| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:25 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 988/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 1.18.0 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: IsoformSwitchAnalyzeR |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.18.0.tar.gz |
| StartedAt: 2022-10-18 20:16:41 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:25:21 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 519.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 5.1Mb
sub-directories of 1Mb or more:
R 1.0Mb
extdata 3.0Mb
* 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
isoformSwitchAnalysisCombined 32.166 1.402 33.568
IsoformSwitchTestDEXSeq 32.949 0.454 33.389
importSalmonData 25.933 2.451 38.100
prepareSalmonFilesDataFrame 9.081 0.684 14.402
extractSequence 9.684 0.016 9.701
analyzeORF 9.158 0.024 9.183
extractTopSwitches 8.491 0.056 8.547
extractSwitchSummary 8.251 0.036 8.287
isoformSwitchAnalysisPart1 7.276 0.160 7.435
analyzeAlternativSplicing 5.848 0.040 5.887
* 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
‘/home/biocbuild/bbs-3.15-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/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 | 32.949 | 0.454 | 33.389 | |
| IsoformSwitchTestDRIMSeq | 4.626 | 0.096 | 4.687 | |
| addORFfromGTF | 0.739 | 0.008 | 0.748 | |
| analyzeAlternativSplicing | 5.848 | 0.040 | 5.887 | |
| analyzeCPAT | 0.048 | 0.008 | 0.057 | |
| analyzeCPC2 | 0.050 | 0.004 | 0.054 | |
| analyzeIUPred2A | 2.211 | 0.024 | 2.237 | |
| analyzeNovelIsoformORF | 0.648 | 0.000 | 0.647 | |
| analyzeORF | 9.158 | 0.024 | 9.183 | |
| analyzePFAM | 0.390 | 0.000 | 0.391 | |
| analyzeSignalP | 0.075 | 0.008 | 0.084 | |
| analyzeSwitchConsequences | 0.894 | 0.011 | 0.905 | |
| expressionAnalysisPlots | 0.819 | 0.000 | 0.819 | |
| extractConsequenceEnrichment | 0.433 | 0.004 | 0.437 | |
| extractConsequenceEnrichmentComparison | 0.689 | 0.032 | 0.721 | |
| extractConsequenceSummary | 0.681 | 0.004 | 0.685 | |
| extractGeneExpression | 0.049 | 0.000 | 0.049 | |
| extractGenomeWideAnalysis | 2.349 | 0.032 | 2.381 | |
| extractGenomeWideSplicingAnalysis | 2.294 | 0.008 | 2.302 | |
| extractSequence | 9.684 | 0.016 | 9.701 | |
| extractSplicingEnrichment | 1.029 | 0.012 | 1.041 | |
| extractSplicingEnrichmentComparison | 1.178 | 0.004 | 1.182 | |
| extractSplicingSummary | 0.921 | 0.000 | 0.921 | |
| extractSwitchOverlap | 0.37 | 0.00 | 0.37 | |
| extractSwitchSummary | 8.251 | 0.036 | 8.287 | |
| extractTopSwitches | 8.491 | 0.056 | 8.547 | |
| getCDS | 0 | 0 | 0 | |
| importCufflinksGalaxyData | 0.000 | 0.000 | 0.001 | |
| importGTF | 0.758 | 0.012 | 0.770 | |
| importIsoformExpression | 0.797 | 0.128 | 0.869 | |
| importRdata | 1.424 | 0.123 | 1.517 | |
| importSalmonData | 25.933 | 2.451 | 38.100 | |
| isoformSwitchAnalysisCombined | 32.166 | 1.402 | 33.568 | |
| isoformSwitchAnalysisPart1 | 7.276 | 0.160 | 7.435 | |
| isoformSwitchAnalysisPart2 | 2.669 | 0.100 | 2.770 | |
| isoformToGeneExp | 1.852 | 0.113 | 1.932 | |
| isoformToIsoformFraction | 0.256 | 0.085 | 0.299 | |
| preFilter | 0.022 | 0.004 | 0.026 | |
| prepareSalmonFilesDataFrame | 9.081 | 0.684 | 14.402 | |
| subsetSwitchAnalyzeRlist | 0.024 | 0.004 | 0.027 | |
| switchAnalyzeRlist | 1.385 | 0.204 | 1.552 | |
| switchPlot | 2.849 | 0.136 | 2.985 | |
| switchPlotTranscript | 1.654 | 0.068 | 1.721 | |
| testData | 0.02 | 0.00 | 0.02 | |