| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:52 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1063/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 2.3.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: IsoformSwitchAnalyzeR |
| Version: 2.3.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.3.0.tar.gz |
| StartedAt: 2024-03-28 06:32:47 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 06:49:26 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 998.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.3.0’
* 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 (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
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
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'
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'
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'
isoformSwitchTestSatuRn: no visible global function definition for
'rowData'
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 '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 assay 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
metadata 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 queryHits
ref_gene_id rowData setdff sigEval sigLevel sigLevelPos significance
splicingResult subjectHits 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IsoformSwitchTestDEXSeq 95.091 0.707 96.045
importSalmonData 90.908 0.839 139.012
prepareSalmonFilesDataFrame 79.555 0.577 91.386
isoformSwitchAnalysisCombined 60.265 0.754 61.157
extractSequence 13.378 0.060 13.467
analyzeORF 12.939 0.044 13.009
extractTopSwitches 11.328 0.028 11.379
extractSwitchSummary 11.230 0.016 11.268
isoformSwitchAnalysisPart1 10.878 0.056 10.959
analyzeAlternativSplicing 9.873 0.012 9.904
isoformToGeneExp 7.123 0.100 7.218
isoformSwitchAnalysisPart2 6.017 0.067 6.090
extractGenomeWideAnalysis 5.709 0.140 5.861
extractGenomeWideSplicingAnalysis 4.971 0.032 5.011
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 | 95.091 | 0.707 | 96.045 | |
| IsoformSwitchTestSatuRn | 4.817 | 0.076 | 4.879 | |
| addORFfromGTF | 2.069 | 0.064 | 2.137 | |
| analyzeAlternativSplicing | 9.873 | 0.012 | 9.904 | |
| analyzeCPAT | 0.065 | 0.000 | 0.066 | |
| analyzeCPC2 | 0.056 | 0.004 | 0.061 | |
| analyzeDeepLoc2 | 0.290 | 0.020 | 0.305 | |
| analyzeDeepTMHMM | 0.686 | 0.000 | 0.689 | |
| analyzeIUPred2A | 3.549 | 0.007 | 3.564 | |
| analyzeNovelIsoformORF | 0.880 | 0.004 | 0.885 | |
| analyzeORF | 12.939 | 0.044 | 13.009 | |
| analyzePFAM | 0.706 | 0.004 | 0.713 | |
| analyzeSignalP | 0.112 | 0.000 | 0.114 | |
| analyzeSwitchConsequences | 1.408 | 0.016 | 1.427 | |
| expressionAnalysisPlots | 1.569 | 0.024 | 1.596 | |
| extractConsequenceEnrichment | 0.589 | 0.004 | 0.594 | |
| extractConsequenceEnrichmentComparison | 0.976 | 0.000 | 0.977 | |
| extractConsequenceSummary | 1.167 | 0.000 | 1.170 | |
| extractGeneExpression | 0.05 | 0.00 | 0.05 | |
| extractGenomeWideAnalysis | 5.709 | 0.140 | 5.861 | |
| extractGenomeWideSplicingAnalysis | 4.971 | 0.032 | 5.011 | |
| extractSequence | 13.378 | 0.060 | 13.467 | |
| extractSplicingEnrichment | 1.589 | 0.000 | 1.592 | |
| extractSplicingEnrichmentComparison | 1.838 | 0.004 | 1.845 | |
| extractSplicingSummary | 1.490 | 0.008 | 1.501 | |
| extractSwitchOverlap | 0.491 | 0.000 | 0.492 | |
| extractSwitchSummary | 11.230 | 0.016 | 11.268 | |
| extractTopSwitches | 11.328 | 0.028 | 11.379 | |
| importCufflinksGalaxyData | 0 | 0 | 0 | |
| importGTF | 2.024 | 0.036 | 2.064 | |
| importIsoformExpression | 1.860 | 0.071 | 1.900 | |
| importRdata | 4.550 | 0.060 | 4.607 | |
| importSalmonData | 90.908 | 0.839 | 139.012 | |
| isoformSwitchAnalysisCombined | 60.265 | 0.754 | 61.157 | |
| isoformSwitchAnalysisPart1 | 10.878 | 0.056 | 10.959 | |
| isoformSwitchAnalysisPart2 | 6.017 | 0.067 | 6.090 | |
| isoformToGeneExp | 7.123 | 0.100 | 7.218 | |
| isoformToIsoformFraction | 1.272 | 0.052 | 1.304 | |
| preFilter | 0.029 | 0.000 | 0.029 | |
| prepareSalmonFilesDataFrame | 79.555 | 0.577 | 91.386 | |
| subsetSwitchAnalyzeRlist | 0.027 | 0.000 | 0.027 | |
| switchAnalyzeRlist | 4.530 | 0.063 | 4.584 | |
| switchPlot | 4.146 | 0.020 | 4.177 | |
| switchPlotTranscript | 2.329 | 0.036 | 2.374 | |
| testData | 0.014 | 0.000 | 0.014 | |