Run 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 /wynton/home/cbi/hb/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 /wynton/home/cbi/hb/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 /wynton/home/cbi/hb/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 ```
Run revdep_details(, "AMARETTO")
for more info
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'get_firehoseData':
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 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
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘Downloads’
Run revdep_details(, "amplican")
for more info
Package unavailable to check Rd xrefs: ‘CrispRVariants’
Run revdep_details(, "aroma.core")
for more info
Packages suggested but not available for checking:
'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Run revdep_details(, "aroma.light")
for more info
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.
Run revdep_details(, "autonomics")
for more info
checking examples ... ERROR ``` Running examples in ‘autonomics-Ex.R’ failed The error most likely occurred in:
Name: create_design
Title: Create design
Aliases: create_design
** Examples
file <- download_data('billing19.rnacounts.txt') ... unique(create_design(object)) Design: ~1 Intercept E00_R1 1
file <- download_data('atkin18.somascan.adat') object <- read_somascan(file, plot=FALSE) Error in (1 + f_col):n_col : NA/NaN argument Calls: read_somascan -> .read_somascan Execution halted ```
checking tests ...
``
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 50 lines of output:
── Error ('test_3_read_somascan_atkin18.R:14:5'): read_somascan(file, subgroupvar = NULL) works ──
Error in
(1 + f_col):n_col`: NA/NaN argument
Backtrace:
▆
(1 + f_col):n_col
: NA/NaN argument
Backtrace:
▆[ FAIL 9 | WARN 0 | SKIP 0 | PASS 74 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘using_autonomics.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-2.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-3.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-4.png" but not available. trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts.csv.gz?tool=geoquery' Content type 'application/x-gzip' length 8347405 bytes (8.0 MB) ================================================== downloaded 8.0 MB ... Quitting from lines 199-202 [unnamed-chunk-11] (using_autonomics.Rmd) Error: processing vignette 'using_autonomics.Rmd' failed with diagnostics: NA/NaN argument --- failed re-building ‘using_autonomics.Rmd’
SUMMARY: processing the following file failed: ‘using_autonomics.Rmd’
Error: Vignette re-building failed. Execution halted ```
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.
Run revdep_details(, "bahc")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "BASiCS")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "BatchQC")
for more info
checking R code for possible problems ... NOTE
gene_plot: no visible global function definition for ‘boxplot’
gene_plot: no visible binding for global variable ‘batch’
gls.series.C: no visible global function definition for ‘lm.fit’
sample_plot: no visible global function definition for ‘boxplot’
sample_plot: no visible binding for global variable ‘batch’
Undefined global functions or variables:
batch boxplot lm.fit
Consider adding
importFrom("graphics", "boxplot")
importFrom("stats", "lm.fit")
to your NAMESPACE file.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘batchQC.html’ ‘batchqc_report.Rmd’ ‘batchqc_report.html’
‘batchqc_report.knit.md’ ‘batchqc_report_files’ ‘libs’
Run 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 5.6Mb
sub-directories of 1Mb or more:
libs 5.4Mb
Run revdep_details(, "BayesianPlatformDesignTimeTrend")
for more info
checking installed package size ... NOTE
installed size is 38.4Mb
sub-directories of 1Mb or more:
libs 38.0Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "baystability")
for more info
Namespaces in Imports field not imported from:
‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
All declared Imports should be used.
Run revdep_details(, "bingat")
for more info
Package unavailable to check Rd xrefs: ‘genalg’
Run 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 ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘DSS’
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.
Run 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 ‘/wynton/home/cbi/hb/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.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘GEOquery’ ‘GSE13015’ ‘R.methodsS3’ ‘R.oo’ ‘R.utils’ ‘data.table’
‘hms’ ‘progress’ ‘readr’ ‘tzdb’ ‘vroom’
Run revdep_details(, "bnbc")
for more info
checkRd: (5) ContactGroup-class.Rd:72-74: \item in \describe must have non-empty label
Run revdep_details(, "bnem")
for more info
Namespace in Imports field not imported from: ‘rmarkdown’
All declared Imports should be used.
Run revdep_details(, "brms")
for more info
Package suggested but not available for checking: ‘cmdstanr’
Run 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
... seqlevelsStyle(my_cds) # UCSC [1] "UCSC" seqlevelsStyle(snps) # NCBI [1] "NCBI" seqlevelsStyle(my_cds) <- seqlevelsStyle(snps) Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable to find FTP dir for assembly GCF_000001405.40 in https://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’
‘forgeMaskedBSgenomeDataPkg’
‘getBatchesByOverlapsFromOnDiskLongTable’
‘getBatchesBySeqnameFromOnDiskLongTable’
‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
‘getRowsByIdFromOnDiskLongTable’
‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’
...
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 for portable file names ... NOTE ``` Found the following non-portable file path: BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R
Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely ‘inst/CITATION’ should be used instead.
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.
Run revdep_details(, "BSW")
for more info
'LazyData' is specified without a 'data' directory
Run 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
Run revdep_details(, "cardelino")
for more info
Package which this enhances but not available for checking: ‘doMC’
Run revdep_details(, "CATALYST")
for more info
checking examples ... ERROR ``` Running examples in ‘CATALYST-Ex.R’ failed The error most likely occurred in:
Name: plotDR
Title: Plot reduced dimensions
Aliases: plotDR
** Examples
construct SCE & run clustering
...
run clustering & dimension reduction
sce <- cluster(sce) o running FlowSOM clustering... o running ConsensusClusterPlus metaclustering... sce <- runDR(sce, dr = "UMAP", cells = 100) Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: runDR ... irlba_tsvd_normalized_laplacian_init -> irlba_spectral_tsvd Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor
... 13. │ └─uwot:::irlba_spectral_tsvd(L, ndim + 1) 14. │ ├─base::suppressWarnings(...) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─irlba::irlba(L, nv = n, nu = 0, maxit = iters) 17. └─base::.handleSimpleError(...) 18. └─base (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 731 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘differential.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/delta-area-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/plotCounts-1-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/plotCounts-2-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/pbMDS-1-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/pbMDS-2-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/clrDR-1-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/clrDR-2-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/differential_files/figure-html/plotExprHeatmap-sample-1.png" but not available. ... The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/preprocessing_files/figure-html/plotScatter-4-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/preprocessing_files/figure-html/plotScatter-5-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CATALYST/new/CATALYST.Rcheck/vign_test/CATALYST/vignettes/preprocessing_files/figure-html/sce2fcs-gating-1.png" but not available. --- finished re-building ‘preprocessing.Rmd’
SUMMARY: processing the following file failed: ‘differential.Rmd’
Error: Vignette re-building failed. Execution halted ```
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:
‘.cluster_cols’
Run revdep_details(, "ccImpute")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "celda")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-celda_CG.R:174:3'): Testing celdaUmap and celdaTsne with celda_CG ──
Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters)
: function 'as_cholmod_sparse' not provided by package 'Matrix'
Backtrace:
▆
...
18. └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose)
19. └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
20. └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
21. ├─base::suppressWarnings(...)
22. │ └─base::withCallingHandlers(...)
23. └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 90 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘celda.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/plot_umap-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/plot_umap-2.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/plot_umap-3.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/celda_heatmap-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/propmap-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/module_heatmap-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/unnamed-chunk-3-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/celda/new/celda.Rcheck/vign_test/celda/vignettes/celda_files/figure-html/module_split_rpc-1.png" but not available. ... Quitting from lines 76-77 [decontX] (decontX.Rmd) Error: processing vignette 'decontX.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘decontX.Rmd’
SUMMARY: processing the following file failed: ‘decontX.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
Run 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 ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/CelliD/new/CelliD.Rcheck/00install.out’ for details.
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'as(, "dsTMatrix")' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
Run revdep_details(, "cellWise")
for more info
installed size is 6.7Mb
sub-directories of 1Mb or more:
libs 6.3Mb
Run revdep_details(, "CEMiTool")
for more info
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.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘BiocVersion’ ‘module.tsv’ ‘modules_genes.gmt’ ‘parameters.tsv’
‘selected_genes.txt’ ‘summary_eigengene.tsv’ ‘summary_mean.tsv’
‘summary_median.tsv’
Run 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 'GenomicRanges::sort' by 'globaltest::sort' 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 ‘/wynton/home/cbi/hb/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 documentation object 'champ.SVD': ‘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 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 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.
Run 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.68 \NewDocumentCommand \citeproctext{}{}
Error: processing vignette 'ChemoSpec2D.Rmd' failed with diagnostics: LaTeX failed to compile /wynton/home/cbi/hb/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 ```
Run 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 [2023-12-10 12:48:41] INFO [2023-12-10 12:48:41] $x INFO [2023-12-10 12:48:41] $x$TF1 INFO [2023-12-10 12:48:41] [1] 3 4 5 INFO [2023-12-10 12:48:41] INFO [2023-12-10 12:48:41] $x$TF2 ... 6. └─BSgenome (local) .local(x, ...) 7. └─BSgenome:::.extractFromBSgenomeMultipleSequences(...) 8. ├─BiocGenerics::lapply(...) 9. └─base::lapply(...)
[ FAIL 1 | WARN 2 | SKIP 6 | PASS 312 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown --- finished re-building ‘ChIPpeakAnno.Rmd’
--- re-building ‘FAQs.Rmd’ using rmarkdown --- finished re-building ‘FAQs.Rmd’
--- re-building ‘pipeline.Rmd’ using rmarkdown
Quitting from lines 154-166 [workflow3] (pipeline.Rmd) ... Quitting from lines 65-72 [annotate] (quickStart.Rmd) Error: processing vignette 'quickStart.Rmd' failed with diagnostics: 'length.out' must be a non-negative number --- failed re-building ‘quickStart.Rmd’
SUMMARY: processing the following files failed: ‘pipeline.Rmd’ ‘quickStart.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE
installed size is 10.4Mb
sub-directories of 1Mb or more:
data 9.4Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
All declared Imports should be used.
checking Rd files ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
Run revdep_details(, "cifti")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "cliqueMS")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘qlcMatrix’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "clusterExperiment")
for more info
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 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 cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘scRNAseq’, ‘ConsensusClusterPlus’
Run revdep_details(, "clustifyr")
for more info
gmt_to_list: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
Run 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 for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocManager’
'library' or 'require' call not declared from: ‘BiocManager’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘BiocVersion’ ‘dataset_n272x978.gct’ ‘dataset_n272x978.gctx’
Run revdep_details(, "cna")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘cna.Rnw’ using Sweave
Registered S3 method overwritten by 'cna':
method from
some.data.frame car
Error: processing vignette 'cna.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cna.tex' failed.
LaTeX errors:
! LaTeX Error: File
nicefrac.sty' not found.
... 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 ```
Run revdep_details(, "CNVScope")
for more info
Namespace in Imports field not imported from: 'Hmisc'
All declared Imports should be used.
Run revdep_details(, "coin")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘Implementation.Rnw’ using Sweave Loading required package: survival Loading required package: grid --- finished re-building ‘Implementation.Rnw’
--- re-building ‘LegoCondInf.Rnw’ using Sweave Loading required package: coin Loading required package: survival Error: processing vignette 'LegoCondInf.Rnw' failed with diagnostics: ... Warning in .local(object, ...) : p-values may be incorrect due to violation of the subset pivotality condition --- finished re-building ‘coin.Rnw’
SUMMARY: processing the following file failed: ‘LegoCondInf.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "compcodeR")
for more info
Packages which this enhances but not available for checking:
'rpanel', 'DSS'
Run revdep_details(, "condiments")
for more info
.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
Run revdep_details(, "conquer")
for more info
installed size is 10.4Mb
sub-directories of 1Mb or more:
libs 10.2Mb
Run revdep_details(, "corrcoverage")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
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
Run 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) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_
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) snprma.Rd:38: Escaped LaTeX specials: \_ \_
checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
checking 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
Run revdep_details(, "crossmeta")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RCurl’ ‘XML’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘GeneMeta’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘BiocVersion’ ‘GSE41845’ ‘hgu95av2.db’
Run revdep_details(, "cSEM")
for more info
Namespace in Imports field not imported from: ‘Rdpack’
All declared Imports should be used.
Run revdep_details(, "cytomapper")
for more info
Package unavailable to check Rd xrefs: ‘CATALYST’
Run revdep_details(, "cytoMEM")
for more info
Found the following files/directories:
‘output files’
Run revdep_details(, "DCATS")
for more info
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
Run revdep_details(, "DeepBlueR")
for more info
Installation failed.
See ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/00install.out’ for details.
* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status
"503"
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) :
Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/DeepBlueR’
* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status
"503"
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) :
Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/DeepBlueR/old/DeepBlueR.Rcheck/DeepBlueR’
Run revdep_details(, "DelayedMatrixStats")
for more info
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.
Run 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. ```
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘dViolin_result’
Run revdep_details(, "DEqMS")
for more info
checking examples ... ERROR ``` Running examples in ‘DEqMS-Ex.R’ failed The error most likely occurred in:
Name: farmsSummary
Title: summarize peptide/PSM intensity into protein level relative
abundance by factor analysis
Aliases: farmsSummary
** Examples
...
dat.psm = eh[["EH1663"]] see ?DEqMS and browseVignettes('DEqMS') for documentation loading from cache
farms method does not tolerate missing values
dat.gene = farmsSummary(dat.psm,group_col=2) Error in loadNamespace(x) : there is no package called ‘farms’ Calls: farmsSummary ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘farms’
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.
Run revdep_details(, "detrendr")
for more info
GNU make is a SystemRequirements.
Run revdep_details(, "DHS.rates")
for more info
Namespace in Imports field not imported from: ‘rlang’
All declared Imports should be used.
Run 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’
Run revdep_details(, "Dino")
for more info
checking examples ... ERROR ``` Running examples in ‘Dino-Ex.R’ failed The error most likely occurred in:
Name: Dino
Title: Normalize scRNAseq data
Aliases: Dino
** Examples
raw data
... ..@ factors : list()
run Dino on raw expression matrix
pbmcSmall_Norm <- Dino(pbmcSmall) Computing sequencing depth Calculating regression slope Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: Dino ... runSVD -> do.call -> -> do.call -> Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 0.112255431313807, 0.107366520001381, 0.47439251594165, 0.277999545324347, 0.201878031561086, 0.292456449500264, 0.0913710355678337, 0.0643945818554276, 0.067168280211569, 0.0996727544738549, 0.179740672602896, 0.192178269400899, 0.524120391782809, 0.305646394906895, 0.297391813942996, 0.148355812914667, 0.0740633589512922, 0.384969821949345, 0.140960010955563, ...
<fn>
(...)<fn>
(...)[ FAIL 2 | WARN 0 | SKIP 0 | PASS 7 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘Dino.Rmd’ using rmarkdown
Quitting from lines 116-117 [normalize data background] (Dino.Rmd) Error: processing vignette 'Dino.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘Dino.Rmd’
SUMMARY: processing the following file failed: ‘Dino.Rmd’
Error: Vignette re-building failed. Execution halted ```
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').
Run 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 39.6Mb
sub-directories of 1Mb or more:
libs 39.2Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run 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: \_
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘DiscoRhythm_report.html’
Run revdep_details(, "dwp")
for more info
Namespaces in Imports field not imported from:
‘GenEst’ ‘expint’ ‘numDeriv’
All declared Imports should be used.
Run revdep_details(, "eaf")
for more info
GNU make is a SystemRequirements.
Run 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
Run 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.
Run revdep_details(, "EpiDISH")
for more info
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.
Run revdep_details(, "epimutacions")
for more info
Packages unavailable to check Rd xrefs: ‘CompQuadForm’, ‘car’
Run revdep_details(, "eseis")
for more info
checking 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_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” 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. ```
Run revdep_details(, "evaluomeR")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
'randomForest', 'flexmix'
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:
‘flexmix’ ‘randomForest’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run 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 documentation object 'InternalFunctions': ‘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. ```
Run revdep_details(, "ExCluster")
for more info
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.
Run 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 ‘/wynton/home/cbi/hb/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 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 for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocManager’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘BiocVersion’
Run 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.
Run revdep_details(, "familial")
for more info
checking examples ... ERROR ``` Running examples in ‘familial-Ex.R’ failed The error most likely occurred in:
Name: center.test
Title: Center test
Aliases: center.test
** Examples
set.seed(123) ... mu = 21000 posterior probabilities: H0 H1 0.59 0.41 optimal decision: indeterminate plot(test) Error in validObject(.Object) : invalid class “FncBand” object: superclass "mMatrix" not defined in the environment of the object's class Calls: plot ... initialize -> initialize -> initMatrix -> validObject Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(familial) > > test_check("familial") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
... 9. └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level) 10. └─methods::new("FncBand", bands, index = obj@index, level = band) 11. ├─methods::initialize(value, ...) 12. └─methods::initialize(value, ...) 13. └─methods (local) initMatrix(.Object, ...) 14. └─methods::validObject(.Object)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 56-57 [unnamed-chunk-3] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class --- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed: ‘vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "FastPCS")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking Rd files ... NOTE
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Run revdep_details(, "FastRCS")
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 7.3Mb
checking Rd files ... NOTE
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Run revdep_details(, "fastverse")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘fastverse_intro.Rmd’ using rmarkdown
Quitting from lines 104-108 [unnamed-chunk-9] (fastverse_intro.Rmd) Error: processing vignette 'fastverse_intro.Rmd' failed with diagnostics: package or namespace load failed for 'fastverse': .onAttach failed in attachNamespace() for 'fastverse', details: call: packageVersion(x) error: there is no package called 'qs' --- failed re-building ‘fastverse_intro.Rmd’
SUMMARY: processing the following file failed: ‘fastverse_intro.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘qs’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
All declared Imports should be used.
Run 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').
Run revdep_details(, "FEAST")
for more info
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
Run 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
Run 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: unable to find FTP dir for assembly GCF_000001405.40 in https://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 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.
Run 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 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
Error: processing vignette 'HowTo-flowCore.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HowTo-flowCore.tex' failed.
LaTeX errors:
! LaTeX Error: File
comment.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... 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 C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 4.2Mb
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: \$
Run 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 cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘doParallel’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘temp’ ‘tmp’
Run revdep_details(, "flowWorkspace")
for more info
checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘flowStats’ Missing link or links in documentation object 'gs_plot_pop_count_cv.Rd': ‘barchart’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘gs_clone’ ‘gs_copy_tree_only’
Undocumented S4 methods:
generic 'dimnames' and siglist 'cytoframe'
generic 'rownames' and siglist 'cytoframe'
generic 'rownames<-' and siglist 'cytoframe'
generic 'show' and siglist 'cytoframe'
generic 'transform' and siglist 'cytoframe'
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 Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'GatingSet-methods': ‘...’
Undocumented arguments in documentation object 'convert' ‘backend’
Undocumented arguments in documentation object 'cs_get_uri' ‘x’
Undocumented arguments in documentation object 'gh_apply_to_new_fcs' ... ‘backend’ ‘backend_dir’
Undocumented arguments in documentation object 'save_gs' ‘cdf’ ‘backend_readonly’
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 compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
-Wno-pedantic
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 34.1Mb
sub-directories of 1Mb or more:
libs 33.4Mb
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
AGPL-3.0-only
Standardizable: FALSE
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘DelayedArray:::simplify_NULL_dimnames’ ‘flowCore:::.estimateLogicle’
‘flowCore:::.spillover_pattern’ ‘flowCore:::checkClass’
‘flowCore:::guid’ ‘flowCore:::logicle_transform’
‘flowCore:::parse_pd_for_read_fs’ ‘flowCore:::txt2spillmatrix’
‘flowCore:::updateTransformKeywords’
‘flowCore:::validFilterResultList’ ‘graph:::.makeEdgeKeys’
‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’
See the note in ?`:::` about the use of this operator.
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
checking compiled code ... NOTE ``` File ‘flowWorkspace/libs/flowWorkspace.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘R_GatingSet.o’, ‘cytoframeAPI.o’, ‘cytosetAPI.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘R_GatingSet.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. ```
Run revdep_details(, "footBayes")
for more info
Namespace in Imports field not imported from: ‘tidyverse’
All declared Imports should be used.
Run 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 The magick package is required to crop "figure/quick_fraser_guide-1.png" but not available. The magick package is required to crop "figure/filter_junctions-1.png" but not available. The magick package is required to crop "figure/sample_covariation-1.png" but not available. The magick package is required to crop "figure/covariation_after_fitting-1.png" but not available. The magick package is required to crop "figure/finding_candidates-1.png" but not available. The magick package is required to crop "figure/figure_findBestQ-1.png" but not available. The magick package is required to crop "figure/result_visualization-1.png" but not available. The magick package is required to crop "figure/result_visualization-2.png" but not available. ... l.45 ^^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 C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
See the note in ?`:::` about the use of this operator.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘FRASER_output’
Run revdep_details(, "funtooNorm")
for more info
checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'show,SampleSet-method': ‘...’
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 for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘plotValidationGraph.pdf’
Run revdep_details(, "gap")
for more info
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘shiny’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘car’
Run revdep_details(, "geneticae")
for more info
Namespaces in Imports field not imported from:
‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
‘reshape2’
All declared Imports should be used.
Run revdep_details(, "GeneTonic")
for more info
Package unavailable to check Rd xrefs: ‘pcaExplorer’
Run 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 ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/genomation/new/genomation.Rcheck/00install.out’ for details.
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
Run 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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 /wynton/home/cbi/hb/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 ```
Run revdep_details(, "ggdmc")
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
Run revdep_details(, "GGPA")
for more info
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 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. ```
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘GGPA-example.Rnw’ using Sweave Loading required package: GGally Loading required package: ggplot2 Loading required package: network
‘network’ 1.18.2 (2023-12-04), part of the Statnet Project ```
Run revdep_details(, "GJRM")
for more info
Package which this enhances but not available for checking: ‘sp’
Run 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 5.3Mb
sub-directories of 1Mb or more:
libs 5.1Mb
Run revdep_details(, "GNET2")
for more info
Found the following files/directories:
‘gene_group_table.csv’ ‘gnet_results.csv’ ‘gnet_results.rda’
‘module_1.tiff’ ‘module_2.tiff’ ‘module_3.tiff’ ‘module_4.tiff’
Run revdep_details(, "GPUmatrix")
for more info
checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘speedglm’ Missing link or links in documentation object 'LR_GradientConjugate_gpumatrix.Rd': ‘Matrix-class’
Missing link or links in documentation object 'gpu.matrix-class.Rd': ‘Matrix-class’
Missing link or links in documentation object 'gpu.matrix.Rd': ‘Matrix-class’
Missing link or links in documentation object 'matrix-product.Rd': ‘%&%’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
Run revdep_details(, "GRaNIE")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘JASPAR2022’
checking R code for possible problems ... NOTE
.performIHW: no visible binding for global variable 'adj_pvalue'
Undefined global functions or variables:
adj_pvalue
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘GRN.network_visualisation.pdf’ ‘TF_peak.fdrCurves_original.pdf’
‘output’
Run revdep_details(, "graper")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "GUIDEseq")
for more info
checking dependencies in R code ... NOTE
':::' call which should be '::': ‘CRISPRseek:::translatePattern’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
plotTracks: warning in scale_x_continuous(label =
xaxis.lab.pos$chromosome, breaks = xaxis.lab.pos$chr.center): partial
argument match of 'label' to 'labels'
.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’
...
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: \_
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘PEtagTestResults’ ‘TS2offtargets3Constructs.xlsx’ ‘barcodes.fa’
‘offTargetsInPeakRegions.xls’ ‘usedBarcode’
Run revdep_details(, "gwasurvivr")
for more info
Found the following files/directories:
‘impute_example.coxph’ ‘impute_example.snps_removed’
‘michigan_example.coxph’ ‘michigan_example.snps_removed’
‘sanger_example.coxph’ ‘sanger_example.snps_removed’
Run 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 ‘/wynton/home/cbi/hb/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
Run revdep_details(, "HACSim")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "Harman")
for more info
Found the following files/directories:
‘hgu95av2cdf’
Run revdep_details(, "hbamr")
for more info
checking installed package size ... NOTE
installed size is 129.6Mb
sub-directories of 1Mb or more:
libs 129.1Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "hermes")
for more info
checking tests ... ``` Running ‘test_dplyr_compatibility.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
... 5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. ├─base::withCallingHandlers(...) 7. └─biomaRt::useEnsembl("ensembl", version = version) 8. └─biomaRt:::.listMarts(...) 9. └─biomaRt:::bmRequest(...) 10. └─httr::stop_for_status(result)
[ FAIL 1 | WARN 2 | SKIP 16 | PASS 815 ] Error: Test failures Execution halted ```
Run 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: Command \textasciigrave unavailable in encoding T1.
Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics: LaTeX failed to compile /wynton/home/cbi/hb/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 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
Run 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
Error: processing vignette 'iNETgrate_inference.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'iNETgrate_inference.tex' failed.
LaTeX errors:
! LaTeX Error: File
commath.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... 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 ```
Run revdep_details(, "InfiniumPurify")
for more info
Package unavailable to check Rd xrefs: ‘minfi’
Run revdep_details(, "IntOMICS")
for more info
Warning: package needs dependence on R (>= 2.10)
Run revdep_details(, "iPath")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
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
Run revdep_details(, "JMbayes2")
for more info
installed size is 5.1Mb
sub-directories of 1Mb or more:
libs 4.7Mb
Run revdep_details(, "kgschart")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "latrend")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘akmedoids’
checking Rd cross-references ... NOTE
Unknown package ‘akmedoids’ in Rd xrefs
Run revdep_details(, "ldsep")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "lemur")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘Introduction.Rmd’ using rmarkdown 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| *******| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| *******| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ... Quitting from lines 106-113 [raw_umap] (Introduction.Rmd) Error: processing vignette 'Introduction.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘Introduction.Rmd’
SUMMARY: processing the following file failed: ‘Introduction.Rmd’
Error: Vignette re-building failed. Execution halted ```
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
harmony_init: no visible global function definition for
‘packageVersion’
Undefined global functions or variables:
packageVersion
Consider adding
importFrom("utils", "packageVersion")
to your NAMESPACE file.
Run revdep_details(, "limorhyde")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: there is no package called 'qs' --- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed: ‘introduction.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘qs’
Run revdep_details(, "Linnorm")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘Linnorm_User_Manual.Rmd’ using rmarkdown ! Undefined control sequence. ...Attaching package: \textquotesingle {}igraph\textquotesingle {} l.988 ...extquotesingle{}igraph\textquotesingle{}}
Error: processing vignette 'Linnorm_User_Manual.Rmd' failed with diagnostics: LaTeX failed to compile /wynton/home/cbi/hb/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 ```
Run 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
Run revdep_details(, "lspartition")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "M3Drop")
for more info
checking dependencies in R code ... WARNING
Package in Depends field not imported from: ‘numDeriv’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported object: ‘scater::exprs’
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
Run revdep_details(, "maEndToEnd")
for more info
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 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’
Run revdep_details(, "magpie")
for more info
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘htmltools’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘test_TRESS.xlsx’ ‘test_strata_TRESS.xlsx’
Run revdep_details(, "MatrixGenerics")
for more info
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’
Run revdep_details(, "mcmcsae")
for more info
installed size is 8.8Mb
sub-directories of 1Mb or more:
libs 7.9Mb
Run 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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 "/wynton/home/cbi/hb/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 documentation object 'getProbeResults' ‘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 examples ... WARNING ``` Found the following significant warnings:
Warning: 'runRegionAnalysis' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
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’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘DiffMeanResults.csv’
Run revdep_details(, "memes")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘ggseqlogo’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run 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: > # but now you have the flexibility as requested by CRAN maintainers. > test_check("metagenomeSeq") Loading required package: metagenomeSeq Loading required package: Biobase Loading required package: BiocGenerics
...
── Failure ('test-norm.R:28:3'): cumNormStat
returns the correct value ───────
cumNormStat(lungData) not equal to 0.7014946.
names for target but not for current
── Failure ('test-norm.R:34:3'): cumNormStatFast
returns the correct value ───
cumNormStatFast(lungData) not equal to 0.7014946.
names for target but not for current
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted ```
Run revdep_details(, "metamicrobiomeR")
for more info
Namespace in Imports field not imported from: ‘lmerTest’
All declared Imports should be used.
Run revdep_details(, "MethReg")
for more info
checking examples ... ERROR ``` Running examples in ‘MethReg-Ex.R’ failed The error most likely occurred in:
Name: create_triplet_distance_based
Title: Map DNAm to target genes using distance approaches, and TF to
the DNAm region using JASPAR2020 TFBS.
Aliases: create_triplet_distance_based
** Examples
... + motif.search.window.size = 500, + target.method = "closest.gene" + ) Finding target genes Removing regions overlapping promoter regions o Get promoter regions for hg38 o Remove promoter regions Looking for TFBS Error: JASPAR2022 package is needed for this function to work. Please install it. Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:
| | 0% |====================================================|100% ~0 s remaining |====================================================|100% Completed after 1 s
| | 0% ... Backtrace: ▆ 1. └─MethReg::get_tf_in_region(...) at test-get_tf_in_region.R:18:5 2. └─MethReg:::check_package("JASPAR2022") 3. └─base::suppressMessages(...) 4. └─base::withCallingHandlers(...)
[ FAIL 2 | WARN 6 | SKIP 3 | PASS 156 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘MethReg.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/MethReg/new/MethReg.Rcheck/vign_test/MethReg/vignettes/MethReg_files/figure-html/workflow-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/MethReg/new/MethReg.Rcheck/vign_test/MethReg/vignettes/MethReg_files/figure-html/plot-1.png" but not available.
Quitting from lines 323-333 [unnamed-chunk-9] (MethReg.Rmd) Error: processing vignette 'MethReg.Rmd' failed with diagnostics: JASPAR2022 package is needed for this function to work. Please install it. --- failed re-building ‘MethReg.Rmd’
SUMMARY: processing the following file failed: ‘MethReg.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... WARNING
Missing or unexported object: ‘downloader::download.file’
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘JASPAR2022’
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘downloader’
A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE
readRemap2022: no visible binding for global variable ‘biotype’
Undefined global functions or variables:
biotype
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘TCGAbiolinks’
Run revdep_details(, "methrix")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘DSS’
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
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘temp’ ‘temp1’
Run revdep_details(, "methylationArrayAnalysis")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes:
Quitting from lines 461-465 [figure10] (methylationArrayAnalysis.Rmd) Error: processing vignette 'methylationArrayAnalysis.Rmd' failed with diagnostics: attempt to set an attribute on NULL --- failed re-building ‘methylationArrayAnalysis.Rmd’
SUMMARY: processing the following file failed: ‘methylationArrayAnalysis.Rmd’
...
trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.4.3.tar.gz' Content type 'application/x-gzip' length 2093488 bytes (2.0 MB) ================================================== downloaded 2.0 MB
trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DMRcatedata_2.20.0.tar.gz' Content type 'application/x-gzip' length 105209 bytes (102 KB) ================================================== downloaded 102 KB ```
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 ‘/wynton/home/cbi/hb/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 DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘DMRcatedata’ ‘cellranger’ ‘readxl’ ‘rematch’
Run 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 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’
Run revdep_details(, "MicrobiomeStat")
for more info
Namespaces in Imports field not imported from:
‘MASS’ ‘Matrix’ ‘utils’
All declared Imports should be used.
Run revdep_details(, "microsamplingDesign")
for more info
checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Warning: The closing backticks on line 165 ("
") in microsamplingDesign.Rmd do not match the opening backticks " ```" on line 163. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
! Undefined control sequence.
l.108 \NewDocumentCommand
\citeproctext{}{}
Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics: LaTeX failed to compile /wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/microsamplingDesign/new/microsamplingDesign.Rcheck/vign_test/microsamplingDesign/vignettes/microsamplingDesign.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See microsamplingDesign.log for more info. --- failed re-building ‘microsamplingDesign.Rmd’
SUMMARY: processing the following file failed: ‘microsamplingDesign.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
Run revdep_details(, "migest")
for more info
Note: found 9 marked UTF-8 strings
Run revdep_details(, "miloR")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: plotMDS
require(MASS) Loading required package: MASS
test_check("miloR") ... 9. └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose) 10. └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE) 11. └─uwot:::irlba_spectral_tsvd(L, ndim + 1) 12. ├─base::suppressWarnings(...) 13. │ └─base::withCallingHandlers(...) 14. └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 179 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘milo_contrasts.Rmd’ using rmarkdown
Quitting from lines 55-61 [unnamed-chunk-3] (milo_contrasts.Rmd) Error: processing vignette 'milo_contrasts.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘milo_contrasts.Rmd’
--- re-building ‘milo_demo.Rmd’ using rmarkdown ...
--- re-building ‘milo_gastrulation.Rmd’ using rmarkdown Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘milo_gastrulation.Rmd’
SUMMARY: processing the following files failed: ‘milo_contrasts.Rmd’ ‘milo_demo.Rmd’
Error: Vignette re-building failed. Execution halted ```
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
.fromMatrix: no visible binding for global variable ‘sce’
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 ‘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 ‘logFC’
plotNhoodMA: no visible binding for global variable ‘Sig’
plotNhoodSizeHist: no visible binding for global variable ‘nh_size’
Undefined global functions or variables:
. ..y.. Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif
label layout logCPM logFC logFC_color logFC_rank nh_size sce size
values weight
Consider adding
importFrom("graphics", "layout")
to your NAMESPACE file.
Run 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 ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/MinimumDistance/new/MinimumDistance.Rcheck/00install.out’ for details.
checking Rd files ... WARNING
checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'coerce' but not in code:
‘as’
checking Rd \usage sections ... WARNING ``` Objects in \usage without \alias in documentation object 'coerce': ‘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 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
Run 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 Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘edge’
Unknown package ‘KEGGprofile’ in Rd xrefs
Run revdep_details(, "MOCHA")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ArchR’
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'purrr'
All declared Imports should be used.
Run revdep_details(, "monocle")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘qlcMatrix’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "MOSim")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘MOSim.Rnw’ using knitr
Quitting from lines 245-271 [code6] (MOSim.Rnw) Error: processing vignette 'MOSim.Rnw' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘MOSim.Rnw’
SUMMARY: processing the following file failed: ‘MOSim.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "motifbreakR")
for more info
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 data for non-ASCII characters ... NOTE
Note: found 6 marked UTF-8 strings
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘grImport2’
Run revdep_details(, "mrfDepth")
for more info
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 7.2Mb
Run 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 Error: processing vignette 'SIRtrans.Rnw' failed with diagnostics: Running 'texi2dvi' on 'SIRtrans.tex' failed. LaTeX errors: ! LaTeX Error: File `bbm.sty' not found.
... 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
Run revdep_details(, "muscat")
for more info
checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘analysis.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/muscData_1.16.0.tar.gz'
Content type 'application/x-gzip' length 236236 bytes (230 KB)
==================================================
downloaded 230 KB
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 non-standard things in the check directory ... NOTE
Found the following files/directories:
‘muscData’
Run 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 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.
Run 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 installed files from ‘inst/doc’ ... NOTE
The following files look like leftovers/mistakes:
‘NanoStringDiff.log’
Please remove them from your package.
checking re-building of vignette outputs ... NOTE ``` 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 ```
Run revdep_details(, "nearBynding")
for more info
Found the following files/directories:
‘all_contexts_heatmap.jpeg’ ‘all_contexts_line.pdf’
‘bamto_sorted.bed’ ‘chr4and5_3UTR.cfg’ ‘chr4and5_3UTR.size’
‘chr4and5_3UTR_bulge.bedGraph’
‘chr4and5_3UTR_bulge_liftOver.bedGraph’
‘chr4and5_3UTR_bulge_liftOver~chr4and5_liftOver.dist’
‘chr4and5_3UTR_exterior.bedGraph’
‘chr4and5_3UTR_exterior_liftOver.bedGraph’
‘chr4and5_3UTR_exterior_liftOver~chr4and5_liftOver.dist’
‘chr4and5_3UTR_hairpin.bedGraph’
...
‘chr4and5_3UTR_internal_liftOver.bedGraph’
‘chr4and5_3UTR_internal_liftOver~chr4and5_liftOver.dist’
‘chr4and5_3UTR_multibranch.bedGraph’
‘chr4and5_3UTR_multibranch_liftOver.bedGraph’
‘chr4and5_3UTR_multibranch_liftOver~chr4and5_liftOver.dist’
‘chr4and5_3UTR_stem.bedGraph’ ‘chr4and5_3UTR_stem_liftOver.bedGraph’
‘chr4and5_3UTR_stem_liftOver~chr4and5_liftOver.dist’
‘chr4and5_liftOver.bedGraph’ ‘chr4and5_sorted.bam’
‘chr4and5_sorted.bam.bai’ ‘stem_heatmap.pdf’ ‘stem_line.jpeg’
‘test.cfg’ ‘test.chain’ ‘test.fa’
Run 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] 182 [1] 183 [1] 184 [1] 185 [1] 186 [1] 187 ... ▆
[ FAIL 2 | WARN 2 | SKIP 1 | PASS 47 ] Error: Test failures Execution halted ```
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
Run revdep_details(, "NormalyzerDE")
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 for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘path’
Run revdep_details(, "numbat")
for more info
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.
Run revdep_details(, "omicplotR")
for more info
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.
Run revdep_details(, "omicsPrint")
for more info
LazyData DB of 7.3 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
Run revdep_details(, "omicsViewer")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘ggseqlogo’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run 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 24.4Mb
sub-directories of 1Mb or more:
libs 23.9Mb
checking 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 for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run 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
Run 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.43 ^^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 R code for possible problems ... NOTE
padjOnSubset: no visible global function definition for ‘bpmapply’
Undefined global functions or variables:
bpmapply
Run 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 Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'summary.panda': ‘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. ```
Run 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.
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘pstat_data.rda’
Run revdep_details(, "pcaMethods")
for more info
Package unavailable to check Rd xrefs: ‘ade4’
Run revdep_details(, "PDATK")
for more info
checking whether package ‘PDATK’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
See ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/PDATK/new/PDATK.Rcheck/00install.out’ for details.
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'rankFeatures-MultiAssayExperiment-method.Rd': ‘[dplyr:ranking]{dplyr::dense_rank}’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking R code for possible problems ... NOTE
.calculateMSMthresholds: no visible binding for global variable
‘funContext’
.plotNetwork: no visible global function definition for ‘legend’
NCSModel: no visible binding for global variable ‘metric’
NCSModel: no visible binding for global variable ‘comparison’
NCSModel: no visible binding for global variable ‘centroid_K’
NCSModel: no visible binding for global variable ‘assay_K’
NetworkCommunitySearchModel: no visible binding for global variable
‘metric’
NetworkCommunitySearchModel: no visible binding for global variable
...
trainModel,NCSModel: no visible binding for global variable
‘cor_threshold’
Undefined global functions or variables:
.error assay_K assay_cohort centroid_K centroid_cohort cluster_label
comparison cor_threshold dev.off feature feature_rank feature_score
funContext ingroup_proportion legend metric missignAssays pdf tmp
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "legend")
to your NAMESPACE file.
Run revdep_details(, "penppml")
for more info
Namespace in Imports field not imported from: ‘fixest’
All declared Imports should be used.
Run revdep_details(, "PepsNMR")
for more info
checkRd: (-1) Normalization.Rd:47: Escaped LaTeX specials: \&
Run revdep_details(, "phosphonormalizer")
for more info
Package which this enhances but not available for checking: ‘MSnbase’
Run revdep_details(, "Pigengene")
for more info
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 for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘C5Trees’ ‘Module_sizes.png’ ‘TomModule.RData’ ‘bn’ ‘bnExample’
‘compacted’ ‘distance_degrees.png’ ‘enriched’ ‘filter_degrees.png’
‘heatmaps’ ‘m1.RData’ ‘membership.csv’ ‘net.RData’ ‘pigengene’
‘pigengene.RData’ ‘pigengene_pvalue.csv’ ‘plots’ ‘treeHeatmaps’
‘trees’ ‘wgOneStep.RData’ ‘wgcna’
Run revdep_details(, "PINSPlus")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "pipeComp")
for more info
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’
Run 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 ‘/wynton/home/cbi/hb/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 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
```
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘out.fasta’
Run revdep_details(, "ProteoMM")
for more info
License components which are templates and need '+ file LICENSE':
MIT
Run revdep_details(, "QDNAseq")
for more info
Run revdep_details(, "Qest")
for more info
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'internals': ‘format.perc’
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. ```
Run revdep_details(, "QFeatures")
for more info
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'QFeatures-aggregate.Rd': ‘sparseMatrix’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
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.
Run 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 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.
Run revdep_details(, "RadioGx")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘magicaxis’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "RBesT")
for more info
checking installed package size ... NOTE
installed size is 28.0Mb
sub-directories of 1Mb or more:
libs 27.4Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "reservr")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: attr { key: "executor_type" value { s: "" } } ...
[ FAIL 18 | WARN 0 | SKIP 1 | PASS 2254 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘distributions.Rmd’ using rmarkdown --- finished re-building ‘distributions.Rmd’
--- re-building ‘tensorflow.Rmd’ using rmarkdown
2023-12-10 18:27:44.856977: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server:/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server:/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server:/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server:/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server:/wynton/home/cbi/shared/software/CBI/_rocky8/JAGS-4.3.2/lib:/wynton/home/cbi/shared/software/CBI/gsl-2.7/lib:/opt/rh/gcc-toolset-10/root/usr/lib64:/opt/rh/gcc-toolset-10/root/usr/lib:/opt/rh/gcc-toolset-10/root/usr/lib64/dyninst:/opt/rh/gcc-toolset-10/root/usr/lib/dyninst:/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.3.2-gcc10/lib64/R/lib:/usr/lib64/openmpi/lib:/wynton/home/cbi/shared/software/CBI/mosh-1.4.0/lib64::
2023-12-10 18:27:44.857032: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303)
2023-12-10 18:27:44.857074: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (dev3): /proc/driver/nvidia/version does not exist
2023-12-10 18:27:44.857660: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
...
Error: processing vignette 'tensorflow.Rmd' failed with diagnostics:
tensorflow.python.framework.errors_impl.InvalidArgumentError: In[0] is not a matrix. Instead it has shape [100] [Op:MatMul]
Run reticulate::py_last_error()
for details.
--- failed re-building ‘tensorflow.Rmd’
SUMMARY: processing the following file failed: ‘tensorflow.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
R 1.5Mb
libs 6.1Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
checking for detritus in the temp directory ... NOTE
Found the following files/directories:
‘__pycache__’ ‘tmpx2o15rqy.py’ ‘tmpxz1igxta.py’
Run 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: File
subfigure.sty' not found.
! Emergency stop.
Error: processing vignette 'RGCCA.Rmd' failed with diagnostics: LaTeX failed to compile /wynton/home/cbi/hb/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 ```
Run revdep_details(, "RJcluster")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "RNAmodR")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c8973130bf5fb_2549' [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c897321b3576f_2537' [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c89738017990_2539' [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c89735425d82_2541' [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c89732f985ad8_2543' [E::idx_find_and_load] Could not retrieve index file for '/wynton/home/cbi/hb/.cache/R/ExperimentHub/1c8973301ccf40_2545' ...
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 898 ] Error: Test failures Execution halted ```
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'
Run revdep_details(, "RnBeads")
for more info
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 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 re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘RnBeads.Rnw’ using Sweave
Error: processing vignette 'RnBeads.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RnBeads.tex' failed.
LaTeX errors:
! LaTeX Error: File
vmargin.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty)
... 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 ```
Run revdep_details(, "robustlm")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "rpm")
for more info
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.6Mb
Run revdep_details(, "rsvddpd")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "rtrend")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking 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_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” 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. ```
Run revdep_details(, "samr")
for more info
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: \#
Run revdep_details(, "scDHA")
for more info
checking tests ...
``
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scDHA)
libtorch is not installed. Use
torch::install_torch()` to download and install libtorch
>
> on_cran <- function() !identical(Sys.getenv("NOT_CRAN"), "true")
>
...
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ] Error: Test failures Execution halted ```
Run revdep_details(, "scISR")
for more info
Namespace in Imports field not imported from: ‘markdown’
All declared Imports should be used.
Run 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 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.
Run revdep_details(, "scMET")
for more info
checking installed package size ... NOTE
installed size is 18.4Mb
sub-directories of 1Mb or more:
libs 18.1Mb
checking 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 for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "scone")
for more info
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
Run revdep_details(, "scp")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘QFeatures_nutshell.Rmd’ using rmarkdown --- finished re-building ‘QFeatures_nutshell.Rmd’
--- re-building ‘advanced.Rmd’ using rmarkdown --- finished re-building ‘advanced.Rmd’
--- re-building ‘read_scp.Rmd’ using rmarkdown [WARNING] Citeproc: citation Amezquita2019-bf not found --- finished re-building ‘read_scp.Rmd’ ... Quitting from lines 943-951 [run_UMAP] (scp.Rmd) Error: processing vignette 'scp.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘scp.Rmd’
SUMMARY: processing the following file failed: ‘scp.Rmd’
Error: Vignette re-building failed. Execution halted ```
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 R code for possible problems ... NOTE
readSCPfromDIANN: no visible global function definition for
‘pivot_wider’
Undefined global functions or variables:
pivot_wider
Run revdep_details(, "scPCA")
for more info
Namespaces in Imports field not imported from:
‘DelayedArray’ ‘matrixStats’
All declared Imports should be used.
Run revdep_details(, "sctransform")
for more info
Package which this enhances but not available for checking: ‘glmGamPoi’
Run 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’
Run revdep_details(, "seeds")
for more info
Package suggested but not available for checking: ‘rsbml’
Run revdep_details(, "seqArchR")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘ggseqlogo’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run 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 7.3Mb
sub-directories of 1Mb or more:
R 1.6Mb
libs 5.0Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘Signac’
Run 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 Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ranger’
checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘assoc_plot.pdf’ ‘assoc_plot_blue_yellow.pdf’ ‘assoc_plot_box.pdf’
‘assoc_plot_fc.pdf’ ‘conf_plot.pdf’ ‘eval.pdf’ ‘interpretion.pdf’
‘siamcat_output.pcl’ ‘siamcat_output.txt’ ‘volcano.pdf’
Run revdep_details(, "SICtools")
for more info
checking whether package ‘SICtools’ can be installed ... WARNING
Found the following significant warnings:
bam.c:128:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
bam_index.c:178:35: 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:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
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]
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
See ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/SICtools/new/SICtools.Rcheck/00install.out’ for details.
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'applyPileups' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
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.
Run revdep_details(, "signifinder")
for more info
Packages unavailable to check Rd xrefs: ‘curatedTCGAData’, ‘EDASeq’
Run revdep_details(, "SimBu")
for more info
checking examples ... ERROR ``` Running examples in ‘SimBu-Ex.R’ failed The error most likely occurred in:
Name: dataset_seurat
Title: Build SummarizedExperiment using a Seurat object
Aliases: dataset_seurat
** Examples
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) ... + count_assay = "counts", + cell_id_col = "ID", + cell_type_col = "cell_type", + tpm_assay = "tpm", + name = "seurat_dataset" + ) Error in value[3L] : Could not access count matrix from Seurat object (counts): Error in doTryCatch(return(expr), name, parentenv, handler): no slot of name "counts" for this object of class "Assay5" Calls: ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. ...
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ] Error: Test failures Execution halted ```
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 ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/SimBu/new/SimBu.Rcheck/00install.out’ for details.
Run 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 6.7Mb
sub-directories of 1Mb or more:
libs 6.0Mb
Run revdep_details(, "sindyr")
for more info
Namespaces in Imports field not imported from:
‘crqa’ ‘plot3D’
All declared Imports should be used.
Run revdep_details(, "Single.mTEC.Transcriptomes")
for more info
installed size is 150.1Mb
sub-directories of 1Mb or more:
data 150.0Mb
Run revdep_details(, "singleCellTK")
for more info
checking examples ... ERROR ``` Running examples in ‘singleCellTK-Ex.R’ failed The error most likely occurred in:
Name: convertSeuratToSCE
Title: convertSeuratToSCE Converts the input seurat object to a sce
object
Aliases: convertSeuratToSCE
** Examples
data(scExample, package = "singleCellTK") seurat <- convertSCEToSeurat(sce) sce <- convertSeuratToSCE(seurat) Error in normarg_assays(assays, as.null.if.no.assay = TRUE) : no slot of name "counts" for this object of class "Assay5" Calls: convertSeuratToSCE ... SingleCellExperiment -> SummarizedExperiment -> normarg_assays Execution halted ```
checking tests ... ``` Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 0.56021914152771, 0.72324200459552, 0.608560503993751, 0.885375554008604, 0.673676308058841, 0.856455999316698, 0.860809184462329, 0.854786269289328, 0.784723738680531, 0.849698625205517, 0.735266553432624, 0.849682214280883, 0.788313998626568, 0.819832968572265, 0.814171620486339, 0.689500279841049, ... Backtrace: ▆
[ FAIL 9 | WARN 23 | SKIP 0 | PASS 121 ] Error: Test failures Execution halted ```
Run revdep_details(, "singscore")
for more info
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
Run revdep_details(, "slasso")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RcppArmadillo’
All declared Imports should be used.
Run revdep_details(, "slingshot")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘conditionsVignette.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-1-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-3-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-5-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-7-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-11-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/slingshot/new/slingshot.Rcheck/vign_test/slingshot/vignettes/conditionsVignette_files/figure-html/unnamed-chunk-16-1.png" but not available. ... Quitting from lines 193-198 [umap] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix' --- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed: ‘vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "sparrow")
for more info
geneSetsStats: no visible binding for global variable ‘direction’
Undefined global functions or variables:
direction
Run 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’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "sparseMatrixStats")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘SummarizedExperiment’
Run revdep_details(, "spathial")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘irlba’ ‘knitr’ ‘rmarkdown’
All declared Imports should be used.
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "spatzie")
for more info
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
Run 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 7.3Mb
sub-directories of 1Mb or more:
R 2.2Mb
libs 4.9Mb
Run revdep_details(, "SPOTlight")
for more info
checking tests ...
``
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> set.seed(321)
> library(testthat)
> library(SPOTlight)
> # plotImage() ----
> test_check("SPOTlight")
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 351 ]
...
Lengths differ: 0 is not 1
── Failure ('test-plotInteractions.R:61:5'): plotInteractions(), which = 'heatmap', tunning ──
na` not equal to "grey50".
1/1 mismatches
x[1]: "#FF7F00"
y[1]: "grey50"
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 351 ] Error: Test failures Execution halted ```
Run revdep_details(, "spqn")
for more info
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.
Run revdep_details(, "stabiliser")
for more info
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
Run revdep_details(, "stapler")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "stm")
for more info
checking re-building of vignette outputs ... NOTE
``
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
Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'stmVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File
ulem.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 ```
Run 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 ‘/wynton/home/cbi/hb/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
Run 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 ```
Run 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 LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "templateICAr")
for more info
Package suggested but not available for checking: ‘INLA’
Run revdep_details(, "tidybulk")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘EGSEA’
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
...
predict prop rc read count ref_genome rotated dimensions sample 1
sample 2 sample a sample b sample_idx samples sdev seurat_clusters
surv_test 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")
to your NAMESPACE file.
Run revdep_details(, "topGO")
for more info
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 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’
checking re-building of vignette outputs ... NOTE ``` 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 ```
Run revdep_details(, "tradeSeq")
for more info
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.
Run revdep_details(, "TRESS")
for more info
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: \&
Run revdep_details(, "VanillaICE")
for more info
checking Rd files ... WARNING
checkRd: (5) VanillaICE.Rd:0-7: Must have a \description
checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'doMC', 'doMPI', 'doSNOW', 'doParallel', 'doRedis'
checking 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 for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘FinalReport6872_baf.rds’ ‘FinalReport6872_gt.rds’
‘FinalReport6872_lrr.rds’
Run 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 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 documentation object 'residuals.MArrayLM2': ‘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 for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘GSEABase’ ‘doParallel’
Run revdep_details(, "Voyager")
for more info
checking examples ... ERROR ``` Running examples in ‘Voyager-Ex.R’ failed The error most likely occurred in:
Name: ElbowPlot
Title: Plot the elbow plot or scree plot for PCA
Aliases: ElbowPlot
** Examples
library(SFEData) ... Loading required package: ggplot2 sfe <- McKellarMuscleData("small") see ?SFEData and browseVignettes('SFEData') for documentation loading from cache require(“SpatialFeatureExperiment”) sfe <- runPCA(sfe, ncomponents = 10, exprs_values = "counts") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: runPCA ... runSVD -> do.call -> -> do.call -> Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 7. └─scater:::.calculate_pca(mat, transposed = !is.null(dimred), ...) 8. ├─BiocSingular::runPCA(...) 9. └─BiocSingular::runPCA(...)
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'variogram-internal.Rd': ‘variogram’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
Run revdep_details(, "vsclust")
for more info
checking for code/documentation mismatches ... WARNING ``` Codoc mismatches from documentation object 'estimClustNum': 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 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
Run revdep_details(, "wateRmelon")
for more info
checking Rd metadata ... WARNING
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 code objects:
‘epicv2clean’ ‘epicv2clean.default’ ‘epicv2clean.gds.class’
Undocumented data sets:
‘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 Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object '.getManifestString' ‘annotation’ Documented arguments not in \usage in documentation object '.getManifestString': ‘x’ ‘obj’ ‘fd’ ‘rn’
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 dependencies in R code ... NOTE
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 R code for possible problems ... NOTE
.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<-’
.buildControlMatrix450k: no visible global function definition for
‘colMeans2’
...
getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex
getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls
hm450.ordering intensitiesByChannel mapToGenome mclapply metadata
methylated methylated<- methylumiR n.sd preprocessNoob preprocessRaw
preprocessSWAN probeAnnotationsCategory projectName pval.detect<-
pvals rowMeans2 seqnames sex_coef subsetByLoci unmethylated
unmethylated<- warn
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
Run revdep_details(, "WaverideR")
for more info
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/WaverideR/new/WaverideR.Rcheck/00install.out’ for details.
Run revdep_details(, "WeMix")
for more info
Package suggested but not available for checking: ‘EdSurvey’
Run revdep_details(, "WGCNA")
for more info
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'empiricalBayesLM.Rd': ‘rlm’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
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