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This page was generated on 2025-08-02 12:05 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1076/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 2.9.1  (landing page)
Kristoffer Vitting-Seerup
Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 Aug 2025)
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: devel
git_last_commit: 14077ce
git_last_commit_date: 2025-07-22 21:32:31 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for IsoformSwitchAnalyzeR on nebbiolo2

To the developers/maintainers of the IsoformSwitchAnalyzeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: IsoformSwitchAnalyzeR
Version: 2.9.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.9.1.tar.gz
StartedAt: 2025-08-01 23:37:41 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 23:50:44 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 783.1 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.9.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'limma', 'DEXSeq', 'satuRn', 'sva', 'ggplot2', 'pfamAnalyzeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IsoformSwitchAnalyzeR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data      1.1Mb
    extdata   4.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyzeNovelIsoformORF: no visible binding for global variable
  'orf_origin'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfStartGenomic'
analyzeNovelIsoformORF: no visible binding for global variable
  'isoform_id'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfEndGenomic'
expressionAnalysisPlot: no visible binding for global variable
  'Condition'
expressionAnalysisPlot: no visible binding for global variable
  'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
  'CI_down'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
  'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceEnrichment: no visible binding for global variable
  'feature2'
extractConsequenceEnrichment: no visible binding for global variable
  'propOfRelevantEvents'
extractConsequenceEnrichment: no visible binding for global variable
  'Significant'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiLo'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiHi'
extractConsequenceEnrichment: no visible binding for global variable
  'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propOfRelevantEvents'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiHi'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiLo'
extractConsequenceGenomeWide: no visible binding for global variable
  'isoform_feature'
extractConsequenceGenomeWide: no visible binding for global variable
  'value'
extractConsequenceGenomeWide: no visible binding for global variable
  'variable'
extractConsequenceGenomeWide: no visible binding for global variable
  'ymax'
extractConsequenceGenomeWide: no visible binding for global variable
  'significance'
extractConsequenceGenomeWide: no visible binding for global variable
  'idNr'
extractConsequenceSummary: no visible binding for global variable
  'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
  'geneFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
  'isoFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractSplicingEnrichment: no visible binding for global variable
  'AStype'
extractSplicingEnrichment: no visible binding for global variable
  'propUp'
extractSplicingEnrichment: no visible binding for global variable
  'Significant'
extractSplicingEnrichment: no visible binding for global variable
  'nTot'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiHi'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiLo'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUp'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiHi'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiLo'
extractSplicingGenomeWide: no visible binding for global variable
  'isoform_feature'
extractSplicingGenomeWide: no visible binding for global variable
  'value'
extractSplicingGenomeWide: no visible binding for global variable
  'variable'
extractSplicingGenomeWide: no visible binding for global variable
  'ymax'
extractSplicingGenomeWide: no visible binding for global variable
  'significance'
extractSplicingGenomeWide: no visible binding for global variable
  'idNr'
extractSplicingSummary: no visible binding for global variable
  'splicingResult'
extractSplicingSummary: no visible binding for global variable
  'geneFraction'
extractSplicingSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractSplicingSummary: no visible binding for global variable
  'isoFraction'
extractSplicingSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractSubCellShifts: no visible binding for global variable 'gene_ref'
extractSubCellShifts: no visible binding for global variable 'gene_id'
extractSubCellShifts: no visible binding for global variable
  'condition_1'
extractSubCellShifts: no visible binding for global variable
  'condition_2'
extractSubCellShifts: no visible binding for global variable
  'isoformUpregulated'
extractSubCellShifts: no visible binding for global variable
  'isoformDownregulated'
extractSubCellShifts: no visible binding for global variable
  'featureCompared'
extractSubCellShifts: no visible binding for global variable
  'isoformsDifferent'
extractSubCellShifts: no visible binding for global variable
  'isoform_id'
extractSubCellShifts: no visible binding for global variable
  'Localizations'
extractSubCellShifts: no visible binding for global variable
  'location_gain'
extractSubCellShifts: no visible binding for global variable
  'location_loss'
extractSubCellShifts: no visible binding for global variable 'n_genes'
extractSubCellShifts: no visible binding for global variable 'n_switch'
extractSubCellShifts: no visible binding for global variable 'Genes'
extractSubCellShifts: no visible binding for global variable 'Switch'
importGTF: no visible binding for global variable 'gene_id'
importGTF: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'isoform_id'
importRdata: no visible binding for global variable 'gene_id'
importRdata: no visible binding for global variable 'ref_gene_id'
importRdata: no visible binding for global variable 'n_ref_gene_ids'
importRdata: no visible binding for global variable 'n_iso_na'
importRdata: no visible binding for global variable 'novel_iso'
importRdata: no visible binding for global variable 'known_ref_gene_id'
importRdata: no visible binding for global variable 'nt_overlap'
importRdata: no visible binding for global variable 'frac_overlap'
importRdata: no visible binding for global variable
  'log2_overlap_ratio'
importRdata: no visible binding for global variable 'has_ref_gene_id'
importRdata: no visible binding for global variable 'has_novel_iso'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_ref'
isoformToGeneExp: no visible binding for global variable 'gene_id'
isoformToGeneExp: no visible binding for global variable 'gene_name'
preFilter: no visible global function definition for 'setdff'
switchPlotTranscript: no visible binding for global variable 'topology'
switchPlotTranscript: no visible binding for global variable 'idNr'
switchPlotTranscript: no visible binding for global variable 'Topology'
switchPlotTranscript: no visible binding for global variable 'topGroup'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
switchPlotTranscript: no visible binding for global variable 'value'
Undefined global functions or variables:
  AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain Genes
  IF Localizations Significant Switch Topology condition_1 condition_2
  feature2 featureCompared frac_overlap geneFraction gene_expression
  gene_id gene_name gene_ref has_novel_iso has_ref_gene_id idNr
  isoFraction isoformDownregulated isoformUpregulated isoform_feature
  isoform_id isoformsDifferent known_ref_gene_id location_gain
  location_loss log2_overlap_ratio nTot n_genes n_iso_na n_ref
  n_ref_gene_ids n_switch novel_iso nrGenesWithConsequences
  nrIsoWithConsequences nt_overlap orfEndGenomic orfStartGenomic
  orf_origin propCiHi propCiLo propOfRelevantEvents propUp propUpCiHi
  propUpCiLo ref_gene_id setdff sigEval sigLevel sigLevelPos
  significance splicingResult switchConsequence topGroup topology value
  variable x xmax xmin y yend ymax ymin
* checking Rd files ... NOTE
checkRd: (-1) isoformToGeneExp.Rd:22: Lost braces; missing escapes or markup?
    22 |     \item{Using the {isoformGeneAnnotation} argument}.
       |                     ^
checkRd: (-1) isoformToIsoformFraction.Rd:23: Lost braces; missing escapes or markup?
    23 |     \item{Using the {isoformGeneAnnotation} argument}.
       |                     ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
IsoformSwitchTestDEXSeq       67.854  2.797  70.660
isoformSwitchAnalysisCombined 45.943  2.840  48.790
importSalmonData              28.925  2.521  39.900
prepareSalmonFilesDataFrame   13.273  1.107  18.184
extractSequence                9.445  0.012   9.456
analyzeORF                     8.991  0.025   9.016
extractTopSwitches             8.927  0.002   8.929
extractSwitchSummary           7.745  0.000   7.746
isoformSwitchAnalysisPart1     7.519  0.004   7.523
analyzeAlternativSplicing      6.269  0.082   6.351
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.


Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** this is package ‘IsoformSwitchAnalyzeR’ version ‘2.9.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IsoformSwitchAnalyzeR)

Tests output


Example timings

IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq67.854 2.79770.660
IsoformSwitchTestSatuRn2.7170.1232.842
addORFfromGTF0.8030.0030.806
analyzeAlternativSplicing6.2690.0826.351
analyzeCPAT0.0540.0030.057
analyzeCPC20.0510.0030.055
analyzeDeepLoc20.2420.0390.282
analyzeDeepTMHMM0.4580.0040.462
analyzeIUPred2A2.3520.0552.407
analyzeNovelIsoformORF0.7220.0170.739
analyzeORF8.9910.0259.016
analyzePFAM0.4750.0090.485
analyzeSignalP0.0830.0040.086
analyzeSwitchConsequences1.0570.0101.067
expressionAnalysisPlots1.1510.0051.156
extractConsequenceEnrichment0.4510.0040.455
extractConsequenceEnrichmentComparison0.7360.0040.740
extractConsequenceSummary0.7650.0190.785
extractGeneExpression0.0460.0010.047
extractGenomeWideAnalysis4.5060.1664.672
extractGenomeWideSplicingAnalysis2.6340.0432.676
extractSequence9.4450.0129.456
extractSplicingEnrichment1.1020.0011.104
extractSplicingEnrichmentComparison1.1960.0021.199
extractSplicingSummary0.9870.0000.988
extractSwitchOverlap0.3630.0030.366
extractSwitchSummary7.7450.0007.746
extractTopSwitches8.9270.0028.929
importCufflinksGalaxyData000
importGTF0.7230.0000.722
importIsoformExpression0.5410.1390.682
importRdata2.2750.0902.368
importSalmonData28.925 2.52139.900
isoformSwitchAnalysisCombined45.943 2.84048.790
isoformSwitchAnalysisPart17.5190.0047.523
isoformSwitchAnalysisPart24.6500.1664.818
isoformToGeneExp2.7800.0922.873
isoformToIsoformFraction0.1850.0730.260
preFilter0.0250.0010.026
prepareSalmonFilesDataFrame13.273 1.10718.184
subsetSwitchAnalyzeRlist0.0240.0010.025
switchAnalyzeRlist2.4000.2242.626
switchPlot3.2600.0293.290
switchPlotTranscript1.7450.0491.794
testData0.0130.0020.015