. └─matrixStats:::tiesMethodMissing() 3. └─base (local) action(msg = msg, package = .packageName)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 378 ] Error: Test failures Execution halted ```
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘methods:::fromNextMethod’ ‘methods:::getGenericFromCall’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.load_next_suggested_package_to_search’

mcmcsae

Version: 0.7.8
GitHub: NA
Source code: https://github.com/cran/mcmcsae
Date/Publication: 2024-12-11 21:00:02 UTC
Number of recursive dependencies: 113

Run revdepcheck::revdep_details(, "mcmcsae") for more info

checking installed package size ... NOTE installed size is 27.1Mb sub-directories of 1Mb or more: R 1.1Mb libs 25.5Mb

MEAL

Version: 1.36.0
GitHub: NA
Source code: https://github.com/cran/MEAL
Date/Publication: 2024-10-29
Number of recursive dependencies: 237

Run revdepcheck::revdep_details(, "MEAL") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘MEAL.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-2.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Volcano 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/QQ-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-2.png" but not available.

... Quitting from lines 157-158 [Regional plot 2 exp] (caseExample.Rmd) Error: processing vignette 'caseExample.Rmd' failed with diagnostics: attempt to set an attribute on NULL --- failed re-building ‘caseExample.Rmd’

SUMMARY: processing the following files failed: ‘MEAL.Rmd’ ‘caseExample.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... WARNING '::' or ':::' import not declared from: 'sva'
checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'getProbeResults.Rd' ‘robust’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE plotRegion: no visible global function definition for ‘subsetByOverlaps’ plotRegion: no visible global function definition for ‘mcols<-’ runRDA: no visible global function definition for ‘rowData’ runSVA: no visible global function definition for ‘resid’ runSVA: no visible global function definition for ‘quantile’ Undefined global functions or variables: mcols<- quantile resid rowData subsetByOverlaps Consider adding importFrom("stats", "quantile", "resid") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘DMRcate’

memes

Version: 1.14.0
GitHub: https://github.com/snystrom/memes
Source code: https://github.com/cran/memes
Date/Publication: 2024-10-29
Number of recursive dependencies: 161

Run revdepcheck::revdep_details(, "memes") for more info

checking S3 generic/method consistency ... WARNING ``` motif_input: function(x, ...) motif_input.universalmotif_df: function(input, path)

motif_input: function(x, ...) motif_input.universalmotif: function(input, path)

... function(x) sequence_input.BStringSet: function(input)

sequence_input: function(x) sequence_input.AAStringSet: function(input) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```
checking Rd files ... NOTE checkRd: (-1) runTomTom.Rd:51: Lost braces; missing escapes or markup? 51 | \item{...}{additional flags passed to tomtom using {cmdfun} formating (see table below for details)} | ^

metabCombiner

Version: 1.16.0
GitHub: NA
Source code: https://github.com/cran/metabCombiner
Date/Publication: 2024-10-29
Number of recursive dependencies: 114

Run revdepcheck::revdep_details(, "metabCombiner") for more info

checking Rd files ... NOTE checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^

MetabolicSurv

Version: 1.1.2
GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv
Source code: https://github.com/cran/MetabolicSurv
Date/Publication: 2021-06-11 08:30:02 UTC
Number of recursive dependencies: 131

Run revdepcheck::revdep_details(, "MetabolicSurv") for more info

checking Rd files ... NOTE checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly

metagenomeSeq

Version: 1.46.0
GitHub: https://github.com/nosson/metagenomeSeq
Source code: https://github.com/cran/metagenomeSeq
Date/Publication: 2024-04-30
Number of recursive dependencies: 144

Run revdepcheck::revdep_details(, "metagenomeSeq") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor ... Component "eb": Component "s2.post": Mean relative difference: 0.002818974 Component "eb": Component "t": Mean relative difference: 0.001476944 Component "eb": Component "df.total": Mean relative difference: 0.002226407 Component "eb": Component "p.value": Mean relative difference: 0.001045802 Component "eb": Component "lods": Mean relative difference: 0.002124969 Component "eb": Component "F": Mean relative difference: 0.002818882

[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted ```

metamicrobiomeR

Version: 1.2
GitHub: https://github.com/nhanhocu/metamicrobiomeR
Source code: https://github.com/cran/metamicrobiomeR
Date/Publication: 2020-11-09 11:20:05 UTC
Number of recursive dependencies: 165

Run revdepcheck::revdep_details(, "metamicrobiomeR") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘lmerTest’ All declared Imports should be used.

MetaNeighbor

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/MetaNeighbor
Date/Publication: 2024-10-29
Number of recursive dependencies: 104

Run revdepcheck::revdep_details(, "MetaNeighbor") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking Rd files ... NOTE checkRd: (-1) extractMetaClusters.Rd:25: Lost braces; missing escapes or markup? 25 | if 1<->2 and 1<->3 are reciprocal top hits, {1, 2, 3} is a meta-cluster, | ^

methrix

Version: 1.20.0
GitHub: https://github.com/CompEpigen/methrix
Source code: https://github.com/cran/methrix
Date/Publication: 2024-10-29
Number of recursive dependencies: 158

Run revdepcheck::revdep_details(, "methrix") for more info

checking R code for possible problems ... NOTE extract_CPGs: no visible global function definition for ‘standardChromosomes’ get_region_summary: no visible binding for global variable ‘..keep’ Undefined global functions or variables: ..keep standardChromosomes

MethylAid

Version: 1.40.0
GitHub: NA
Source code: https://github.com/cran/MethylAid
Date/Publication: 2024-10-29
Number of recursive dependencies: 177

Run revdepcheck::revdep_details(, "MethylAid") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘MethylAid.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'MethylAid.Rnw' failed with diagnostics: unable to run pdflatex on 'MethylAid.tex' LaTeX errors: ! LaTeX Error: Filenowidow.sty' not found.

... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MethylAid.Rnw’

SUMMARY: processing the following file failed: ‘MethylAid.Rnw’

Error: Vignette re-building failed. Execution halted ```

methylationArrayAnalysis

Version: 1.29.0
GitHub: NA
Source code: https://github.com/cran/methylationArrayAnalysis
Date/Publication: 2024-04-30
Number of recursive dependencies: 219

Run revdepcheck::revdep_details(, "methylationArrayAnalysis") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘methylationArrayAnalysis.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure3-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure4-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure5-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure6-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure7-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure8-1.png" but not available. ... See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache cache: /c4/home/henrik/.cache/R/ExperimentHub filename: experimenthub.sqlite3 --- failed re-building ‘methylationArrayAnalysis.Rmd’

SUMMARY: processing the following file failed: ‘methylationArrayAnalysis.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking whether package ‘methylationArrayAnalysis’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'rmarkdown::pdf_document' by 'BiocStyle::pdf_document' when loading 'methylationArrayAnalysis' Warning: replacing previous import 'rmarkdown::html_document' by 'BiocStyle::html_document' when loading 'methylationArrayAnalysis' Warning: replacing previous import 'rmarkdown::md_document' by 'BiocStyle::md_document' when loading 'methylationArrayAnalysis' See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'knitr', 'rmarkdown', 'BiocStyle', 'limma', 'minfi', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'IlluminaHumanMethylation450kmanifest', 'RColorBrewer', 'missMethyl', 'matrixStats', 'minfiData', 'Gviz', 'DMRcate', 'stringr', 'FlowSorted.Blood.450k' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 322.9Mb sub-directories of 1Mb or more: doc 2.6Mb extdata 320.2Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.

methylumi

Version: 2.52.0
GitHub: https://github.com/seandavi/methylumi
Source code: https://github.com/cran/methylumi
Date/Publication: 2024-10-29
Number of recursive dependencies: 174

Run revdepcheck::revdep_details(, "methylumi") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats', 'FDb.InfiniumMethylation.hg19', 'minfi' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 11.9Mb sub-directories of 1Mb or more: R 1.3Mb data 2.7Mb doc 1.9Mb extdata 5.8Mb
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used. ... Packages in Depends field not imported from: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’ ‘reshape2’ ‘scales’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE getBarcodes: warning in list.files(path = path, patt = "idat"): partial argument match of 'patt' to 'pattern' coerce,RangedSummarizedExperiment-GenomicMethylSet: warning in assays(from, withDim = F): partial argument match of 'withDim' to 'withDimnames' .getFinalReportBlock: no visible global function definition for ‘read.table’ .mclapply: no visible global function definition for ‘mclapply’ .parallel : <anonymous>: no visible global function definition for ‘ecdf’ ... subsetCommonProbes text theme_bw title value variable weighted.mean Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "abline", "axis", "box", "lines", "par", "points", "rect", "text", "title") importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset", "p.adjust", "pnorm", "weighted.mean") importFrom("utils", "capture.output", "data", "packageDescription", "packageVersion", "read.csv", "read.delim", "read.table") to your NAMESPACE file.
checking Rd files ... NOTE prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

migest

Version: 2.0.4
GitHub: https://github.com/guyabel/migest
Source code: https://github.com/cran/migest
Date/Publication: 2023-11-18 08:40:02 UTC
Number of recursive dependencies: 47

Run revdepcheck::revdep_details(, "migest") for more info

checking data for non-ASCII characters ... NOTE Note: found 9 marked UTF-8 strings

miloR

Version: 2.2.0
GitHub: https://github.com/MarioniLab/miloR
Source code: https://github.com/cran/miloR
Date/Publication: 2024-10-29
Number of recursive dependencies: 212

Run revdepcheck::revdep_details(, "miloR") for more info

checking installed package size ... NOTE installed size is 35.0Mb sub-directories of 1Mb or more: data 1.8Mb doc 7.9Mb libs 24.5Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’ plotDAbeeswarm: no visible binding for global variable ‘logFC’ plotDAbeeswarm: no visible binding for global variable ‘is_signif’ plotDAbeeswarm: no visible binding for global variable ‘Nhood’ plotDAbeeswarm: no visible binding for global variable ‘logFC_color’ plotNhoodCounts: no visible binding for global variable ‘cond’ plotNhoodCounts: no visible binding for global variable ‘values’ plotNhoodCounts: no visible binding for global variable ‘y’ plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC’ ... plotNhoodMA: no visible binding for global variable ‘Sig’ plotNhoodSizeHist: no visible binding for global variable ‘nh_size’ testNhoods: no visible global function definition for ‘type’ Undefined global functions or variables: . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif label layout logCPM logFC logFC_color logFC_rank nh_size size type values weight y Consider adding importFrom("graphics", "layout") to your NAMESPACE file.

MinimumDistance

Version: 1.50.0
GitHub: NA
Source code: https://github.com/cran/MinimumDistance
Date/Publication: 2024-10-29
Number of recursive dependencies: 90

Run revdepcheck::revdep_details(, "MinimumDistance") for more info

checking whether package ‘MinimumDistance’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/MinimumDistance/new/MinimumDistance.Rcheck/00install.out’ for details.
checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'coercion-methods.Rd' but not in code: ‘as’
checking Rd \usage sections ... WARNING ``` Objects in \usage without \alias in Rd file 'coercion-methods.Rd': ‘as’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking contents of ‘data’ directory ... WARNING Output for data("trioSetListExample", package = "MinimumDistance"): Warning message: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doSNOW’
checking whether startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MatrixGenerics’ All declared Imports should be used.
checking R code for possible problems ... NOTE callDenovoSegments: no visible global function definition for ‘read.bsfiles’ combineRanges: no visible global function definition for ‘RangedData’ getRefGene: no visible global function definition for ‘RangedData’ overlapsCentromere: no visible global function definition for ‘RangedData’ pruneMD: no visible global function definition for ‘RangedDataCBS’ pruneTrioSet: no visible global function definition for ‘RangedDataList’ read.bsfiles2: no visible binding for global variable ‘read.bsfiles’ GenomeAnnotatedDataFrameFrom,character: no visible global function definition for ‘read.bsfiles’ calculateMindist,list: no visible binding for global variable ‘elt’ Undefined global functions or variables: RangedData RangedDataCBS RangedDataList elt read.bsfiles

miRecSurv

Version: 1.0.2
GitHub: NA
Source code: https://github.com/cran/miRecSurv
Date/Publication: 2021-08-17 16:20:05 UTC
Number of recursive dependencies: 8

Run revdepcheck::revdep_details(, "miRecSurv") for more info

checking Rd files ... NOTE checkRd: (-1) sim.data.Rd:11: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:12: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:13: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:14: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:15: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:16: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:17: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:18: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:19: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:20: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:21: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:22: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:23: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:24: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:25: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:26: Lost braces in \enumerate; meant \describe ? checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?

mixOmics

Version: 6.30.0
GitHub: https://github.com/mixOmicsTeam/mixOmics
Source code: https://github.com/cran/mixOmics
Date/Publication: 2024-10-29
Number of recursive dependencies: 100

Run revdepcheck::revdep_details(, "mixOmics") for more info

checking installed package size ... NOTE installed size is 23.3Mb sub-directories of 1Mb or more: R 2.0Mb data 3.3Mb doc 16.5Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gsignal’ All declared Imports should be used.

mnem

Version: 1.22.0
GitHub: https://github.com/cbg-ethz/mnem
Source code: https://github.com/cran/mnem
Date/Publication: 2024-10-29
Number of recursive dependencies: 182

Run revdepcheck::revdep_details(, "mnem") for more info

checking installed package size ... NOTE installed size is 10.5Mb sub-directories of 1Mb or more: data 2.3Mb doc 4.2Mb libs 3.6Mb

moanin

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/moanin
Date/Publication: 2024-10-29
Number of recursive dependencies: 124

Run revdepcheck::revdep_details(, "moanin") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘documentation.Rmd’ using knitr

Quitting from lines 45-49 [unnamed-chunk-2] (documentation.Rmd) Error: processing vignette 'documentation.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘documentation.Rmd’

SUMMARY: processing the following file failed: ‘documentation.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking Rd files ... NOTE checkRd: (-1) DE_timepoints.Rd:129-130: Lost braces in \itemize; meant \describe ? checkRd: (-1) DE_timepoints.Rd:131-132: Lost braces in \itemize; meant \describe ? checkRd: (-1) DE_timepoints.Rd:133-136: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:39-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimate_log_fold_change.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) splines_kmeans.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) splines_kmeans.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) splines_kmeans.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) splines_kmeans_score_and_label.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) splines_kmeans_score_and_label.Rd:72-73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) splines_kmeans_score_and_label.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘edge’ Unknown package ‘KEGGprofile’ in Rd xrefs

MOCHA

Version: 1.1.0
GitHub: NA
Source code: https://github.com/cran/MOCHA
Date/Publication: 2024-01-25 12:20:12 UTC
Number of recursive dependencies: 246

Run revdepcheck::revdep_details(, "MOCHA") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘ArchR’

monocle

Version: 2.34.0
GitHub: NA
Source code: https://github.com/cran/monocle
Date/Publication: 2024-10-29
Number of recursive dependencies: 258

Run revdepcheck::revdep_details(, "monocle") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘monocle-vignette.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics: unable to run pdflatex on 'monocle-vignette.tex' LaTeX errors: ! LaTeX Error: Filesectsty.sty' not found.

... l.37 \sectionfont {\sffamily\bfseries\color{RoyalBlue}\sectionrule{0pt}{0pt}{... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘monocle-vignette.Rnw’

SUMMARY: processing the following file failed: ‘monocle-vignette.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘biocViews’ All declared Imports should be used.
checking R code for possible problems ... NOTE assign_cell_lineage: no visible global function definition for ‘nei’ buildBranchCellDataSet: no visible global function definition for ‘nei’ count_leaf_descendents: no visible global function definition for ‘nei’ cth_classifier_cds: no visible global function definition for ‘nei’ cth_classifier_cell: no visible global function definition for ‘nei’ diff_test_helper: no visible binding for global variable ‘Size_Factor’ exportCDS: no visible binding for global variable ‘use_for_ordering’ extract_good_ordering: no visible global function definition for ‘nei’ fit_model_helper: no visible binding for global variable ‘Size_Factor’ get_next_node_id: no visible binding for '<<-' assignment to ... variable ‘Branch’ project2MST: no visible global function definition for ‘nei’ reverseEmbeddingCDS : <anonymous>: no visible global function definition for ‘quantile’ Undefined global functions or variables: Branch Size_Factor nei next_node pseudocount quantile use_for_ordering Consider adding importFrom("stats", "quantile") to your NAMESPACE file.

moocore

Version: 0.1.2
GitHub: https://github.com/multi-objective/moocore
Source code: https://github.com/cran/moocore
Date/Publication: 2024-09-18 04:50:02 UTC
Number of recursive dependencies: 44

Run revdepcheck::revdep_details(, "moocore") for more info

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

MOSim

Version: 2.2.0
GitHub: https://github.com/ConesaLab/MOSim
Source code: https://github.com/cran/MOSim
Date/Publication: 2024-10-29
Number of recursive dependencies: 217

Run revdepcheck::revdep_details(, "MOSim") for more info

checking whether package ‘MOSim’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/MOSim/new/MOSim.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 5.8Mb
checking R code for possible problems ... NOTE make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.a’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.ao’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq.a’ ... make_association_dataframe : keep_remaining2: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq’ make_association_dataframe: no visible binding for global variable ‘Peak_ID’ make_association_dataframe: no visible binding for global variable ‘Gene_ID’ Undefined global functions or variables: Freq Freq.a Freq.ao Gene_ID Peak_ID cluster
checking Rd files ... NOTE checkRd: (-1) TF_human.Rd:12: Lost braces; missing escapes or markup? 12 | @source {https://tflink.net/} | ^ checkRd: (-1) associationList.Rd:14: Lost braces; missing escapes or markup? 14 | @source {Created in-house to serve as an example} | ^ checkRd: (-1) sc_mosim.Rd:94: Lost braces; missing escapes or markup? 94 | {https://tflink.net/}} | ^ checkRd: (-1) scatac.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:23-28: Lost braces 23 | for (cell_type in unique_cell_types) { | ^

motifbreakR

Version: 2.20.0
GitHub: https://github.com/Simon-Coetzee/motifbreakR
Source code: https://github.com/cran/motifbreakR
Date/Publication: 2024-10-29
Number of recursive dependencies: 196

Run revdepcheck::revdep_details(, "motifbreakR") for more info

checking examples ... ERROR ``` Running examples in ‘motifbreakR-Ex.R’ failed The error most likely occurred in:

Name: snps.from.rsid

Title: Import SNPs from rsid for use in motifbreakR

Aliases: snps.from.rsid

** Examples

library(BSgenome.Hsapiens.UCSC.hg19) ... snps <- as.character(read.table(snps.file)[,1]) snps.mb <- snps.from.rsid(snps[1], + dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37, + search.genome = BSgenome.Hsapiens.UCSC.hg19) Warning in download.file(url, destfile, method, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/': FTP status was '400 Unknown Error' Error in download.file(url, destfile, method, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/' Calls: snps.from.rsid ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘motifbreakR-vignette.Rmd’ using rmarkdown

Quitting from lines 105-112 [fromrsid] (motifbreakR-vignette.Rmd) Error: processing vignette 'motifbreakR-vignette.Rmd' failed with diagnostics: cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/' --- failed re-building ‘motifbreakR-vignette.Rmd’

SUMMARY: processing the following file failed: ‘motifbreakR-vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking for missing documentation entries ... WARNING Undocumented data sets: 'example.pvalue' All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE Package in Depends field not imported from: 'MotifDb' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE biomartToGranges: no visible binding for global variable 'chr_name' biomartToGranges: no visible binding for global variable 'chrom_start' biomartToGranges: no visible binding for global variable 'chrom_end' biomartToGranges: no visible binding for global variable 'SNP_id' biomartToGranges: no visible binding for global variable 'REF' biomartToGranges: no visible binding for global variable 'ALT' calculatePvalue: no visible binding for global variable 'Refpvalue' calculatePvalue: no visible binding for global variable 'Altpvalue' convertPeakFile: no visible binding for global variable 'chr' convertPeakFile: no visible binding for global variable 'name' Undefined global functions or variables: ALT Altpvalue REF Refpvalue SNP_id chr chr_name chrom_end chrom_start name
checking Rd files ... NOTE checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^ checkRd: (-1) calculatePvalue.Rd:7: Lost braces 7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. | ^
checking data for non-ASCII characters ... NOTE Note: found 12 marked UTF-8 strings

mrfDepth

Version: 1.0.17
GitHub: NA
Source code: https://github.com/cran/mrfDepth
Date/Publication: 2024-05-24 21:20:02 UTC
Number of recursive dependencies: 44

Run revdepcheck::revdep_details(, "mrfDepth") for more info

checking installed package size ... NOTE installed size is 21.6Mb sub-directories of 1Mb or more: data 1.6Mb libs 19.6Mb

msqrob2

Version: 1.14.1
GitHub: https://github.com/statOmics/msqrob2
Source code: https://github.com/cran/msqrob2
Date/Publication: 2024-12-23
Number of recursive dependencies: 198

Run revdepcheck::revdep_details(, "msqrob2") for more info

checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.vcovUnscaled’
checking R code for possible problems ... NOTE .noridge_msqrobLmer: no visible binding for global variable ‘w’ .ridge_msqrobLmer: no visible binding for global variable ‘w’ Undefined global functions or variables: w

mult.latent.reg

Version: 0.2.1
GitHub: NA
Source code: https://github.com/cran/mult.latent.reg
Date/Publication: 2024-11-15 15:50:02 UTC
Number of recursive dependencies: 12

Run revdepcheck::revdep_details(, "mult.latent.reg") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘npmlreg’

MultiBD

Version: 0.2.0
GitHub: NA
Source code: https://github.com/cran/MultiBD
Date/Publication: 2016-12-05 18:28:46
Number of recursive dependencies: 74

Run revdepcheck::revdep_details(, "MultiBD") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘SIR-MCMC.Rmd’ using rmarkdown --- finished re-building ‘SIR-MCMC.Rmd’

--- re-building ‘SIRtrans.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'SIRtrans.Rnw' failed with diagnostics: unable to run pdflatex on 'SIRtrans.tex' LaTeX errors: ... l.75 \usepackage {amsmath}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘SIRtrans.Rnw’

SUMMARY: processing the following file failed: ‘SIRtrans.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 10.4Mb sub-directories of 1Mb or more: libs 8.8Mb

multistateQTL

Version: 1.2.0
GitHub: https://github.com/dunstone-a/multistateQTL
Source code: https://github.com/cran/multistateQTL
Date/Publication: 2024-10-29
Number of recursive dependencies: 143

Run revdepcheck::revdep_details(, "multistateQTL") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Rtsne’

muscat

Version: 1.20.0
GitHub: https://github.com/HelenaLC/muscat
Source code: https://github.com/cran/muscat
Date/Publication: 2024-11-06
Number of recursive dependencies: 242

Run revdepcheck::revdep_details(, "muscat") for more info

checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: doc 7.4Mb
checking R code for possible problems ... NOTE pbHeatmap: no visible binding for global variable ‘gene’ pbHeatmap: no visible binding for global variable ‘p_adj.loc’ pbHeatmap: no visible binding for global variable ‘logFC’ Undefined global functions or variables: gene logFC p_adj.loc
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘cowplot’ ‘tidyr’

muscData

Version: 1.20.0
GitHub: https://github.com/HelenaLC/muscData
Source code: https://github.com/cran/muscData
Date/Publication: 2024-11-05
Number of recursive dependencies: 279

Run revdepcheck::revdep_details(, "muscData") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘Crowell19_4vs4’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘SingleCellExperiment’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

mvgam

Version: 1.1.3
GitHub: https://github.com/nicholasjclark/mvgam
Source code: https://github.com/cran/mvgam
Date/Publication: 2024-09-04 03:40:02 UTC
Number of recursive dependencies: 147

Run revdepcheck::revdep_details(, "mvgam") for more info

checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘cmdstanr’

Packages which this enhances but not available for checking: 'gratia', 'tidyr' ```
checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: R 1.9Mb doc 2.0Mb libs 2.6Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘cmdstanr’, ‘patchwork’

mvpd

Version: 0.0.4
GitHub: https://github.com/swihart/mvpd
Source code: https://github.com/cran/mvpd
Date/Publication: 2023-09-03 14:20:02 UTC
Number of recursive dependencies: 50

Run revdepcheck::revdep_details(, "mvpd") for more info

checking Rd files ... NOTE checkRd: (-1) dmvss.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dmvss.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dmvss.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dmvss.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dmvss.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pmvss.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pmvss.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pmvss.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pmvss.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly

mzipmed

Version: 1.4.0
GitHub: NA
Source code: https://github.com/cran/mzipmed
Date/Publication: 2023-07-07 16:30:02 UTC
Number of recursive dependencies: 31

Run revdepcheck::revdep_details(, "mzipmed") for more info

checking Rd files ... NOTE checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup? 22 | @source {Simulated to serve as an example} | ^

NanoStringDiff

Version: 1.36.0
GitHub: NA
Source code: https://github.com/cran/NanoStringDiff
Date/Publication: 2024-10-29
Number of recursive dependencies: 48

Run revdepcheck::revdep_details(, "NanoStringDiff") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘compute.baseSigma’ ‘est.dispersion’ ‘fun5’ ‘glmfit.OneGroup’ ‘glmfit.full’ ‘glmfit.reduce’ ‘rnegbinom’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘NanoStringDiff.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:
```
IQR, mad, sd, var, xtabs
```
... l.37 \sectionfont {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘NanoStringDiff.Rnw’

SUMMARY: processing the following file failed: ‘NanoStringDiff.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking Rd contents ... NOTE Auto-generated content requiring editing in Rd file 'NanoStringDiff-package.Rd': \references: ‘This optional section can contain literature or other refere...’ \seealso: ‘Optional links to other man pages’ \examples: ‘\dontrun{ ## Optional simple examples of the most impor...’
checking installed files from ‘inst/doc’ ... NOTE The following files look like leftovers/mistakes: ‘NanoStringDiff.log’ Please remove them from your package.

nearBynding

Version: 1.16.0
GitHub: NA
Source code: https://github.com/cran/nearBynding
Date/Publication: 2024-10-29
Number of recursive dependencies: 119

Run revdepcheck::revdep_details(, "nearBynding") for more info

checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: extdata 6.9Mb

netZooR

Version: 1.10.0
GitHub: https://github.com/netZoo/netZooR
Source code: https://github.com/cran/netZooR
Date/Publication: 2024-10-30
Number of recursive dependencies: 231

Run revdepcheck::revdep_details(, "netZooR") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [1] 187 [1] 188 [1] 189 [1] 190 [1] 191 [1] 192 ... Backtrace: ▆
1. └─netZooR::pandaPy(...) at test-panda.R:29:4
2. └─reticulate::source_python(pandapath, convert = TRUE)
3. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
4. └─reticulate:::py_run_file_impl(file, local, convert)
[ FAIL 1 | WARN 9 | SKIP 1 | PASS 48 ] Error: Test failures Execution halted ```
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 1.5Mb extdata 2.9Mb
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘matrixcalc’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE estimatePenaltyParameters: no visible global function definition for ‘matrix.trace’ runEgret: no visible binding for global variable ‘NA12878’ show,panda: no visible global function definition for ‘print.panda’ Undefined global functions or variables: NA12878 matrix.trace print.panda
checking Rd files ... NOTE checkRd: (-1) condorCluster.Rd:39: Lost braces; missing escapes or markup? 39 | in the modularity for each iteration. Default is min(10^{-4},1/(number of edges)), | ^ checkRd: (-1) dragon.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dragon.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dragon.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dragon.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dragon.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) dragon.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly

nn2poly

Version: 0.1.2
GitHub: NA
Source code: https://github.com/cran/nn2poly
Date/Publication: 2024-11-11 15:20:02 UTC
Number of recursive dependencies: 97

Run revdepcheck::revdep_details(, "nn2poly") for more info

checking C++ specification ... NOTE Specified C++14: please drop specification unless essential

nnSVG

Version: 1.10.0
GitHub: https://github.com/lmweber/nnSVG
Source code: https://github.com/cran/nnSVG
Date/Publication: 2024-10-29
Number of recursive dependencies: 150

Run revdepcheck::revdep_details(, "nnSVG") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

NormalyzerDE

Version: 1.24.0
GitHub: https://github.com/ComputationalProteomics/NormalyzerDE
Source code: https://github.com/cran/NormalyzerDE
Date/Publication: 2024-10-29
Number of recursive dependencies: 134

Run revdepcheck::revdep_details(, "NormalyzerDE") for more info

checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'NormalyzerEvaluationResults.Rd': NormalyzerEvaluationResults Code: function(nr, categoricalAnova = TRUE) Docs: function(nr) Argument names in code not in docs: categoricalAnova NormalyzerEvaluationResults Code: function(nr, categoricalAnova = TRUE) Docs: function(nr) Argument names in code not in docs: categoricalAnova
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'calculateFeatureCV.Rd': ‘sampleReplicateGroups’

Documented arguments not in \usage in Rd file 'verifySummarizedExperiment.Rd': ‘fullMatrix’ ‘designMatrix’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

numbat

Version: 1.4.2
GitHub: https://github.com/kharchenkolab/numbat
Source code: https://github.com/cran/numbat
Date/Publication: 2024-09-20 12:20:07 UTC
Number of recursive dependencies: 141

Run revdepcheck::revdep_details(, "numbat") for more info

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 4.2Mb libs 1.2Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

omicplotR

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/omicplotR
Date/Publication: 2024-10-29
Number of recursive dependencies: 105

Run revdepcheck::revdep_details(, "omicplotR") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘ALDEx2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

omicsPrint

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/omicsPrint
Date/Publication: 2024-10-29
Number of recursive dependencies: 141

Run revdepcheck::revdep_details(, "omicsPrint") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘omicsPrint.Rmd’ using rmarkdown trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100940/matrix/GSE100940_series_matrix.txt.gz'

Quitting from lines 251-261 [downloadretry] (omicsPrint.Rmd) Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics: cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100940/matrix/GSE100940_series_matrix.txt.gz' --- failed re-building ‘omicsPrint.Rmd’

SUMMARY: processing the following file failed: ‘omicsPrint.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking LazyData ... WARNING LazyData DB of 7.3 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE installed size is 8.8Mb sub-directories of 1Mb or more: data 7.4Mb doc 1.3Mb

omicsViewer

Version: 1.10.0
GitHub: https://github.com/mengchen18/omicsViewer
Source code: https://github.com/cran/omicsViewer
Date/Publication: 2024-10-29
Number of recursive dependencies: 187

Run revdepcheck::revdep_details(, "omicsViewer") for more info

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: extdata 4.8Mb

OncoBayes2

Version: 0.8-9
GitHub: NA
Source code: https://github.com/cran/OncoBayes2
Date/Publication: 2023-07-20 18:40:05 UTC
Number of recursive dependencies: 99

Run revdepcheck::revdep_details(, "OncoBayes2") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 195.0Mb sub-directories of 1Mb or more: libs 193.0Mb
checking whether startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking Rd files ... NOTE checkRd: (-1) summary.blrm_trial.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:31-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) summary.blrm_trial.Rd:34: Lost braces in \itemize; meant \describe ?
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

OptHoldoutSize

Version: 0.1.0.0
GitHub: NA
Source code: https://github.com/cran/OptHoldoutSize
Date/Publication: 2022-02-18 12:20:02 UTC
Number of recursive dependencies: 35

Run revdepcheck::revdep_details(, "OptHoldoutSize") for more info

checking Rd files ... NOTE checkRd: (-1) optimal_holdout_size.Rd:30: Lost braces; missing escapes or markup? 30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data. | ^

OptimalDesign

Version: 1.0.1
GitHub: NA
Source code: https://github.com/cran/OptimalDesign
Date/Publication: 2019-12-02 08:50:07 UTC
Number of recursive dependencies: 37

Run revdepcheck::revdep_details(, "OptimalDesign") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'gurobi', 'slam'
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

OUTRIDER

Version: 1.24.0
GitHub: https://github.com/gagneurlab/OUTRIDER
Source code: https://github.com/cran/OUTRIDER
Date/Publication: 2024-10-29
Number of recursive dependencies: 202

Run revdepcheck::revdep_details(, "OUTRIDER") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘OUTRIDER.Rnw’ using knitr The magick package is required to crop "figure/deVsOutlier-1.png" but not available. The magick package is required to crop "figure/quick_guide-1.png" but not available. The magick package is required to crop "figure/filtering-1.png" but not available. The magick package is required to crop "figure/filtering-2.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-1.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-2.png" but not available. The magick package is required to crop "figure/controlling_for_confounders-1.png" but not available. The magick package is required to crop "figure/aberrantperSample-1.png" but not available. ... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘OUTRIDER.Rnw’

SUMMARY: processing the following file failed: ‘OUTRIDER.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: doc 2.4Mb libs 3.1Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs' See the note in ?`:::` about the use of this operator.
checking Rd files ... NOTE checkRd: (-1) results.Rd:48-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:68-71: Lost braces in \itemize; \value handles \item{}{} directly

pandaR

Version: 1.38.0
GitHub: NA
Source code: https://github.com/cran/pandaR
Date/Publication: 2024-10-29
Number of recursive dependencies: 59

Run revdepcheck::revdep_details(, "pandaR") for more info

checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
checking LazyData ... WARNING LazyData DB of 9.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE installed size is 9.4Mb sub-directories of 1Mb or more: data 9.0Mb
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in Rd file 'summary.panda.Rd': ‘summary.panda’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

pARI

Version: 1.1.2
GitHub: https://github.com/angeella/pARI
Source code: https://github.com/cran/pARI
Date/Publication: 2024-09-06 18:50:06 UTC
Number of recursive dependencies: 33

Run revdepcheck::revdep_details(, "pARI") for more info

checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: libs 6.0Mb

PathoStat

Version: 1.32.0
GitHub: https://github.com/mani2012/PathoStat
Source code: https://github.com/cran/PathoStat
Date/Publication: 2024-10-29
Number of recursive dependencies: 197

Run revdepcheck::revdep_details(, "PathoStat") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ComplexHeatmap’ ‘RColorBrewer’ All declared Imports should be used.

pcaMethods

Version: 1.98.0
GitHub: https://github.com/hredestig/pcamethods
Source code: https://github.com/cran/pcaMethods
Date/Publication: 2024-10-29
Number of recursive dependencies: 32

Run revdepcheck::revdep_details(, "pcaMethods") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ade4’

pecora

Version: 0.1.1
GitHub: NA
Source code: https://github.com/cran/pecora
Date/Publication: 2021-11-05 13:10:02 UTC
Number of recursive dependencies: 3

Run revdepcheck::revdep_details(, "pecora") for more info

checking examples ... ERROR ``` Running examples in ‘pecora-Ex.R’ failed The error most likely occurred in:

Name: pecora-package

Title: pecora-package

Aliases: pecora-package pecora.package pecorapackage

Keywords: package

** Examples

X <- matrix(rnorm(100*20), nrow=20) out <- oneSample(X = X) pv <- t2p(Test = out, alternative = "two.sided") Error in tiesMethodMissing() : [matrixStats (>= 1.3.0)] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank(). See also ?matrixStats::matrixStats.options Calls: t2p -> rowRanks -> tiesMethodMissing -> action Execution halted ```

penppml

Version: 0.2.3
GitHub: https://github.com/tomzylkin/penppml
Source code: https://github.com/cran/penppml
Date/Publication: 2023-09-08 14:10:02 UTC
Number of recursive dependencies: 130

Run revdepcheck::revdep_details(, "penppml") for more info

checking installed package size ... NOTE installed size is 13.3Mb sub-directories of 1Mb or more: data 1.8Mb libs 11.1Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘fixest’ All declared Imports should be used.

PepsNMR

Version: 1.24.0
GitHub: https://github.com/ManonMartin/PepsNMR
Source code: https://github.com/cran/PepsNMR
Date/Publication: 2024-10-29
Number of recursive dependencies: 65

Run revdepcheck::revdep_details(, "PepsNMR") for more info

checking Rd files ... NOTE checkRd: (-1) Normalization.Rd:47: Escaped LaTeX specials: \&

phosphonormalizer

Version: 1.30.0
GitHub: NA
Source code: https://github.com/cran/phosphonormalizer
Date/Publication: 2024-10-29
Number of recursive dependencies: 44

Run revdepcheck::revdep_details(, "phosphonormalizer") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘MSnbase’

Pigengene

Version: 1.32.0
GitHub: NA
Source code: https://github.com/cran/Pigengene
Date/Publication: 2024-10-29
Number of recursive dependencies: 189

Run revdepcheck::revdep_details(, "Pigengene") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘Pigengene_inference.Rnw’ using knitr Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'Pigengene_inference.Rnw' failed with diagnostics: unable to run pdflatex on 'Pigengene_inference.tex' LaTeX errors: ! LaTeX Error: Filenowidow.sty' not found.

... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘Pigengene_inference.Rnw’

SUMMARY: processing the following file failed: ‘Pigengene_inference.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ``` Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn")

one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db ```
checking Rd files ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? ... checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:77-79: Lost braces in \itemize; meant \describe ?

pipeComp

Version: 1.16.0
GitHub: https://github.com/plger/pipeComp
Source code: https://github.com/cran/pipeComp
Date/Publication: 2024-10-29
Number of recursive dependencies: 212

Run revdepcheck::revdep_details(, "pipeComp") for more info

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.0Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
checking R code for possible problems ... NOTE scrna_describeDatasets: no visible binding for global variable ‘cluster’ scrna_describeDatasets: no visible binding for global variable ‘nb’ scrna_describeDatasets : pf: no visible binding for global variable ‘.x’ scrna_describeDatasets : rd: no visible binding for global variable ‘y’ scrna_describeDatasets : rd: no visible binding for global variable ‘cluster’ scrna_evalPlot_filtering: no visible binding for global variable ‘max.lost’ ... scrna_evalPlot_filtering: no visible binding for global variable ‘doubletmethod’ scrna_evalPlot_filtering: no visible binding for global variable ‘method’ scrna_evalPlot_overall: no visible binding for global variable ‘true.nbClusts’ scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’ Undefined global functions or variables: .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb true.nbClusts y
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘edgeR’ ‘sva’

PlackettLuce

Version: 0.4.3
GitHub: https://github.com/hturner/PlackettLuce
Source code: https://github.com/cran/PlackettLuce
Date/Publication: 2023-06-16 14:30:02 UTC
Number of recursive dependencies: 181

Run revdepcheck::revdep_details(, "PlackettLuce") for more info

checking Rd files ... NOTE checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup? 27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\}, | ^ checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup? 27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\}, | ^ checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup? 27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\}, | ^ checkRd: (-1) rankings.Rd:127: Lost braces; missing escapes or markup? 127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in | ^

pmp

Version: 1.18.0
GitHub: NA
Source code: https://github.com/cran/pmp
Date/Publication: 2024-10-29
Number of recursive dependencies: 107

Run revdepcheck::revdep_details(, "pmp") for more info

checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: data 1.8Mb doc 6.0Mb

PolySTest

Version: 1.0.2
GitHub: https://github.com/computproteomics/PolySTest
Source code: https://github.com/cran/PolySTest
Date/Publication: 2024-11-28
Number of recursive dependencies: 142

Run revdepcheck::revdep_details(, "PolySTest") for more info

checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in parse(con): 11:41: unexpected ',' 10: year="2020", 11: doi="10.1074/mcp.RA119.001777"), ^
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: doc 4.3Mb shiny 1.4Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE perm_unpaired: no visible binding for global variable ‘NumTests’ permtest_paired: no visible binding for global variable ‘NumTests’ Undefined global functions or variables: NumTests

priorsense

Version: 1.0.4
GitHub: NA
Source code: https://github.com/cran/priorsense
Date/Publication: 2024-11-01 12:30:02 UTC
Number of recursive dependencies: 112

Run revdepcheck::revdep_details(, "priorsense") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'cmdstanr', 'iwmm'

PRONE

Version: 1.0.0
GitHub: https://github.com/lisiarend/PRONE
Source code: https://github.com/cran/PRONE
Date/Publication: 2024-10-29
Number of recursive dependencies: 285

Run revdepcheck::revdep_details(, "PRONE") for more info

checking installed package size ... NOTE installed size is 13.5Mb sub-directories of 1Mb or more: doc 10.4Mb help 1.1Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘NormalyzerDE:::calculateAvgMadMem’ ‘NormalyzerDE:::calculateAvgReplicateVariation’ ‘NormalyzerDE:::calculatePercentageAvgDiffInMat’ ‘NormalyzerDE:::calculateReplicateCV’ ‘NormalyzerDE:::calculateSummarizedCorrelationVector’ See the note in ?`:::` about the use of this operator.

ProteoDisco

Version: 1.12.0
GitHub: https://github.com/ErasmusMC-CCBC/ProteoDisco
Source code: https://github.com/cran/ProteoDisco
Date/Publication: 2024-10-29
Number of recursive dependencies: 186

Run revdepcheck::revdep_details(, "ProteoDisco") for more info

checking whether package ‘ProteoDisco’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ProteoDisco/new/ProteoDisco.Rcheck/00install.out’ for details.
checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'ProteoDiscography' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking Rd files ... NOTE checkRd: (-1) checkProteotypicFragments.Rd:25: Lost braces; missing escapes or markup? 25 | \item{x}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) checkProteotypicFragments.Rd:39: Lost braces; missing escapes or markup? 39 | {ProteoDiscography} with an additional column specifying the number of proteotypic fragments per record. | ^ checkRd: (-1) generateJunctionModels.Rd:36: Lost braces; missing escapes or markup? 36 | of the given {ProteoDiscography}; strand-information is taken into account. If no strand-information is given, the nearest (or overlapping) known | ^ checkRd: (-1) importGenomicVariants.MAF.Rd:17: Lost braces; missing escapes or markup? ... | ^ checkRd: (-1) importTranscriptSequences.Rd:15: Lost braces; missing escapes or markup? 15 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^ checkRd: (-1) incorporateGenomicVariants.Rd:34: Lost braces; missing escapes or markup? 34 | \code{incorporateMutations} Incorporates SNV, MNV and InDels present in the {ProteoDiscography} on the transcripts. | ^ checkRd: (-1) incorporateGenomicVariants.Rd:17: Lost braces; missing escapes or markup? 17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.} | ^
checking data for non-ASCII characters ... NOTE ``` Error loading dataset 'ProteoDiscographyExample.hg19': Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed

```

ProteoMM

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/ProteoMM
Date/Publication: 2024-10-29
Number of recursive dependencies: 99

Run revdepcheck::revdep_details(, "ProteoMM") for more info

checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT

QDNAseq

Version: 1.42.0
GitHub: https://github.com/ccagc/QDNAseq
Source code: https://github.com/cran/QDNAseq
Date/Publication: 2024-10-29
Number of recursive dependencies: 94

Run revdepcheck::revdep_details(, "QDNAseq") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave EM algorithm started ...

Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. ... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’

SUMMARY: processing the following file failed: ‘QDNAseq.Rnw’

Error: Vignette re-building failed. Execution halted ```

QFeatures

Version: 1.16.0
GitHub: https://github.com/RforMassSpectrometry/QFeatures
Source code: https://github.com/cran/QFeatures
Date/Publication: 2024-10-29
Number of recursive dependencies: 173

Run revdepcheck::revdep_details(, "QFeatures") for more info

checking Rd cross-references ... WARNING ``` Missing link or links in Rd file 'QFeatures-aggregate.Rd': ‘sparseMatrix’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: doc 5.2Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘MultiAssayExperiment:::.sampleMapFromData’ See the note in ?`:::` about the use of this operator.

RaceID

Version: 0.3.9
GitHub: NA
Source code: https://github.com/cran/RaceID
Date/Publication: 2024-11-24 22:50:02 UTC
Number of recursive dependencies: 142

Run revdepcheck::revdep_details(, "RaceID") for more info

checking installed package size ... NOTE installed size is 11.9Mb sub-directories of 1Mb or more: data 2.1Mb doc 6.6Mb libs 2.3Mb

rADA

Version: 1.1.9
GitHub: NA
Source code: https://github.com/cran/rADA
Date/Publication: 2021-03-23 19:40:06 UTC
Number of recursive dependencies: 104

Run revdepcheck::revdep_details(, "rADA") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘rada_vignette.Rmd’ using knitr

Quitting from lines 62-70 [unnamed-chunk-2] (rada_vignette.Rmd) Error: processing vignette 'rada_vignette.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette.Rmd’

--- re-building ‘rada_vignette_supplemental.Rmd’ using knitr ... Quitting from lines 62-70 [unnamed-chunk-2] (rada_vignette_supplemental.Rmd) Error: processing vignette 'rada_vignette_supplemental.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette_supplemental.Rmd’

SUMMARY: processing the following files failed: ‘rada_vignette.Rmd’ ‘rada_vignette_supplemental.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: doc 6.8Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’ All declared Imports should be used.

RadioGx

Version: 2.10.0
GitHub: NA
Source code: https://github.com/cran/RadioGx
Date/Publication: 2024-10-29
Number of recursive dependencies: 149

Run revdepcheck::revdep_details(, "RadioGx") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 3.5Mb
checking data for non-ASCII characters ... NOTE Note: found 52 marked UTF-8 strings

RBesT

Version: 1.7-4
GitHub: https://github.com/Novartis/RBesT
Source code: https://github.com/cran/RBesT
Date/Publication: 2024-11-21 14:10:03 UTC
Number of recursive dependencies: 142

Run revdepcheck::revdep_details(, "RBesT") for more info

checking installed package size ... NOTE installed size is 101.5Mb sub-directories of 1Mb or more: libs 99.5Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

regsem

Version: 1.9.5
GitHub: https://github.com/Rjacobucci/regsem
Source code: https://github.com/cran/regsem
Date/Publication: 2023-06-02 09:00:02 UTC
Number of recursive dependencies: 163

Run revdepcheck::revdep_details(, "regsem") for more info

checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: libs 5.9Mb

reservr

Version: 0.0.3
GitHub: https://github.com/AshesITR/reservr
Source code: https://github.com/cran/reservr
Date/Publication: 2024-06-24 16:40:02 UTC
Number of recursive dependencies: 133

Run revdepcheck::revdep_details(, "reservr") for more info

checking installed package size ... NOTE installed size is 18.7Mb sub-directories of 1Mb or more: R 1.5Mb doc 1.2Mb libs 15.7Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

RGCCA

Version: 3.0.3
GitHub: https://github.com/rgcca-factory/RGCCA
Source code: https://github.com/cran/RGCCA
Date/Publication: 2023-12-11 21:00:06 UTC
Number of recursive dependencies: 190

Run revdepcheck::revdep_details(, "RGCCA") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘RGCCA.Rmd’ using rmarkdown ! LaTeX Error: Fileifsym.sty' not found.

! Emergency stop.

Error: processing vignette 'RGCCA.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RGCCA/new/RGCCA.Rcheck/vign_test/RGCCA/vignettes/RGCCA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RGCCA.log for more info. --- failed re-building ‘RGCCA.Rmd’

SUMMARY: processing the following file failed: ‘RGCCA.Rmd’

Error: Vignette re-building failed. Execution halted ```

RiboDiPA

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/RiboDiPA
Date/Publication: 2024-10-29
Number of recursive dependencies: 153

Run revdepcheck::revdep_details(, "RiboDiPA") for more info

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 2.9Mb doc 1.5Mb libs 1.4Mb
checking R code for possible problems ... NOTE .pMappingChr: no visible global function definition for ‘pcoverageByTranscript’ Undefined global functions or variables: pcoverageByTranscript

RJcluster

Version: 3.2.4
GitHub: NA
Source code: https://github.com/cran/RJcluster
Date/Publication: 2022-02-14 21:30:02 UTC
Number of recursive dependencies: 52

Run revdepcheck::revdep_details(, "RJcluster") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: libs 7.1Mb

RNAmodR

Version: 1.20.0
GitHub: https://github.com/FelixErnst/RNAmodR
Source code: https://github.com/cran/RNAmodR
Date/Publication: 2024-10-29
Number of recursive dependencies: 189

Run revdepcheck::revdep_details(, "RNAmodR") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'Biostrings:::XString' 'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::prepare_objects_to_bind' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.get_inosine_score'
checking Rd files ... NOTE checkRd: (-1) ModInosine-functions.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine-functions.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine.Rd:39-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine.Rd:43-44: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) plotData.Rd:122-124: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:125-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:128-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:130-131: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:99-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:106-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) subsetByCoord.Rd:128-129: Lost braces in \itemize; \value handles \item{}{} directly
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'RNAmodR-internals.Rd': ‘object’ ‘range’ ‘data’ ‘modType’ ‘scoreFun’ ‘source’ ‘type’ ‘j’ ‘value’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

RnBeads

Version: 2.24.0
GitHub: NA
Source code: https://github.com/cran/RnBeads
Date/Publication: 2024-10-29
Number of recursive dependencies: 274

Run revdepcheck::revdep_details(, "RnBeads") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘RnBeads.Rnw’ using Sweave Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'RnBeads.Rnw' failed with diagnostics: unable to run pdflatex on 'RnBeads.tex' LaTeX errors: ! LaTeX Error: Filevmargin.sty' not found.

Type X to quit or to proceed, ... l.10 \usepackage [english,american]{babel}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘RnBeads_Annotations.Rnw’

SUMMARY: processing the following files failed: ‘RnBeads.Rnw’ ‘RnBeads_Annotations.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster', 'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma', 'matrixStats', 'illuminaio', 'methylumi', 'plyr' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: R 3.2Mb doc 4.1Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘qvalue’ A package should be listed in only one of these fields.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE Package in Depends field not imported from: 'grid' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: 'Gviz:::.getBMFeatureMap' 'doParallel:::.options' 'grDevices:::.smoothScatterCalcDensity' 'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k' 'minfi:::.normalizeFunnorm450k' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .stopImplicitCluster: no visible global function definition for ‘stopCluster’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘phenoData’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘assayDataElementNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘featureNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘varLabels’ ... plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable refText reg.type region.size registerDoParallel relative.coord removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore size solve.QP stopCluster sva target texthere tsne type types ucscTableQuery universeCounts useMart v var.diff varFit varLabels x x2 xmlValue y y2 yint Consider adding importFrom("stats", "setNames") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) as.RnBeadRawSet.Rd:9: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.RnBeadRawSet.Rd:10: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.RnBeadRawSet.Rd:11: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:60-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReportPlot.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReportPlot.Rd:49: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) createReportPlot.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:41-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:46: Lost braces in \itemize; meant \describe ?

robustlm

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/robustlm
Date/Publication: 2021-03-22 15:40:02 UTC
Number of recursive dependencies: 28

Run revdepcheck::revdep_details(, "robustlm") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

rpm

Version: 0.7-3
GitHub: https://github.com/handcock/rpm
Source code: https://github.com/cran/rpm
Date/Publication: 2024-04-18 08:20:03 UTC
Number of recursive dependencies: 65

Run revdepcheck::revdep_details(, "rpm") for more info

checking installed package size ... NOTE installed size is 13.4Mb sub-directories of 1Mb or more: libs 12.9Mb

rsvddpd

Version: 1.0.0
GitHub: https://github.com/subroy13/rsvddpd
Source code: https://github.com/cran/rsvddpd
Date/Publication: 2021-10-27 14:30:02 UTC
Number of recursive dependencies: 34

Run revdepcheck::revdep_details(, "rsvddpd") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

rtrend

Version: 0.1.5
GitHub: https://github.com/rpkgs/rtrend
Source code: https://github.com/cran/rtrend
Date/Publication: 2024-01-11 03:30:02 UTC
Number of recursive dependencies: 60

Run revdepcheck::revdep_details(, "rtrend") for more info

checking whether startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```

samr

Version: 3.0
GitHub: NA
Source code: https://github.com/cran/samr
Date/Publication: 2018-10-16 10:00:03 UTC
Number of recursive dependencies: 43

Run revdepcheck::revdep_details(, "samr") for more info

checking Rd files ... NOTE checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$ checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \# checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#

SANvi

Version: 0.1.1
GitHub: https://github.com/fradenti/SANvi
Source code: https://github.com/cran/SANvi
Date/Publication: 2024-05-15 11:40:06 UTC
Number of recursive dependencies: 15

Run revdepcheck::revdep_details(, "SANvi") for more info

checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: libs 9.3Mb

scDataviz

Version: 1.16.0
GitHub: https://github.com/kevinblighe/scDataviz
Source code: https://github.com/cran/scDataviz
Date/Publication: 2024-10-29
Number of recursive dependencies: 188

Run revdepcheck::revdep_details(, "scDataviz") for more info

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: doc 6.1Mb

scDesign3

Version: 1.4.0
GitHub: https://github.com/SONGDONGYUAN1994/scDesign3
Source code: https://github.com/cran/scDesign3
Date/Publication: 2024-10-29
Number of recursive dependencies: 140

Run revdepcheck::revdep_details(, "scDesign3") for more info

checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

scDHA

Version: 1.2.2
GitHub: https://github.com/duct317/scDHA
Source code: https://github.com/cran/scDHA
Date/Publication: 2024-04-02 22:42:03 UTC
Number of recursive dependencies: 61

Run revdepcheck::revdep_details(, "scDHA") for more info

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: data 3.2Mb libs 4.4Mb

scISR

Version: 0.1.1
GitHub: https://github.com/duct317/scISR
Source code: https://github.com/cran/scISR
Date/Publication: 2022-06-30 06:20:08 UTC
Number of recursive dependencies: 47

Run revdepcheck::revdep_details(, "scISR") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘markdown’ All declared Imports should be used.

scmap

Version: 1.28.0
GitHub: https://github.com/hemberg-lab/scmap
Source code: https://github.com/cran/scmap
Date/Publication: 2024-10-29
Number of recursive dependencies: 90

Run revdepcheck::revdep_details(, "scmap") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘scmap.Rmd’ using rmarkdown

Quitting from lines 15-17 [knitr-options] (scmap.Rmd) Error: processing vignette 'scmap.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘scmap.Rmd’

SUMMARY: processing the following file failed: ‘scmap.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 2.6Mb doc 1.1Mb libs 2.3Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Biobase’ All declared Imports should be used.

scMET

Version: 1.8.0
GitHub: https://github.com/andreaskapou/scMET
Source code: https://github.com/cran/scMET
Date/Publication: 2024-10-29
Number of recursive dependencies: 115

Run revdepcheck::revdep_details(, "scMET") for more info

checking installed package size ... NOTE installed size is 70.7Mb sub-directories of 1Mb or more: doc 3.7Mb libs 65.7Mb
checking whether startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking Rd files ... NOTE checkRd: (-1) scmet_differential.Rd:70: Lost braces; missing escapes or markup? 70 | calibration is performed, and `alpha_{E}`` is set to | ^
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

scMultiSim

Version: 1.2.0
GitHub: https://github.com/ZhangLabGT/scMultiSim
Source code: https://github.com/cran/scMultiSim
Date/Publication: 2024-10-29
Number of recursive dependencies: 140

Run revdepcheck::revdep_details(, "scMultiSim") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/shiny-app/www/.prettierrc These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 3.7Mb doc 1.6Mb
checking R code for possible problems ... NOTE .SpatialGrid: no visible global function definition for ‘new’ .amplifyOneCell: no visible binding for global variable ‘len2nfrag’ .atacSeq: no visible binding for global variable ‘dens_nonzero’ .check_opt: no visible binding for global variable ‘val’ .check_opt: no visible binding for global variable ‘checker’ .check_opt: no visible binding for global variable ‘desc’ .check_opt: no visible binding for global variable ‘check’ .check_opt: no visible binding for global variable ‘err_msg’ .check_opt: no visible global function definition for ‘check’ .continuousCIFParamNormal : <anonymous>: no visible binding for global ... path_len paths prcomp regulator rmultinom rowVars target tips to total_ncell val value vx_knn vx_knn2 vx_knn_normalized vx_knn_normalized2 vx_normalized vx_normalized2 vx_raw vx_raw2 vy_knn vy_knn2 vy_knn_normalized vy_knn_normalized2 vy_normalized vy_normalized2 vy_raw vy_raw2 x xend y yend Consider adding importFrom("methods", "new") importFrom("stats", "prcomp", "rmultinom") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

scone

Version: 1.30.0
GitHub: https://github.com/YosefLab/scone
Source code: https://github.com/cran/scone
Date/Publication: 2024-10-29
Number of recursive dependencies: 270

Run revdepcheck::revdep_details(, "scone") for more info

checking R code for possible problems ... NOTE sconeReport: no visible global function definition for ‘visNetworkOutput’ sconeReport: no visible global function definition for ‘plotlyOutput’ sconeReport : server: no visible global function definition for ‘renderVisNetwork’ sconeReport : server: no visible global function definition for ‘%>%’ sconeReport : server: no visible global function definition for ‘visNetwork’ sconeReport : server: no visible global function definition for ‘visHierarchicalLayout’ ... sconeReport : server: no visible global function definition for ‘geom_point’ sconeReport : server: no visible global function definition for ‘guides’ Undefined global functions or variables: %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork scale_fill_manual theme visEdges visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput visNetworkProxy visOptions visSelectNodes ylim
checking Rd files ... NOTE checkRd: (-1) estimate_ziber.Rd:57: Lost braces; missing escapes or markup? 57 | expression rate (Z in {0,1}). Detection conditioned on expression is a | ^ checkRd: (-1) estimate_ziber.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) estimate_ziber.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly ... checkRd: (-1) score_matrix.Rd:98-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) score_matrix.Rd:100-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) score_matrix.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:85-87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) score_matrix.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly

scp

Version: 1.16.0
GitHub: https://github.com/UCLouvain-CBIO/scp
Source code: https://github.com/cran/scp
Date/Publication: 2024-10-29
Number of recursive dependencies: 196

Run revdepcheck::revdep_details(, "scp") for more info

checking installed package size ... NOTE installed size is 12.4Mb sub-directories of 1Mb or more: doc 11.2Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘MultiAssayExperiment:::.sampleMapFromData’ ‘QFeatures:::.get_Hits’ ‘QFeatures:::.normIndex’ See the note in ?`:::` about the use of this operator.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘dplyr’

scPCA

Version: 1.20.0
GitHub: https://github.com/PhilBoileau/scPCA
Source code: https://github.com/cran/scPCA
Date/Publication: 2024-10-29
Number of recursive dependencies: 169

Run revdepcheck::revdep_details(, "scPCA") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DelayedArray’ ‘matrixStats’ All declared Imports should be used.

scpoisson

Version: 0.0.1
GitHub: NA
Source code: https://github.com/cran/scpoisson
Date/Publication: 2022-08-17 06:50:02 UTC
Number of recursive dependencies: 202

Run revdepcheck::revdep_details(, "scpoisson") for more info

checking Rd files ... NOTE checkRd: (-1) HclustDepart.Rd:23: Lost braces; missing escapes or markup? 23 | \item{\code{res2}}: {a data frame contains two columns: names (cell names) and clusters (cluster label)} | ^ checkRd: (-1) HclustDepart.Rd:24-26: Lost braces 24 | \item{\code{sigclust_p}}: {a matrix with cells to cluster as rows, split index as columns, | ^ checkRd: (-1) HclustDepart.Rd:27-29: Lost braces 27 | \item{\code{sigclust_z}}: {a matrix with cells to cluster as rows, split index as columns, | ^ checkRd: (-1) LouvainDepart.Rd:38: Lost braces; missing escapes or markup? ... | ^ checkRd: (-1) sigp.Rd:21: Lost braces 21 | \item{\code{shc_result}}: {a \code{shc} S3-object as defined in sigclust2 package} | ^ checkRd: (-1) sigp.Rd:22: Lost braces; missing escapes or markup? 22 | \item{\code{clust2}}: {a vector with group index for each cell} | ^ checkRd: (-1) sigp.Rd:23: Lost braces; missing escapes or markup? 23 | \item{\code{clust_dat}}: {a matrix of data representation used as input for hierarchical clustering} | ^

sctransform

Version: 0.4.1
GitHub: https://github.com/satijalab/sctransform
Source code: https://github.com/cran/sctransform
Date/Publication: 2023-10-19 04:40:02 UTC
Number of recursive dependencies: 67

Run revdepcheck::revdep_details(, "sctransform") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘glmGamPoi’

sechm

Version: 1.14.0
GitHub: https://github.com/plger/sechm
Source code: https://github.com/cran/sechm
Date/Publication: 2024-10-29
Number of recursive dependencies: 93

Run revdepcheck::revdep_details(, "sechm") for more info

checking R code for possible problems ... NOTE homogenizeDEA: no visible global function definition for ‘head’ homogenizeDEA: no visible global function definition for ‘p.adjust’ setRowAttr : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: head p.adjust setNames Consider adding importFrom("stats", "p.adjust", "setNames") importFrom("utils", "head") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ggplot2’

seeds

Version: 0.9.1
GitHub: https://github.com/Newmi1988/seeds
Source code: https://github.com/cran/seeds
Date/Publication: 2020-07-14 00:00:02 UTC
Number of recursive dependencies: 89

Run revdepcheck::revdep_details(, "seeds") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rsbml’

sensobol

Version: 1.1.5
GitHub: https://github.com/arnaldpuy/sensobol
Source code: https://github.com/cran/sensobol
Date/Publication: 2024-02-21 13:40:02 UTC
Number of recursive dependencies: 87

Run revdepcheck::revdep_details(, "sensobol") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: doc 3.5Mb libs 1.4Mb

seqArchR

Version: 1.10.0
GitHub: https://github.com/snikumbh/seqArchR
Source code: https://github.com/cran/seqArchR
Date/Publication: 2024-12-23
Number of recursive dependencies: 121

Run revdepcheck::revdep_details(, "seqArchR") for more info

checking examples ... ERROR ``` Running examples in ‘seqArchR-Ex.R’ failed The error most likely occurred in:

Name: seqArchR

Title: seqArchR: A package for de novo discovery of different sequence

architectures

Aliases: seqArchR

** Examples

... ── Outer chunk 1 of 1 [Size: 200] ──

── Inner chunk 1 of 2 [Size: 100] Error: BiocParallel errors 2 remote errors, element index: 1, 51 98 unevaluated and other errors first remote error: Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn' Run reticulate::py_last_error() for details. Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...)
1. └─BiocParallel:::.bpinit(...) ── Error ('test_seqArchR_main.R:149:5'): seqArchR (cv) works when timeFlag is FALSE ── ...
  1. └─seqArchR:::.handle_chunk_w_NMF2(...)
  2. └─seqArchR:::.stability_model_select_pyNMF2(...)
  3. └─seqArchR:::.perform_multiple_NMF_runs(...)
  4. ├─BiocParallel::bplapply(...)
  5. └─BiocParallel::bplapply(...)
2. └─BiocParallel:::.bpinit(...)
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] Error: Test failures Execution halted ```

Seurat

Version: 5.1.0
GitHub: https://github.com/satijalab/seurat
Source code: https://github.com/cran/Seurat
Date/Publication: 2024-05-10 17:23:17 UTC
Number of recursive dependencies: 266

Run revdepcheck::revdep_details(, "Seurat") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'BPCells', 'presto'
checking installed package size ... NOTE installed size is 16.0Mb sub-directories of 1Mb or more: R 1.7Mb libs 13.4Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Signac’

SIAMCAT

Version: 2.10.0
GitHub: NA
Source code: https://github.com/cran/SIAMCAT
Date/Publication: 2024-10-29
Number of recursive dependencies: 203

Run revdepcheck::revdep_details(, "SIAMCAT") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 23.7Mb sub-directories of 1Mb or more: doc 18.6Mb extdata 2.1Mb help 1.9Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ranger’

SICtools

Version: 1.36.0
GitHub: NA
Source code: https://github.com/cran/SICtools
Date/Publication: 2024-10-29
Number of recursive dependencies: 51

Run revdepcheck::revdep_details(, "SICtools") for more info

checking whether package ‘SICtools’ can be installed ... WARNING Found the following significant warnings: bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] errmod.c:79:15: warning: self-comparison always evaluates to false [-Wtautological-compare] bam_tview_curses.c:142:18: warning: ‘base’ is used uninitialized [-Wuninitialized] md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] bamcheck.c:1515:15: warning: pointer ‘stats’ used after ‘free’ [-Wuse-after-free] Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SICtools/new/SICtools.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats', 'plyr', 'GenomicRanges', 'IRanges' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE .indelDiffFunc: no visible global function definition for ‘fisher.test’ .indelDiffFunc: no visible global function definition for ‘dist’ indelDiff: no visible global function definition for ‘read.delim’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘fisher.test’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘dist’ Undefined global functions or variables: dist fisher.test read.delim Consider adding importFrom("stats", "dist", "fisher.test") importFrom("utils", "read.delim") to your NAMESPACE file.

sigminer

Version: 2.3.1
GitHub: https://github.com/ShixiangWang/sigminer
Source code: https://github.com/cran/sigminer
Date/Publication: 2024-05-11 08:50:02 UTC
Number of recursive dependencies: 209

Run revdepcheck::revdep_details(, "sigminer") for more info

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: extdata 1.0Mb help 1.7Mb libs 1.6Mb

SimBu

Version: 1.8.0
GitHub: https://github.com/omnideconv/SimBu
Source code: https://github.com/cran/SimBu
Date/Publication: 2024-10-29
Number of recursive dependencies: 199

Run revdepcheck::revdep_details(, "SimBu") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions .pre-commit-config.yaml .prettierignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking whether package ‘SimBu’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SimBu/new/SimBu.Rcheck/00install.out’ for details.

simona

Version: 1.4.0
GitHub: https://github.com/jokergoo/simona
Source code: https://github.com/cran/simona
Date/Publication: 2024-10-29
Number of recursive dependencies: 147

Run revdepcheck::revdep_details(, "simona") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 17.3Mb sub-directories of 1Mb or more: libs 15.5Mb

simPop

Version: 2.1.3
GitHub: https://github.com/statistikat/simPop
Source code: https://github.com/cran/simPop
Date/Publication: 2024-01-08 10:40:02 UTC
Number of recursive dependencies: 117

Run revdepcheck::revdep_details(, "simPop") for more info

checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: data 2.0Mb libs 5.7Mb

Single.mTEC.Transcriptomes

Version: 1.34.0
GitHub: NA
Source code: https://github.com/cran/Single.mTEC.Transcriptomes
Date/Publication: 2024-10-31
Number of recursive dependencies: 177

Run revdepcheck::revdep_details(, "Single.mTEC.Transcriptomes") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘mTECs.Rnw’ using knitr The magick package is required to crop "figure/Figure_1C_variableNoMarker-1.png" but not available. The magick package is required to crop "figure/Figure_1A_trasvsgenes-1.png" but not available. The magick package is required to crop "figure/Figure_Supp1_percentageTRAs-1.png" but not available. The magick package is required to crop "figure/Figure_1B_saturation-1.png" but not available. The magick package is required to crop "figure/Figure_Supp2_traenrichment-1.png" but not available. The magick package is required to crop "figure/Figure_1D1_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D2_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D3_histogramAire-1.png" but not available. ... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘mTECs.Rnw’

SUMMARY: processing the following file failed: ‘mTECs.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 916.9Mb sub-directories of 1Mb or more: data 903.6Mb doc 13.2Mb
checking Rd metadata ... NOTE Invalid package aliases in Rd file 'Single.mTec.Transcriptomes-package.Rd': ‘Single.mTec.Transcriptomes-package’

singleCellTK

Version: 2.16.0
GitHub: https://github.com/compbiomed/singleCellTK
Source code: https://github.com/cran/singleCellTK
Date/Publication: 2024-10-29
Number of recursive dependencies: 405

Run revdepcheck::revdep_details(, "singleCellTK") for more info

checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: R 1.0Mb extdata 1.5Mb shiny 3.0Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

singscore

Version: 1.26.0
GitHub: https://github.com/DavisLaboratory/singscore
Source code: https://github.com/cran/singscore
Date/Publication: 2024-10-29
Number of recursive dependencies: 145

Run revdepcheck::revdep_details(, "singscore") for more info

checking R code for possible problems ... NOTE plotDispersion: no visible binding for global variable ‘Score’ plotDispersion: no visible binding for global variable ‘Dispersion’ plotDispersion: no visible binding for global variable ‘Class’ plotDispersion: no visible binding for global variable ‘SampleText’ plotDispersion: no visible binding for global variable ‘SampleLabel’ plotRankDensity_intl: no visible binding for global variable ‘Ranks’ plotRankDensity_intl: no visible binding for global variable ‘upDown’ plotRankDensity_intl: no visible binding for global variable ‘..density..’ plotRankDensity_intl: no visible binding for global variable ‘EntrezID’ ... plotScoreLandscape: no visible binding for global variable ‘sc1’ plotScoreLandscape: no visible binding for global variable ‘sc2’ projectScoreLandscape: no visible binding for global variable ‘SampleText’ projectScoreLandscape: no visible binding for global variable ‘Class’ projectScoreLandscape: no visible binding for global variable ‘SampleLabel’ Undefined global functions or variables: ..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText Score sc1 sc2 upDown

slasso

Version: 1.0.0
GitHub: https://github.com/unina-sfere/slasso
Source code: https://github.com/cran/slasso
Date/Publication: 2021-10-15 07:40:02 UTC
Number of recursive dependencies: 96

Run revdepcheck::revdep_details(, "slasso") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: R 4.5Mb libs 1.5Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RcppArmadillo’ All declared Imports should be used.

slingshot

Version: 2.14.0
GitHub: https://github.com/kstreet13/slingshot
Source code: https://github.com/cran/slingshot
Date/Publication: 2024-10-29
Number of recursive dependencies: 187

Run revdepcheck::revdep_details(, "slingshot") for more info

checking Rd files ... NOTE checkRd: (-1) SlingshotDataSet-class.Rd:76-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:79-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:81-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:83-84: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:85-87: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:88-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:96-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:100-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:105-112: Lost braces in \itemize; meant \describe ? ... checkRd: (-1) slingParams.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:45-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:49-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:54-61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:62-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:68-70: Lost braces in \itemize; \value handles \item{}{} directly

SpaNorm

Version: 1.0.0
GitHub: https://github.com/bhuvad/SpaNorm
Source code: https://github.com/cran/SpaNorm
Date/Publication: 2024-10-29
Number of recursive dependencies: 222

Run revdepcheck::revdep_details(, "SpaNorm") for more info

checking installed package size ... NOTE installed size is 8.5Mb sub-directories of 1Mb or more: data 4.2Mb doc 4.0Mb
checking R code for possible problems ... NOTE plotSpatial: no visible binding for global variable ‘x’ plotSpatial: no visible binding for global variable ‘y’ plotSpatial: no visible binding for global variable ‘colour’ plotSpatial: no visible binding for global variable ‘r’ Undefined global functions or variables: colour r x y

sparrow

Version: 1.12.0
GitHub: https://github.com/lianos/sparrow
Source code: https://github.com/cran/sparrow
Date/Publication: 2024-10-29
Number of recursive dependencies: 205

Run revdepcheck::revdep_details(, "sparrow") for more info

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: R 1.1Mb doc 2.1Mb extdata 2.1Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking R code for possible problems ... NOTE geneSetsStats: no visible binding for global variable ‘direction’ Undefined global functions or variables: direction

SparseArray

Version: 1.6.0
GitHub: https://github.com/Bioconductor/SparseArray
Source code: https://github.com/cran/SparseArray
Date/Publication: 2024-10-29
Number of recursive dependencies: 99

Run revdepcheck::revdep_details(, "SparseArray") for more info

checking compiled code ... NOTE ``` File ‘SparseArray/libs/SparseArray.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’, ‘Rf_isBlankString’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

sparseMatrixStats

Version: 1.18.0
GitHub: https://github.com/const-ae/sparseMatrixStats
Source code: https://github.com/cran/sparseMatrixStats
Date/Publication: 2024-10-29
Number of recursive dependencies: 57

Run revdepcheck::revdep_details(, "sparseMatrixStats") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: libs 5.3Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘SummarizedExperiment’

spatzie

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/spatzie
Date/Publication: 2024-10-29
Number of recursive dependencies: 192

Run revdepcheck::revdep_details(, "spatzie") for more info

checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

splatter

Version: 1.30.0
GitHub: https://github.com/Oshlack/splatter
Source code: https://github.com/cran/splatter
Date/Publication: 2024-10-29
Number of recursive dependencies: 250

Run revdepcheck::revdep_details(, "splatter") for more info

checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: doc 9.4Mb

SpliceWiz

Version: 1.8.0
GitHub: https://github.com/alexchwong/SpliceWiz
Source code: https://github.com/cran/SpliceWiz
Date/Publication: 2024-10-29
Number of recursive dependencies: 204

Run revdepcheck::revdep_details(, "SpliceWiz") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 20.3Mb sub-directories of 1Mb or more: R 2.3Mb doc 6.1Mb libs 10.8Mb
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.

SPOTlight

Version: 1.10.0
GitHub: https://github.com/MarcElosua/SPOTlight
Source code: https://github.com/cran/SPOTlight
Date/Publication: 2024-10-29
Number of recursive dependencies: 199

Run revdepcheck::revdep_details(, "SPOTlight") for more info

checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: doc 4.7Mb

spqn

Version: 1.18.0
GitHub: https://github.com/hansenlab/spqn
Source code: https://github.com/cran/spqn
Date/Publication: 2024-10-29
Number of recursive dependencies: 78

Run revdepcheck::revdep_details(, "spqn") for more info

checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘BiocGenerics’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

stabiliser

Version: 1.0.6
GitHub: NA
Source code: https://github.com/cran/stabiliser
Date/Publication: 2023-05-17 11:00:05 UTC
Number of recursive dependencies: 148

Run revdepcheck::revdep_details(, "stabiliser") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘knitr’ All declared Imports should be used.

stapler

Version: 0.7.1
GitHub: https://github.com/muschellij2/stapler
Source code: https://github.com/cran/stapler
Date/Publication: 2020-01-09 18:50:06 UTC
Number of recursive dependencies: 56

Run revdepcheck::revdep_details(, "stapler") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

staRdom

Version: 1.1.28
GitHub: https://github.com/MatthiasPucher/staRdom
Source code: https://github.com/cran/staRdom
Date/Publication: 2023-06-16 08:20:02 UTC
Number of recursive dependencies: 147

Run revdepcheck::revdep_details(, "staRdom") for more info

checking Rd files ... NOTE checkRd: (-1) abs_parms.Rd:67: Lost braces; missing escapes or markup? 67 | \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression | ^ checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup? 68 | \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression | ^ checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup? 69 | \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression | ^ checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup? ... | ^ checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup? 72 | \item E4:E6 ratio $a_{465}$/$a_{665}$ | ^ checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup? 73 | \item $a_{254}$ absorbance at 254 nm | ^ checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup? 74 | \item $a_{300}$ absorbance at 300 nm | ^

stm

Version: 1.3.7
GitHub: https://github.com/bstewart/stm
Source code: https://github.com/cran/stm
Date/Publication: 2023-12-01 22:30:02 UTC
Number of recursive dependencies: 80

Run revdepcheck::revdep_details(, "stm") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘stmVignette.Rnw’ using Sweave stm v1.3.7 successfully loaded. See ?stm for help. Papers, resources, and other materials at structuraltopicmodel.com Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error: processing vignette 'stmVignette.Rnw' failed with diagnostics: unable to run pdflatex on 'stmVignette.tex' LaTeX errors: ! LaTeX Error: Fileulem.sty' not found. ... l.57 ^^M

! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'stmVignette.Rnw'

SUMMARY: processing the following file failed: 'stmVignette.Rnw'

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 2.5Mb libs 3.2Mb

summarytools

Version: 1.0.1
GitHub: https://github.com/dcomtois/summarytools
Source code: https://github.com/cran/summarytools
Date/Publication: 2022-05-20 07:30:05 UTC
Number of recursive dependencies: 74

Run revdepcheck::revdep_details(, "summarytools") for more info

checking whether package ‘summarytools’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/summarytools/new/summarytools.Rcheck/00install.out’ for details.
checking data for non-ASCII characters ... NOTE Note: found 78 marked UTF-8 strings

SuperCell

Version: 1.0.1
GitHub: https://github.com/GfellerLab/SuperCell
Source code: https://github.com/cran/SuperCell
Date/Publication: 2024-10-25 11:30:02 UTC
Number of recursive dependencies: 252

Run revdepcheck::revdep_details(, "SuperCell") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘velocyto.R’

surveyPrev

Version: 1.0.0
GitHub: https://github.com/richardli/surveyPrev
Source code: https://github.com/cran/surveyPrev
Date/Publication: 2024-04-10 19:50:02 UTC
Number of recursive dependencies: 166

Run revdepcheck::revdep_details(, "surveyPrev") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 3.0Mb doc 2.5Mb

susieR

Version: 0.12.35
GitHub: https://github.com/stephenslab/susieR
Source code: https://github.com/cran/susieR
Date/Publication: 2023-02-17 17:50:02 UTC
Number of recursive dependencies: 76

Run revdepcheck::revdep_details(, "susieR") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘finemapping.Rmd’ using rmarkdown --- finished re-building ‘finemapping.Rmd’

--- re-building ‘finemapping_summary_statistics.Rmd’ using rmarkdown --- finished re-building ‘finemapping_summary_statistics.Rmd’

--- re-building ‘mwe.Rmd’ using rmarkdown --- finished re-building ‘mwe.Rmd’

... l.8 \usepackage {xspace}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘trendfiltering_derivations.Rnw’

SUMMARY: processing the following file failed: ‘trendfiltering_derivations.Rnw’

Error: Vignette re-building failed. Execution halted ```

sva

Version: 3.54.0
GitHub: NA
Source code: https://github.com/cran/sva
Date/Publication: 2024-10-29
Number of recursive dependencies: 98

Run revdepcheck::revdep_details(, "sva") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘sva.Rnw’ using Sweave Loading required package: mgcv Loading required package: nlme This is mgcv 1.9-1. For overview type 'help("mgcv-package")'. Loading required package: genefilter Loading required package: BiocParallel Loading required package: Biobase Loading required package: BiocGenerics

... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘sva.Rnw’

SUMMARY: processing the following file failed: ‘sva.Rnw’

Error: Vignette re-building failed. Execution halted ```

TCA

Version: 1.2.1
GitHub: https://github.com/cozygene/TCA
Source code: https://github.com/cran/TCA
Date/Publication: 2021-02-14 21:50:06 UTC
Number of recursive dependencies: 60

Run revdepcheck::revdep_details(, "TCA") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup? 35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.} | ^
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

templateICAr

Version: 0.9.1
GitHub: https://github.com/mandymejia/templateICAr
Source code: https://github.com/cran/templateICAr
Date/Publication: 2024-11-21 16:50:02 UTC
Number of recursive dependencies: 133

Run revdepcheck::revdep_details(, "templateICAr") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’

tidybulk

Version: 1.18.0
GitHub: https://github.com/stemangiola/tidybulk
Source code: https://github.com/cran/tidybulk
Date/Publication: 2024-10-29
Number of recursive dependencies: 404

Run revdepcheck::revdep_details(, "tidybulk") for more info

checking R code for possible problems ... NOTE .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘group_name’ .aggregate_duplicates_se: no visible binding for global variable ‘group’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ... sample b sample_idx samples sdev se_data seurat_clusters surv_test tagwise.dispersion temp term test tot tot_filt transcript transcript_upper tt_columns update.formula upper value variable vcov web_page where with_groups x Consider adding importFrom("base", "sample") importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik", "predict", "update.formula", "vcov") importFrom("utils", "combn") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) remove_redundancy-methods.Rd:158-175: Lost braces 158 | select_closest_pairs = function(df) { | ^ checkRd: (-1) remove_redundancy-methods.Rd:161-171: Lost braces 161 | while (df |> nrow() > 0) { | ^ checkRd: (-1) rotate_dimensions-methods.Rd:126-134: Lost braces 126 | rotation = function(m, d) { | ^
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk.Rd': ‘log_transform’

Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk_SE.Rd': ‘.abundance’ ‘.feature’ ‘.element’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

TopDom

Version: 0.10.1
GitHub: https://github.com/HenrikBengtsson/TopDom
Source code: https://github.com/cran/TopDom
Date/Publication: 2021-05-06 07:40:03 UTC
Number of recursive dependencies: 36

Run revdepcheck::revdep_details(, "TopDom") for more info

checking Rd files ... NOTE checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup? 21 | Recommended range is in {5, ..., 20}.} | ^

topGO

Version: 2.58.0
GitHub: NA
Source code: https://github.com/cran/topGO
Date/Publication: 2024-10-29
Number of recursive dependencies: 58

Run revdepcheck::revdep_details(, "topGO") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘topGO.Rnw’ using Sweave

Loading required package: xtable Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

... l.11 \usepackage {caption}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘topGO.Rnw’

SUMMARY: processing the following file failed: ‘topGO.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi', 'SparseM' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking whether startup messages can be suppressed ... NOTE ```

groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Rgraphviz’ ‘multtest’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing object imported by a ':::' call: ‘globaltest:::globaltest’

tradeSeq

Version: 1.20.0
GitHub: https://github.com/statOmics/tradeSeq
Source code: https://github.com/cran/tradeSeq
Date/Publication: 2024-10-29
Number of recursive dependencies: 178

Run revdepcheck::revdep_details(, "tradeSeq") for more info

checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: doc 6.6Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Biobase’ ‘igraph’ All declared Imports should be used.
checking R code for possible problems ... NOTE .earlyDETest: no visible binding for global variable ‘X1’ .earlyDETest: no visible binding for global variable ‘X2’ .findKnots: no visible binding for global variable ‘t1’ .findKnots: no visible binding for global variable ‘l1’ .plotGeneCount: no visible binding for global variable ‘dim1’ .plotGeneCount: no visible binding for global variable ‘dim2’ .plotSmoothers: no visible binding for global variable ‘time’ .plotSmoothers: no visible binding for global variable ‘gene_count’ .plotSmoothers: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ... ‘pCol’ .plotSmoothers_sce: no visible binding for global variable ‘time’ .plotSmoothers_sce: no visible binding for global variable ‘gene_count’ .plotSmoothers_sce: no visible binding for global variable ‘lineage’ .plotSmoothers_sce: no visible binding for global variable ‘pCol’ Undefined global functions or variables: X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time Consider adding importFrom("stats", "time") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) fitGAM.Rd:151-154: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:155-156: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:157-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:159-160: Lost braces in \itemize; meant \describe ?

TRESS

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/TRESS
Date/Publication: 2024-10-29
Number of recursive dependencies: 86

Run revdepcheck::revdep_details(, "TRESS") for more info

checking package dependencies ... NOTE Vignette dependency required without any vignettes:: ‘knitr’
checking Rd files ... NOTE checkRd: (-1) CallCandidates.Rd:61: Escaped LaTeX specials: \& checkRd: (-1) CallCandidates.Rd:63: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.multiRep.Rd:7: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.paramEsti.Rd:10: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.paramEsti.Rd:23: Escaped LaTeX specials: \& checkRd: (-1) findBumps.Rd:8: Escaped LaTeX specials: \&

VanillaICE

Version: 1.68.0
GitHub: NA
Source code: https://github.com/cran/VanillaICE
Date/Publication: 2024-10-29
Number of recursive dependencies: 87

Run revdepcheck::revdep_details(, "VanillaICE") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMC', 'doMPI', 'doSNOW', 'doParallel', 'doRedis'
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: R 1.2Mb doc 1.1Mb extdata 2.1Mb
checking whether startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’ ‘MatrixGenerics’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) TransitionParam.Rd:27: Lost braces; missing escapes or markup? 27 | computed as e^{-2*d/taup}, where d is the distance between markers | ^

variancePartition

Version: 1.36.2
GitHub: https://github.com/DiseaseNeuroGenomics/variancePartition
Source code: https://github.com/cran/variancePartition
Date/Publication: 2024-11-08
Number of recursive dependencies: 202

Run revdepcheck::revdep_details(, "variancePartition") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘FAQ.Rmd’ using rmarkdown --- finished re-building ‘FAQ.Rmd’

--- re-building ‘additional_visualization.Rmd’ using rmarkdown --- finished re-building ‘additional_visualization.Rmd’

--- re-building ‘dream.Rmd’ using rmarkdown --- finished re-building ‘dream.Rmd’

... --- finished re-building ‘rnd_effects.Rmd’

--- re-building ‘variancePartition.Rmd’ using rmarkdown --- finished re-building ‘variancePartition.Rmd’

SUMMARY: processing the following file failed: ‘mvtests.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘zenith’
checking installed package size ... NOTE installed size is 8.5Mb sub-directories of 1Mb or more: data 1.3Mb doc 6.0Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘lmerTest:::as_lmerModLT’ See the note in ?`:::` about the use of this operator.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in Rd file 'residuals.MArrayLM2.Rd': ‘residuals.MArrayLM2’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘GSEABase’ ‘doParallel’

VaSP

Version: 1.18.0
GitHub: https://github.com/yuhuihui2011/VaSP
Source code: https://github.com/cran/VaSP
Date/Publication: 2024-10-29
Number of recursive dependencies: 96

Run revdepcheck::revdep_details(, "VaSP") for more info

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 3.5Mb

Voyager

Version: 1.8.1
GitHub: https://github.com/pachterlab/voyager
Source code: https://github.com/cran/Voyager
Date/Publication: 2024-11-01
Number of recursive dependencies: 235

Run revdepcheck::revdep_details(, "Voyager") for more info

checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (16): 'test-bivariate.R:130:5', 'test-bivariate.R:151:5', 'test-gstat.R:187:5', 'test-plot.R:356:5', 'test-plot.R:402:5', 'test-plot.R:439:5', 'test-plot.R:457:5', 'test-plot.R:471:5', 'test-plot.R:521:5', 'test-plot.R:599:5', 'test-plot.R:632:5', 'test-plot.R:654:5', 'test-plot.R:814:5', 'test-plot.R:849:5', ... • plot/plotcorrelogram-coldata-i.svg • plot/plotcorrelogram-continuous-color-by.svg • plot/plotcorrelogram-one-gene-c.svg • plot/plotcorrelogram-one-gene-corr.svg • plot/plotcorrelogram-specify-gene-and-coldata-i.svg • plot/plotdimloadings-not-balanced.svg • plot/with-subset-freqpoly.svg • plot/with-subset.svg Error: Test failures Execution halted
checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: doc 4.9Mb
checking R code for possible problems ... NOTE .get_tx_df: no visible binding for global variable ‘cell_col’ .get_tx_df: no visible global function definition for ‘getTechTxFields’ .get_tx_df: no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : <anonymous>: no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : <anonymous>: no visible global function definition for ‘rowGeometryNames’ .get_tx_df : <anonymous>: no visible global function definition for ‘st_is_empty’ .get_tx_df : <anonymous>: no visible global function definition for ‘readSelectTx’ .plot_var_sf: no visible binding for global variable ‘gene’ plotTxBin2D: no visible binding for global variable ‘X’ plotTxBin2D: no visible binding for global variable ‘Y’ Undefined global functions or variables: X Y cell_col gdalParquetAvailable gene getTechTxFields readSelectTx rowGeometryNames st_is_empty

vsclust

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/vsclust
Date/Publication: 2024-10-29
Number of recursive dependencies: 162

Run revdepcheck::revdep_details(, "vsclust") for more info

checking for code/documentation mismatches ... WARNING ``` Codoc mismatches from Rd file 'estimClustNum.Rd': estimClustNum Code: function(dat, maxClust = 25, scaling = "standardize", cores = 1) Docs: function(dat, maxClust = 25, cores = 1) Argument names in code not in docs: scaling Mismatches in argument names: Position: 3 Code: scaling Docs: cores

... runClustWrapper Code: function(dat, NClust, proteins = NULL, VSClust = TRUE, scaling = "standardize", cores, verbose = FALSE) Docs: function(dat, NClust, proteins = NULL, VSClust = TRUE, cores, verbose = FALSE) Argument names in code not in docs: scaling Mismatches in argument names: Position: 5 Code: scaling Docs: cores Position: 6 Code: cores Docs: verbose ```
checking installed package size ... NOTE installed size is 8.5Mb sub-directories of 1Mb or more: doc 4.7Mb libs 1.9Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE runFuncEnrich: no visible global function definition for ‘compareCluster’ runFuncEnrich: no visible global function definition for ‘new’ Undefined global functions or variables: compareCluster new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd files ... NOTE prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples

wateRmelon

Version: 2.12.0
GitHub: NA
Source code: https://github.com/cran/wateRmelon
Date/Publication: 2024-10-29
Number of recursive dependencies: 186

Run revdepcheck::revdep_details(, "wateRmelon") for more info

checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘R.utils’ Packages in Depends field not imported from: ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘matrixStats’ ‘methylumi’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘minfi:::.annoGet’ ‘minfi:::.availableAnnotation’ ‘minfi:::.isRGOrStop’ See the note in ?`:::` about the use of this operator.
checking Rd metadata ... WARNING Rd files with duplicated alias 'NChannelSetToMethyLumiSet2': ‘NChannelSetToMethyLumiSet2.Rd’ ‘wm_internal.Rd’ Rd files with duplicated alias 'fot': ‘dot-getManifestString.Rd’ ‘got.Rd’ Rd files with duplicated alias 'got': ‘dot-getManifestString.Rd’ ‘got.Rd’
checking for missing documentation entries ... WARNING Undocumented data sets: ‘ageCoefs’ ‘epicV2.controls’ ‘sex_coef’ Undocumented S4 methods: generic 'adjustedDasen' and siglist 'MethyLumiSet' generic 'adjustedDasen' and siglist 'MethylSet' generic 'adjustedDasen' and siglist 'RGChannelSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'readEPIC.Rd': readEPIC Code: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, two = TRUE, ...) Docs: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, ...) Argument names in code not in docs: two Mismatches in argument names: Position: 8 Code: two Docs: ...
checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'canno.Rd' ‘name’

Undocumented arguments in Rd file 'dot-createAnnotation.Rd' ‘object’

Documented arguments not in \usage in Rd file 'dot-getManifestString.Rd': ‘x’ ‘obj’ ‘fd’ ‘rn’

Undocumented arguments in Rd file 'epicv2clean.default.Rd' ... Undocumented arguments in Rd file 'readPepo.Rd' ‘oob’ Documented arguments not in \usage in Rd file 'readPepo.Rd': ‘keep’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE readPepo: warning in dir(idatdir, patt = "idat"): partial argument match of 'patt' to 'pattern' .adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no visible global function definition for ‘colQuantiles’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getMeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getUnmeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘assay<-’ ... getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls hm450.ordering intensitiesByChannel letterFrequency mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd oligonucleotideFrequency preprocessNoob preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pvals rowMeans2 seqnames sex_coef subsetByLoci unmethylated unmethylated<- warn Consider adding importFrom("utils", "head") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) combo.Rd:24: Lost braces; missing escapes or markup? 24 | and \code{phenoData} are joined on \code{sampleName} . \code{featureData} and {annotation} are taken from | ^
checking Rd contents ... NOTE Argument items with no description in Rd file 'read.manifest.Rd': ‘file’ Argument items with no description in Rd file 'wm_internal.Rd': ‘mats’ ‘chans’ ‘parallel’ ‘protocol.data’ ‘IDAT’ ‘force’

WaverideR

Version: 0.3.2
GitHub: https://github.com/stratigraphy/WaverideR
Source code: https://github.com/cran/WaverideR
Date/Publication: 2023-09-06 15:40:02 UTC
Number of recursive dependencies: 164

Run revdepcheck::revdep_details(, "WaverideR") for more info

checking whether package ‘WaverideR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/WaverideR/new/WaverideR.Rcheck/00install.out’ for details.
checking Rd files ... NOTE checkRd: (-1) anchor_points_grey.Rd:9: Lost braces 9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr | ^ checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces 206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates | ^ checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces 40 | link[WaverideR]{analyze_wavelet} wavelet function | ^ checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces 41 | To create a list use the link[base]{list} function} | ^ checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces 44 | To create the matrix use the link[base]{cbind} function and only add the | ^

winputall

Version: 1.0.1
GitHub: NA
Source code: https://github.com/cran/winputall
Date/Publication: 2024-06-07 14:40:02 UTC
Number of recursive dependencies: 102

Run revdepcheck::revdep_details(, "winputall") for more info

checking installed package size ... NOTE installed size is 103.2Mb sub-directories of 1Mb or more: libs 102.8Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

WQM

Version: 0.1.4
GitHub: NA
Source code: https://github.com/cran/WQM
Date/Publication: 2024-10-11 08:00:18 UTC
Number of recursive dependencies: 81

Run revdepcheck::revdep_details(, "WQM") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘wmtsa’

zinbwave

Version: 1.28.0
GitHub: https://github.com/drisso/zinbwave
Source code: https://github.com/cran/zinbwave
Date/Publication: 2024-10-29
Number of recursive dependencies: 169

Run revdepcheck::revdep_details(, "zinbwave") for more info

checking Rd files ... NOTE checkRd: (-1) zinbSim.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) zinbSim.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) zinbSim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) zinbSim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly

zitools

Version: 1.0.0
GitHub: https://github.com/kreutz-lab/zitools
Source code: https://github.com/cran/zitools
Date/Publication: 2024-10-29
Number of recursive dependencies: 176

Run revdepcheck::revdep_details(, "zitools") for more info

checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'rowQuantiles.Rd': \S4method{rowQuantiles}{Zi} Code: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ..., useNames = TRUE, drop = TRUE) Docs: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = TRUE, type = 7L, ..., useNames = TRUE, drop = TRUE) Argument names in code not in docs: digits ... = 1, by = 0.25), na.rm = TRUE, type = 7L, ..., useNames = TRUE, drop = TRUE) Argument names in code not in docs: digits Mismatches in argument names: Position: 7 Code: digits Docs: ... Position: 8 Code: ... Docs: useNames Position: 9 Code: useNames Docs: drop Mismatches in argument default values: Name: 'na.rm' Code: FALSE Docs: TRUE
checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘zitools_tutorial.Rmd’ using rmarkdown ! LaTeX Error: Filetitling.sty' not found.

! Emergency stop.

Error: processing vignette 'zitools_tutorial.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/zitools/new/zitools.Rcheck/vign_test/zitools/vignettes/zitools_tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See zitools_tutorial.log for more info. --- failed re-building ‘zitools_tutorial.Rmd’

SUMMARY: processing the following file failed: ‘zitools_tutorial.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF.
checking R code for possible problems ... NOTE calcWeights: no visible global function definition for ‘predict’ omit_str_zero: no visible global function definition for ‘predict’ Undefined global functions or variables: predict Consider adding importFrom("stats", "predict") to your NAMESPACE file.

HenrikBengtsson/matrixStats documentation built on Jan. 11, 2025, 7:46 p.m.

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HenrikBengtsson/matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors)

revdep/R_MATRIXSTATS_TIES_METHOD_MISSING=defunct/problems.md In HenrikBengtsson/matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

abcrf

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airpart

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AlpsNMR

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AMARETTO

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amplican

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apollo

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aroma.affymetrix

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aroma.core

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aroma.light

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autonomics

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bage

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bahc

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Banksy

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BASiCS

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BatchQC

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BayesfMRI

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BayesianPlatformDesignTimeTrend

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bcf

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bingat

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BioNERO

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biscuiteer

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blackbox

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BloodGen3Module

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bmm

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bnbc

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bnclassify

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bnem

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brms

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BSgenome

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Name: SNPlocs-class

Title: SNPlocs objects

Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs

ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs

OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method

providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName

releaseName,SNPlocs-method referenceGenome

BSW

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bulkAnalyseR

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bumphunter

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CARBayesST

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cardelino

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CATALYST

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causalOT

HenrikBengtsson/matrixStats
Functions that Apply to Rows and Columns of Matrices (and to Vectors)

revdep/R_MATRIXSTATS_TIES_METHOD_MISSING=defunct/problems.md
In HenrikBengtsson/matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)