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This page was generated on 2022-01-21 13:07:57 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 machv2


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? here 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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 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 -0500 (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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.16.0.tar.gz
StartedAt: 2022-01-20 14:17:56 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:34:49 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 1012.9 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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  6.3Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   4.2Mb
* 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       107.379  0.993 108.935
isoformSwitchAnalysisCombined  66.759  3.337  70.214
importSalmonData               47.951  1.909  67.049
extractSequence                34.176  0.196  34.400
analyzeORF                     32.650  0.208  32.890
extractTopSwitches             32.348  0.160  32.553
extractSwitchSummary           31.490  0.145  31.660
isoformSwitchAnalysisPart1     30.441  0.152  30.620
prepareSalmonFilesDataFrame    18.186  0.313  25.335
analyzeAlternativSplicing      14.293  0.031  14.340
IsoformSwitchTestDRIMSeq       10.249  0.148  10.529
switchPlot                      6.374  0.018   6.403
isoformSwitchAnalysisPart2      5.792  0.037   5.838
extractGenomeWideAnalysis       5.325  0.113   5.443
analyzeIUPred2A                 5.003  0.051   5.058
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.



Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
IsoformSwitchTestDEXSeq107.379 0.993108.935
IsoformSwitchTestDRIMSeq10.249 0.14810.529
addORFfromGTF1.7160.0131.730
analyzeAlternativSplicing14.293 0.03114.340
analyzeCPAT0.0940.0060.101
analyzeCPC20.0810.0060.086
analyzeIUPred2A5.0030.0515.058
analyzeNovelIsoformORF1.3260.0091.336
analyzeORF32.650 0.20832.890
analyzePFAM0.8470.0070.856
analyzeSignalP0.1300.0060.137
analyzeSwitchConsequences1.7660.0251.794
expressionAnalysisPlots1.4620.0081.471
extractConsequenceEnrichment0.7060.0080.714
extractConsequenceEnrichmentComparison1.3370.0091.346
extractConsequenceSummary1.3020.0071.310
extractGeneExpression0.0750.0050.081
extractGenomeWideAnalysis5.3250.1135.443
extractGenomeWideSplicingAnalysis3.8720.0683.945
extractSequence34.176 0.19634.400
extractSplicingEnrichment2.0990.0142.118
extractSplicingEnrichmentComparison2.1660.0172.190
extractSplicingSummary1.7030.0101.713
extractSwitchOverlap0.7520.0130.766
extractSwitchSummary31.490 0.14531.660
extractTopSwitches32.348 0.16032.553
getCDS0.0000.0010.001
importCufflinksGalaxyData0.0010.0010.002
importGTF1.6320.0091.644
importIsoformExpression1.4290.1181.511
importRdata3.0830.0713.136
importSalmonData47.951 1.90967.049
isoformSwitchAnalysisCombined66.759 3.33770.214
isoformSwitchAnalysisPart130.441 0.15230.620
isoformSwitchAnalysisPart25.7920.0375.838
isoformToGeneExp3.6390.1993.817
isoformToIsoformFraction0.4310.0600.463
preFilter0.0480.0030.052
prepareSalmonFilesDataFrame18.186 0.31325.335
subsetSwitchAnalyzeRlist0.0510.0030.054
switchAnalyzeRlist3.0650.0713.106
switchPlot6.3740.0186.403
switchPlotTranscript4.4050.0094.417
testData0.0300.0040.035