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This page was generated on 2024-05-04 11:40:41 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1076/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 2.4.0  (landing page)
Kristoffer Vitting-Seerup
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: RELEASE_3_19
git_last_commit: 7835f1d
git_last_commit_date: 2024-04-30 10:58:30 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for IsoformSwitchAnalyzeR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IsoformSwitchAnalyzeR
Version: 2.4.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.4.0.tar.gz
StartedAt: 2024-05-04 08:47:29 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 09:02:25 -0000 (Sat, 04 May 2024)
EllapsedTime: 896.7 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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.
* 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 (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    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           95.919  1.762  97.845
isoformSwitchAnalysisCombined     63.133  0.884  64.187
importSalmonData                  33.165  1.030  84.699
prepareSalmonFilesDataFrame       18.613  0.248  37.129
extractSequence                   15.065  0.451  15.551
analyzeORF                        13.267  0.052  13.344
isoformSwitchAnalysisPart1        12.417  0.028  12.468
extractSwitchSummary              12.017  0.135  12.183
extractTopSwitches                12.003  0.128  12.159
analyzeAlternativSplicing         10.091  0.040  10.150
extractGenomeWideSplicingAnalysis  5.546  0.403   5.964
extractGenomeWideAnalysis          4.721  0.311   5.043
isoformSwitchAnalysisPart2         4.924  0.088   5.013
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.


Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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
IsoformSwitchTestDEXSeq95.919 1.76297.845
IsoformSwitchTestSatuRn4.0200.0884.090
addORFfromGTF1.1620.0081.172
analyzeAlternativSplicing10.091 0.04010.150
analyzeCPAT0.0730.0000.074
analyzeCPC20.0700.0000.071
analyzeDeepLoc20.3110.0240.328
analyzeDeepTMHMM0.7340.0000.736
analyzeIUPred2A3.6910.0363.734
analyzeNovelIsoformORF0.9740.0040.980
analyzeORF13.267 0.05213.344
analyzePFAM0.6690.0000.672
analyzeSignalP0.1480.0040.153
analyzeSwitchConsequences1.3930.0001.396
expressionAnalysisPlots1.6210.0001.624
extractConsequenceEnrichment0.6560.0030.661
extractConsequenceEnrichmentComparison0.9810.0000.984
extractConsequenceSummary1.1310.0031.138
extractGeneExpression0.0590.0080.066
extractGenomeWideAnalysis4.7210.3115.043
extractGenomeWideSplicingAnalysis5.5460.4035.964
extractSequence15.065 0.45115.551
extractSplicingEnrichment1.5790.0161.599
extractSplicingEnrichmentComparison1.8910.0121.907
extractSplicingSummary1.5180.0281.549
extractSwitchOverlap0.4980.0200.519
extractSwitchSummary12.017 0.13512.183
extractTopSwitches12.003 0.12812.159
importCufflinksGalaxyData0.0000.0000.001
importGTF1.1340.0081.144
importIsoformExpression0.8770.0950.933
importRdata3.6400.0923.725
importSalmonData33.165 1.03084.699
isoformSwitchAnalysisCombined63.133 0.88464.187
isoformSwitchAnalysisPart112.417 0.02812.468
isoformSwitchAnalysisPart24.9240.0885.013
isoformToGeneExp4.3950.0874.465
isoformToIsoformFraction0.2890.0440.308
preFilter0.030.000.03
prepareSalmonFilesDataFrame18.613 0.24837.129
subsetSwitchAnalyzeRlist0.0290.0000.029
switchAnalyzeRlist3.5420.1113.633
switchPlot4.3350.0124.355
switchPlotTranscript2.4570.0202.482
testData0.0150.0000.016