Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:31 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for IsoformSwitchAnalyzeR on nebbiolo2


To the developers/maintainers of the IsoformSwitchAnalyzeR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 963/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 1.16.0  (landing page)
Kristoffer Vitting-Seerup
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: RELEASE_3_14
git_last_commit: 5eb5b2b
git_last_commit_date: 2021-10-26 12:35:46 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IsoformSwitchAnalyzeR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.16.0.tar.gz
StartedAt: 2022-04-12 07:56:28 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:05:51 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 562.7 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   4.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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
analyzeIUPred2A: no visible global function definition for 'queryHits'
analyzeIUPred2A: no visible global function definition for
  'subjectHits'
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'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'queryHits'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'subjectHits'
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'
grangesFracOverlap: no visible global function definition for
  'queryHits'
grangesFracOverlap: no visible global function definition for
  'subjectHits'
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 global function definition for 'queryHits'
importRdata: no visible global function definition for 'subjectHits'
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'
importSalmonData: no visible global function definition for 'metadata'
importSalmonData: no visible global function definition for 'assay'
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 global function definition for
  'queryHits'
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'
Undefined global functions or variables:
  AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain IF
  Significant assay feature2 frac_overlap geneFraction gene_expression
  gene_id gene_name has_novel_iso has_ref_gene_id idNr isoFraction
  isoform_feature isoform_id known_ref_gene_id log2_overlap_ratio
  metadata nTot n_iso_na n_ref n_ref_gene_ids novel_iso
  nrGenesWithConsequences nrIsoWithConsequences nt_overlap
  orfEndGenomic orfStartGenomic orf_origin propCiHi propCiLo
  propOfRelevantEvents propUp propUpCiHi propUpCiLo queryHits
  ref_gene_id setdff sigEval sigLevel sigLevelPos significance
  splicingResult subjectHits switchConsequence value variable x xmax
  xmin y yend ymax ymin
* checking Rd files ... OK
* 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       54.570  1.037  55.594
isoformSwitchAnalysisCombined 34.940  1.496  36.437
importSalmonData              28.575  2.206  42.134
extractSequence               16.541  0.096  16.637
analyzeORF                    16.050  0.164  16.214
extractTopSwitches            15.590  0.060  15.649
extractSwitchSummary          15.385  0.140  15.524
isoformSwitchAnalysisPart1    14.715  0.300  15.016
prepareSalmonFilesDataFrame   10.299  0.681  17.135
analyzeAlternativSplicing      6.100  0.008   6.109
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.



Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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
IsoformSwitchTestDEXSeq54.570 1.03755.594
IsoformSwitchTestDRIMSeq4.5110.2014.668
addORFfromGTF0.8310.0040.835
analyzeAlternativSplicing6.1000.0086.109
analyzeCPAT0.0530.0000.053
analyzeCPC20.0440.0040.048
analyzeIUPred2A2.2490.0202.269
analyzeNovelIsoformORF0.6470.0040.650
analyzeORF16.050 0.16416.214
analyzePFAM0.4040.0000.404
analyzeSignalP0.0730.0040.077
analyzeSwitchConsequences0.8530.0120.866
expressionAnalysisPlots0.7820.0320.815
extractConsequenceEnrichment0.4500.0160.466
extractConsequenceEnrichmentComparison0.6130.0070.622
extractConsequenceSummary0.6490.0130.661
extractGeneExpression0.0500.0000.051
extractGenomeWideAnalysis2.0830.0072.091
extractGenomeWideSplicingAnalysis2.2040.0122.216
extractSequence16.541 0.09616.637
extractSplicingEnrichment1.0030.0401.043
extractSplicingEnrichmentComparison1.1150.0161.131
extractSplicingSummary0.8290.0000.830
extractSwitchOverlap0.4220.0080.430
extractSwitchSummary15.385 0.14015.524
extractTopSwitches15.590 0.06015.649
getCDS000
importCufflinksGalaxyData000
importGTF0.8800.0160.895
importIsoformExpression0.7650.1330.836
importRdata1.5810.1041.632
importSalmonData28.575 2.20642.134
isoformSwitchAnalysisCombined34.940 1.49636.437
isoformSwitchAnalysisPart114.715 0.30015.016
isoformSwitchAnalysisPart22.8570.0602.918
isoformToGeneExp2.0220.0972.070
isoformToIsoformFraction0.2400.1050.300
preFilter0.0200.0040.025
prepareSalmonFilesDataFrame10.299 0.68117.135
subsetSwitchAnalyzeRlist0.0290.0000.029
switchAnalyzeRlist1.6430.2291.821
switchPlot3.3560.1683.524
switchPlotTranscript2.2500.0722.322
testData0.0170.0000.017