Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1060/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IsoformSwitchAnalyzeR 2.7.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: IsoformSwitchAnalyzeR |
Version: 2.7.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.7.0.tar.gz |
StartedAt: 2024-12-24 07:59:13 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 08:14:05 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 892.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IsoformSwitchAnalyzeR.Rcheck |
Warnings: 6 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IsoformSwitchAnalyzeR’ version ‘2.7.0’ * checking package namespace information ... OK * checking package dependencies ... INFO 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. Imports includes 30 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 7.0Mb 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... WARNING Warning: program compiled against libxml 212 using older 211 * 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 91.163 1.976 93.357 isoformSwitchAnalysisCombined 61.199 1.039 62.371 importSalmonData 40.510 3.383 93.594 prepareSalmonFilesDataFrame 17.914 1.268 30.842 analyzeORF 12.399 0.060 12.495 extractSequence 12.421 0.032 12.478 extractSwitchSummary 10.837 0.028 10.885 extractTopSwitches 10.729 0.028 10.774 isoformSwitchAnalysisPart1 10.708 0.008 10.744 analyzeAlternativSplicing 9.822 0.092 9.934 isoformSwitchAnalysisPart2 6.179 0.087 6.281 extractGenomeWideAnalysis 5.881 0.112 6.007 extractGenomeWideSplicingAnalysis 5.140 0.028 5.179 * 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: 6 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’ for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (IsoformSwitchAnalyzeR)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
name | user | system | elapsed | |
IsoformSwitchTestDEXSeq | 91.163 | 1.976 | 93.357 | |
IsoformSwitchTestSatuRn | 3.941 | 0.067 | 4.017 | |
addORFfromGTF | 1.116 | 0.000 | 1.118 | |
analyzeAlternativSplicing | 9.822 | 0.092 | 9.934 | |
analyzeCPAT | 0.063 | 0.004 | 0.069 | |
analyzeCPC2 | 0.060 | 0.004 | 0.065 | |
analyzeDeepLoc2 | 0.296 | 0.015 | 0.314 | |
analyzeDeepTMHMM | 0.719 | 0.017 | 0.739 | |
analyzeIUPred2A | 3.612 | 0.031 | 3.657 | |
analyzeNovelIsoformORF | 0.979 | 0.008 | 0.990 | |
analyzeORF | 12.399 | 0.060 | 12.495 | |
analyzePFAM | 0.695 | 0.008 | 0.707 | |
analyzeSignalP | 0.115 | 0.008 | 0.127 | |
analyzeSwitchConsequences | 1.440 | 0.032 | 1.476 | |
expressionAnalysisPlots | 1.589 | 0.008 | 1.601 | |
extractConsequenceEnrichment | 0.621 | 0.000 | 0.622 | |
extractConsequenceEnrichmentComparison | 1.011 | 0.004 | 1.017 | |
extractConsequenceSummary | 1.142 | 0.008 | 1.152 | |
extractGeneExpression | 0.052 | 0.004 | 0.056 | |
extractGenomeWideAnalysis | 5.881 | 0.112 | 6.007 | |
extractGenomeWideSplicingAnalysis | 5.140 | 0.028 | 5.179 | |
extractSequence | 12.421 | 0.032 | 12.478 | |
extractSplicingEnrichment | 1.599 | 0.000 | 1.603 | |
extractSplicingEnrichmentComparison | 1.847 | 0.008 | 1.859 | |
extractSplicingSummary | 1.509 | 0.000 | 1.512 | |
extractSwitchOverlap | 0.469 | 0.000 | 0.470 | |
extractSwitchSummary | 10.837 | 0.028 | 10.885 | |
extractTopSwitches | 10.729 | 0.028 | 10.774 | |
importCufflinksGalaxyData | 0 | 0 | 0 | |
importGTF | 1.081 | 0.000 | 1.082 | |
importIsoformExpression | 0.773 | 0.083 | 0.860 | |
importRdata | 3.515 | 0.043 | 3.576 | |
importSalmonData | 40.510 | 3.383 | 93.594 | |
isoformSwitchAnalysisCombined | 61.199 | 1.039 | 62.371 | |
isoformSwitchAnalysisPart1 | 10.708 | 0.008 | 10.744 | |
isoformSwitchAnalysisPart2 | 6.179 | 0.087 | 6.281 | |
isoformToGeneExp | 4.376 | 0.052 | 4.446 | |
isoformToIsoformFraction | 0.284 | 0.055 | 0.341 | |
preFilter | 0.030 | 0.000 | 0.031 | |
prepareSalmonFilesDataFrame | 17.914 | 1.268 | 30.842 | |
subsetSwitchAnalyzeRlist | 0.025 | 0.004 | 0.029 | |
switchAnalyzeRlist | 3.796 | 0.111 | 3.914 | |
switchPlot | 4.736 | 0.115 | 4.864 | |
switchPlotTranscript | 2.596 | 0.035 | 2.639 | |
testData | 0.014 | 0.000 | 0.014 | |