revdep/problems.md

In HenrikBengtsson/parallelly: Enhancing the 'parallel' Package

adea

• Version: 1.5.2
• GitHub: NA
• Source code: https://github.com/cran/adea
• Date/Publication: 2024-11-12 18:00:02 UTC
• Number of recursive dependencies: 54

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

In both

• checking package dependencies ... ERROR ``` Package required but not available: ‘ROI.plugin.symphony’

  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

bootUR

• Version: 1.0.4
• GitHub: https://github.com/smeekes/bootUR
• Source code: https://github.com/cran/bootUR
• Date/Publication: 2024-05-20 09:30:02 UTC
• Number of recursive dependencies: 68

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

In both

• checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: libs 6.2Mb

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

breathteststan

• Version: 0.8.9
• GitHub: https://github.com/dmenne/breathteststan
• Source code: https://github.com/cran/breathteststan
• Date/Publication: 2025-01-08 09:00:07 UTC
• Number of recursive dependencies: 152

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

In both

• checking installed package size ... NOTE installed size is 64.0Mb sub-directories of 1Mb or more: libs 63.7Mb

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

COTAN

• Version: 2.6.2
• GitHub: https://github.com/seriph78/COTAN
• Source code: https://github.com/cran/COTAN
• Date/Publication: 2025-01-19
• Number of recursive dependencies: 276

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

In both

• checking installed package size ... NOTE installed size is 13.6Mb sub-directories of 1Mb or more: doc 11.8Mb

• checking dependencies in R code ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator.

• checking R code for possible problems ... NOTE mergeUniformCellsClusters : fromMergedName: warning in vapply(currentClNames, function(clName, mergedName) {: partial argument match of 'FUN.VAL' to 'FUN.VALUE' mergeUniformCellsClusters : fromMergedName: warning in return(str_detect(mergedName, clName)): partial argument match of 'FUN.VAL' to 'FUN.VALUE' mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL = logical(1L), mergedClName): partial argument match of 'FUN.VAL' to 'FUN.VALUE' ECDPlot: no visible binding for global variable ‘.’ ... ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot obj objSeurat observedNN observedNY observedY observedYN observedYY pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm type types useTorch usedMaxResolution values violinwidth width x xmax xmaxv xminv y zoomedNuPlot

decoupleR

• Version: 2.12.0
• GitHub: https://github.com/saezlab/decoupleR
• Source code: https://github.com/cran/decoupleR
• Date/Publication: 2024-10-29
• Number of recursive dependencies: 268

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

In both

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

  Name: get_collectri

  Title: CollecTRI gene regulatory network. Wrapper to access CollecTRI

  gene regulatory network. CollecTRI is a comprehensive resource

  containing a curated collection of transcription factors (TFs) and

  their target genes. It is an expansion of DoRothEA. Each interaction

  is weighted by its mode of regulation (either positive or negative).

  Aliases: get_collectri

  ** Examples

  collectri <- get_collectri(organism='human', split_complexes=FALSE) [2025-01-29 07:41:10] [WARN] [OmnipathR] Accessing collectri as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. Error in if (.keep) . else select(., -!!evs_col) : argument is of length zero Calls: get_collectri ... tidyselect_data_has_predicates -> unnest_evidences -> %>% Execution halted ```

• checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:

  1. ├─OmnipathR:::has_column(., "evidences")
  2. │ ├─col %in% colnames(data)
  3. │ └─base::colnames(data)
  4. │ └─base::is.data.frame(x)
  5. ├─OmnipathR::filter_evidences(...)
  6. │ └─expr(...) %>% eval_select(data) %>% names %>% ... ...
  7. ├─OmnipathR:::is_empty_2(.)
  8. │ └─value %>% ...
  9. ├─tidyselect::eval_select(., data)
  10. │ └─tidyselect::tidyselect_data_has_predicates(data)
  11. └─OmnipathR::unnest_evidences(., .keep = .keep)
  12. └─... %>% ...

  [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ] Error: Test failures Execution halted ```

• checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘decoupleR.Rmd’ using rmarkdown [WARNING] Could not fetch resource https://github.com/saezlab/decoupleR/blob/master/inst/figures/net_plot.png?raw=1: HttpExceptionRequest Request { host = "github.com" port = 443 secure = True requestHeaders = [] path = "/saezlab/decoupleR/blob/master/inst/figures/net_plot.png" queryString = "?raw=1" method = "GET" ... Quitting from lines 86-88 [collectri] (tf_sc.Rmd) Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘tf_sc.Rmd’

  SUMMARY: processing the following files failed: ‘tf_bk.Rmd’ ‘tf_sc.Rmd’

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

• checking Rd cross-references ... WARNING ``` Missing link or links in Rd file 'run_gsva.Rd': ‘GSVA::gsva’ ‘GeneSetCollection’

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

• checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: doc 8.9Mb extdata 1.4Mb

desla

• Version: 0.3.0
• GitHub: https://github.com/RobertAdamek/desla
• Source code: https://github.com/cran/desla
• Date/Publication: 2023-06-29 11:50:06 UTC
• Number of recursive dependencies: 35

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

In both

• checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: libs 7.3Mb

gastempt

• Version: 0.7.0
• GitHub: https://github.com/dmenne/gastempt
• Source code: https://github.com/cran/gastempt
• Date/Publication: 2024-12-20 07:50:02 UTC
• Number of recursive dependencies: 109

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

In both

• checking installed package size ... NOTE installed size is 176.3Mb sub-directories of 1Mb or more: libs 175.8Mb

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

gtfstools

• Version: 1.4.0
• GitHub: https://github.com/ipeaGIT/gtfstools
• Source code: https://github.com/cran/gtfstools
• Date/Publication: 2025-01-09 00:40:02 UTC
• Number of recursive dependencies: 90

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

In both

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

InPAS

• Version: 2.14.1
• GitHub: NA
• Source code: https://github.com/cran/InPAS
• Date/Publication: 2024-12-23
• Number of recursive dependencies: 165

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

In both

• checking Rd cross-references ... WARNING ``` Missing link or links in Rd file 'get_ssRleCov.Rd': ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’

  Missing link or links in Rd file 'set_globals.Rd': ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’

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

• 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: ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’ ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’ ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’ ‘search_distalCPs’ ‘search_proximalCPs’

• checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd': ‘gcCompensationensation’

  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. ```

JMbayes2

• Version: 0.5-0
• GitHub: https://github.com/drizopoulos/JMbayes2
• Source code: https://github.com/cran/JMbayes2
• Date/Publication: 2024-05-30 07:30:03 UTC
• Number of recursive dependencies: 77

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

In both

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

mappp

• Version: 1.0.0
• GitHub: https://github.com/cole-brokamp/mappp
• Source code: https://github.com/cran/mappp
• Date/Publication: 2022-01-25 09:22:42 UTC
• Number of recursive dependencies: 35

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

In both

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

mmrm

• Version: 0.3.14
• GitHub: https://github.com/openpharma/mmrm
• Source code: https://github.com/cran/mmrm
• Date/Publication: 2024-09-27 23:30:01 UTC
• Number of recursive dependencies: 176

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

In both

• checking installed package size ... NOTE installed size is 188.8Mb sub-directories of 1Mb or more: libs 187.0Mb

NCC

• Version: 1.0
• GitHub: https://github.com/pavlakrotka/NCC
• Source code: https://github.com/cran/NCC
• Date/Publication: 2023-03-03 09:10:10 UTC
• Number of recursive dependencies: 116

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

In both

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

nebula

• Version: 1.5.3
• GitHub: https://github.com/lhe17/nebula
• Source code: https://github.com/cran/nebula
• Date/Publication: 2024-02-15 23:00:02 UTC
• Number of recursive dependencies: 173

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

In both

• checking installed package size ... NOTE installed size is 35.4Mb sub-directories of 1Mb or more: libs 33.7Mb

outliers.ts.oga

• Version: 0.0.1
• GitHub: NA
• Source code: https://github.com/cran/outliers.ts.oga
• Date/Publication: 2024-05-28 17:00:02 UTC
• Number of recursive dependencies: 155

Run revdepcheck::revdep_details(, "outliers.ts.oga") for more info

In both

• checking whether package ‘outliers.ts.oga’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/futureverse/parallelly/revdep/checks/outliers.ts.oga/new/outliers.ts.oga.Rcheck/00install.out’ for details.

pmartR

• Version: 2.4.6
• GitHub: https://github.com/pmartR/pmartR
• Source code: https://github.com/cran/pmartR
• Date/Publication: 2024-10-14 21:10:02 UTC
• Number of recursive dependencies: 147

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

In both

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

• checking installed package size ... NOTE installed size is 10.5Mb sub-directories of 1Mb or more: libs 8.0Mb

QDNAseq

• Version: 1.42.0
• GitHub: https://github.com/ccagc/QDNAseq
• Source code: https://github.com/cran/QDNAseq
• Date/Publication: 2024-10-29
• Number of recursive dependencies: 94

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

In both

• checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave EM algorithm started ...

  Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. ... l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’

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

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

qtl2pleio

• Version: 1.4.3
• GitHub: https://github.com/fboehm/qtl2pleio
• Source code: https://github.com/cran/qtl2pleio
• Date/Publication: 2020-12-02 22:50:02 UTC
• Number of recursive dependencies: 129

Run revdepcheck::revdep_details(, "qtl2pleio") for more info

In both

• checking installed package size ... NOTE installed size is 36.9Mb sub-directories of 1Mb or more: libs 36.6Mb

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

ResIN

• Version: 2.0.0
• GitHub: https://github.com/pwarncke77/ResIN
• Source code: https://github.com/cran/ResIN
• Date/Publication: 2024-10-04 10:40:03 UTC
• Number of recursive dependencies: 111

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

In both

• checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

scruff

• Version: 1.24.0
• GitHub: https://github.com/campbio/scruff
• Source code: https://github.com/cran/scruff
• Date/Publication: 2024-10-29
• Number of recursive dependencies: 180

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

In both

• checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 2.4Mb doc 1.7Mb

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

• checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads' See the note in ?`:::` about the use of this operator.

• checking foreign function calls ... NOTE Foreign function call to a different package: .Call(ShortRead:::.set_omp_threads, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.

• checking R code for possible problems ... NOTE .plotFracProteinCodingGenes: no visible binding for global variable 'genes' .plotGenes: no visible binding for global variable 'genes' .plotGenesPerMillionReads: no visible binding for global variable 'genes' Undefined global functions or variables: genes

SimDesign

• Version: 2.18
• GitHub: https://github.com/philchalmers/SimDesign
• Source code: https://github.com/cran/SimDesign
• Date/Publication: 2024-12-14 08:10:07 UTC
• Number of recursive dependencies: 135

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

In both

• checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: doc 6.5Mb

streetscape

• Version: 1.0.5
• GitHub: NA
• Source code: https://github.com/cran/streetscape
• Date/Publication: 2025-01-21 14:50:03 UTC
• Number of recursive dependencies: 139

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

In both

• checking data for ASCII and uncompressed saves ... WARNING 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_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatMessages” 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?) code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

• checking whether startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPolygons” 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. ```

targets

• Version: 1.10.0
• GitHub: https://github.com/ropensci/targets
• Source code: https://github.com/cran/targets
• Date/Publication: 2025-01-13 15:00:01 UTC
• Number of recursive dependencies: 160

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

In both

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

TDApplied

• Version: 3.0.4
• GitHub: https://github.com/shaelebrown/TDApplied
• Source code: https://github.com/cran/TDApplied
• Date/Publication: 2024-10-29 08:30:02 UTC
• Number of recursive dependencies: 84

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

In both

• checking installed package size ... NOTE installed size is 13.0Mb sub-directories of 1Mb or more: doc 8.2Mb libs 4.4Mb

HenrikBengtsson/parallelly documentation built on Feb. 24, 2025, 2:40 a.m.