| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:35 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 992/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 1.21.0 (landing page) Kristoffer Vitting-Seerup
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: IsoformSwitchAnalyzeR |
| Version: 1.21.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.21.0.tar.gz |
| StartedAt: 2022-12-29 00:47:16 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:55:29 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 493.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.21.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.21.0'
* 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 whether package 'IsoformSwitchAnalyzeR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 1.0Mb
extdata 4.2Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/IsoformSwitchAnalyzeR/libs/x64/IsoformSwitchAnalyzeR.dll':
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
importSalmonData 31.70 1.08 41.58
isoformSwitchAnalysisCombined 31.01 1.76 32.99
IsoformSwitchTestDEXSeq 31.66 0.43 32.11
prepareSalmonFilesDataFrame 14.37 0.22 18.62
extractSequence 8.22 0.09 8.31
isoformSwitchAnalysisPart1 8.16 0.05 8.22
extractTopSwitches 7.89 0.06 7.96
extractSwitchSummary 7.72 0.05 7.77
analyzeORF 7.34 0.05 7.39
IsoformSwitchTestDRIMSeq 5.31 0.25 5.73
analyzeAlternativSplicing 5.20 0.08 5.28
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'IsoformSwitchAnalyzeR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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 | 31.66 | 0.43 | 32.11 | |
| IsoformSwitchTestDRIMSeq | 5.31 | 0.25 | 5.73 | |
| addORFfromGTF | 0.76 | 0.00 | 0.76 | |
| analyzeAlternativSplicing | 5.20 | 0.08 | 5.28 | |
| analyzeCPAT | 0.03 | 0.02 | 0.05 | |
| analyzeCPC2 | 0.05 | 0.00 | 0.04 | |
| analyzeIUPred2A | 1.86 | 0.04 | 1.95 | |
| analyzeNovelIsoformORF | 0.52 | 0.00 | 0.52 | |
| analyzeORF | 7.34 | 0.05 | 7.39 | |
| analyzePFAM | 0.33 | 0.03 | 0.36 | |
| analyzeSignalP | 0.08 | 0.00 | 0.08 | |
| analyzeSwitchConsequences | 0.92 | 0.02 | 0.93 | |
| expressionAnalysisPlots | 0.81 | 0.01 | 0.83 | |
| extractConsequenceEnrichment | 0.52 | 0.00 | 0.52 | |
| extractConsequenceEnrichmentComparison | 0.91 | 0.02 | 0.92 | |
| extractConsequenceSummary | 0.62 | 0.05 | 0.67 | |
| extractGeneExpression | 0.06 | 0.00 | 0.06 | |
| extractGenomeWideAnalysis | 2.36 | 0.00 | 2.36 | |
| extractGenomeWideSplicingAnalysis | 2.33 | 0.03 | 2.36 | |
| extractSequence | 8.22 | 0.09 | 8.31 | |
| extractSplicingEnrichment | 1.17 | 0.00 | 1.18 | |
| extractSplicingEnrichmentComparison | 1.44 | 0.02 | 1.45 | |
| extractSplicingSummary | 1.06 | 0.01 | 1.08 | |
| extractSwitchOverlap | 0.31 | 0.03 | 0.34 | |
| extractSwitchSummary | 7.72 | 0.05 | 7.77 | |
| extractTopSwitches | 7.89 | 0.06 | 7.96 | |
| getCDS | 0 | 0 | 0 | |
| importCufflinksGalaxyData | 0 | 0 | 0 | |
| importGTF | 0.92 | 0.00 | 0.92 | |
| importIsoformExpression | 1.20 | 0.30 | 1.26 | |
| importRdata | 1.66 | 0.14 | 1.76 | |
| importSalmonData | 31.70 | 1.08 | 41.58 | |
| isoformSwitchAnalysisCombined | 31.01 | 1.76 | 32.99 | |
| isoformSwitchAnalysisPart1 | 8.16 | 0.05 | 8.22 | |
| isoformSwitchAnalysisPart2 | 2.70 | 0.11 | 2.84 | |
| isoformToGeneExp | 2.22 | 0.16 | 2.43 | |
| isoformToIsoformFraction | 0.42 | 0.17 | 0.50 | |
| preFilter | 0.02 | 0.01 | 0.03 | |
| prepareSalmonFilesDataFrame | 14.37 | 0.22 | 18.62 | |
| subsetSwitchAnalyzeRlist | 0.03 | 0.00 | 0.03 | |
| switchAnalyzeRlist | 1.60 | 0.14 | 1.71 | |
| switchPlot | 3.31 | 0.07 | 3.37 | |
| switchPlotTranscript | 1.28 | 0.03 | 1.31 | |
| testData | 0.02 | 0.00 | 0.02 | |