Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1054/2255 | 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 | ERROR | skipped | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_2.5.0.tar.gz |
StartedAt: 2024-08-21 02:00:42 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:13:40 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 777.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IsoformSwitchAnalyzeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'IsoformSwitchAnalyzeR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'IsoformSwitchAnalyzeR' version '2.5.0' * 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 whether package 'IsoformSwitchAnalyzeR' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: R 1.0Mb data 1.1Mb extdata 4.3Mb * 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/IsoformSwitchAnalyzeR/libs/x64/IsoformSwitchAnalyzeR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed IsoformSwitchTestDEXSeq 81.32 0.69 82.28 isoformSwitchAnalysisCombined 60.55 4.41 64.86 importSalmonData 42.64 1.57 52.96 prepareSalmonFilesDataFrame 20.45 0.60 24.90 extractSequence 11.86 0.20 12.08 analyzeORF 10.47 0.16 10.63 extractTopSwitches 10.08 0.09 10.18 extractSwitchSummary 9.83 0.08 9.90 isoformSwitchAnalysisPart1 9.45 0.13 9.56 analyzeAlternativSplicing 7.39 0.16 7.54 isoformSwitchAnalysisPart2 5.59 0.42 5.97 extractGenomeWideAnalysis 5.21 0.19 5.39 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log' for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'IsoformSwitchAnalyzeR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs/x64 ** 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 ** 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 | 81.32 | 0.69 | 82.28 | |
IsoformSwitchTestSatuRn | 3.64 | 0.16 | 3.88 | |
addORFfromGTF | 1.25 | 0.01 | 1.28 | |
analyzeAlternativSplicing | 7.39 | 0.16 | 7.54 | |
analyzeCPAT | 0.08 | 0.02 | 0.10 | |
analyzeCPC2 | 0.06 | 0.01 | 0.10 | |
analyzeDeepLoc2 | 0.38 | 0.06 | 0.43 | |
analyzeDeepTMHMM | 0.43 | 0.07 | 0.54 | |
analyzeIUPred2A | 3.08 | 0.04 | 3.18 | |
analyzeNovelIsoformORF | 0.9 | 0.0 | 0.9 | |
analyzeORF | 10.47 | 0.16 | 10.63 | |
analyzePFAM | 0.62 | 0.05 | 0.68 | |
analyzeSignalP | 0.10 | 0.01 | 0.13 | |
analyzeSwitchConsequences | 1.18 | 0.08 | 1.26 | |
expressionAnalysisPlots | 1.33 | 0.02 | 1.35 | |
extractConsequenceEnrichment | 0.41 | 0.01 | 0.42 | |
extractConsequenceEnrichmentComparison | 0.65 | 0.03 | 0.69 | |
extractConsequenceSummary | 1.02 | 0.00 | 1.02 | |
extractGeneExpression | 0.04 | 0.03 | 0.08 | |
extractGenomeWideAnalysis | 5.21 | 0.19 | 5.39 | |
extractGenomeWideSplicingAnalysis | 2.96 | 0.08 | 3.04 | |
extractSequence | 11.86 | 0.20 | 12.08 | |
extractSplicingEnrichment | 1.50 | 0.03 | 1.53 | |
extractSplicingEnrichmentComparison | 1.50 | 0.04 | 1.53 | |
extractSplicingSummary | 1.22 | 0.04 | 1.27 | |
extractSwitchOverlap | 0.56 | 0.05 | 0.97 | |
extractSwitchSummary | 9.83 | 0.08 | 9.90 | |
extractTopSwitches | 10.08 | 0.09 | 10.18 | |
importCufflinksGalaxyData | 0 | 0 | 0 | |
importGTF | 1.08 | 0.00 | 1.09 | |
importIsoformExpression | 1.28 | 0.24 | 1.56 | |
importRdata | 3.70 | 0.14 | 3.89 | |
importSalmonData | 42.64 | 1.57 | 52.96 | |
isoformSwitchAnalysisCombined | 60.55 | 4.41 | 64.86 | |
isoformSwitchAnalysisPart1 | 9.45 | 0.13 | 9.56 | |
isoformSwitchAnalysisPart2 | 5.59 | 0.42 | 5.97 | |
isoformToGeneExp | 4.38 | 0.31 | 4.74 | |
isoformToIsoformFraction | 0.58 | 0.12 | 0.76 | |
preFilter | 0.04 | 0.00 | 0.05 | |
prepareSalmonFilesDataFrame | 20.45 | 0.60 | 24.90 | |
subsetSwitchAnalyzeRlist | 0.03 | 0.00 | 0.03 | |
switchAnalyzeRlist | 3.25 | 0.19 | 3.47 | |
switchPlot | 4.21 | 0.04 | 4.25 | |
switchPlotTranscript | 2.18 | 0.02 | 2.20 | |
testData | 0.04 | 0.00 | 0.03 | |