Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-20 13:54 -0400 (Sat, 20 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
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 1050/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IsoformSwitchAnalyzeR 2.5.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: IsoformSwitchAnalyzeR |
Version: 2.5.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.5.0.tar.gz |
StartedAt: 2024-07-20 02:20:04 -0400 (Sat, 20 Jul 2024) |
EndedAt: 2024-07-20 02:31:20 -0400 (Sat, 20 Jul 2024) |
EllapsedTime: 676.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: IsoformSwitchAnalyzeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings IsoformSwitchAnalyzeR_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IsoformSwitchAnalyzeR’ version ‘2.5.0’ * 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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE 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 ... ERROR Running examples in ‘IsoformSwitchAnalyzeR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: importSalmonData > ### Title: Direct creation of a switchAnalyzeRlist from Salmon > ### quantification > ### Aliases: importSalmonData > > ### ** Examples > > ### Please note > # The way of importing files in the following example with > # "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is > # specialized way of accessing the example data in the IsoformSwitchAnalyzeR package > # and not something you need to do - just supply the string e.g. > # parentDir = "individual_quantifications_in_subdir/" to the functions > # path (e.g. "myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument > > ### Prepare data.frame with quant file info > salmonDf <- prepareSalmonFileDataFrame( + system.file("extdata/drosophila", package="IsoformSwitchAnalyzeR") + ) Found 4 Salmon quantifications of interest Adding NAs as conditions. Please modify these manually. > > ### Add conditions > salmonDf$condition <- c('wt','wt','ko','ko') > > ### Create switchAnalyzeRlist > aSwitchList <- importSalmonData(salmonDf) Importing quantification data... Error in checkAssays2Txps(assays, txps) : none of the transcripts in the quantification files are in the GTF Calls: importSalmonData -> suppressMessages -> withCallingHandlers Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘IsoformSwitchAnalyzeR.Rmd’ using rmarkdown Quitting from lines 1154-1158 [unnamed-chunk-37] (IsoformSwitchAnalyzeR.Rmd) Error: processing vignette 'IsoformSwitchAnalyzeR.Rmd' failed with diagnostics: none of the transcripts in the quantification files are in the GTF --- failed re-building ‘IsoformSwitchAnalyzeR.Rmd’ SUMMARY: processing the following file failed: ‘IsoformSwitchAnalyzeR.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’ for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
name | user | system | elapsed | |
IsoformSwitchTestDEXSeq | 63.012 | 1.180 | 64.184 | |
IsoformSwitchTestSatuRn | 2.576 | 0.080 | 2.626 | |
addORFfromGTF | 0.746 | 0.000 | 0.746 | |
analyzeAlternativSplicing | 5.715 | 0.032 | 5.746 | |
analyzeCPAT | 0.077 | 0.000 | 0.077 | |
analyzeCPC2 | 0.048 | 0.004 | 0.051 | |
analyzeDeepLoc2 | 0.218 | 0.020 | 0.225 | |
analyzeDeepTMHMM | 0.419 | 0.000 | 0.419 | |
analyzeIUPred2A | 2.214 | 0.032 | 2.247 | |
analyzeNovelIsoformORF | 0.552 | 0.004 | 0.556 | |
analyzeORF | 8.653 | 0.068 | 8.721 | |
analyzePFAM | 0.407 | 0.000 | 0.407 | |
analyzeSignalP | 0.080 | 0.004 | 0.084 | |
analyzeSwitchConsequences | 0.937 | 0.000 | 0.937 | |
expressionAnalysisPlots | 1.011 | 0.004 | 1.014 | |
extractConsequenceEnrichment | 0.432 | 0.004 | 0.436 | |
extractConsequenceEnrichmentComparison | 0.602 | 0.008 | 0.610 | |
extractConsequenceSummary | 0.713 | 0.016 | 0.728 | |
extractGeneExpression | 0.038 | 0.000 | 0.038 | |
extractGenomeWideAnalysis | 3.916 | 0.116 | 4.032 | |
extractGenomeWideSplicingAnalysis | 2.491 | 0.016 | 2.507 | |
extractSequence | 8.735 | 0.020 | 8.755 | |
extractSplicingEnrichment | 0.982 | 0.000 | 0.982 | |
extractSplicingEnrichmentComparison | 1.159 | 0.016 | 1.176 | |
extractSplicingSummary | 0.925 | 0.004 | 0.929 | |
extractSwitchOverlap | 0.322 | 0.000 | 0.323 | |
extractSwitchSummary | 7.659 | 0.028 | 7.688 | |
extractTopSwitches | 7.936 | 0.040 | 7.976 | |
importCufflinksGalaxyData | 0.001 | 0.000 | 0.000 | |
importGTF | 0.723 | 0.004 | 0.728 | |
importIsoformExpression | 0.610 | 0.116 | 0.677 | |
importRdata | 2.268 | 0.168 | 2.406 | |