| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 966/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IsoformSwitchAnalyzeR 1.17.04 (landing page) Kristoffer Vitting-Seerup
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.17.04 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.17.04.tar.gz |
| StartedAt: 2022-03-17 19:24:01 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:33:03 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 542.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.17.04.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IsoformSwitchAnalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IsoformSwitchAnalyzeR' version '1.17.04'
* 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
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
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 'D:/biocbuild/bbs-3.15-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. 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 37.59 0.39 43.22
importSalmonData 32.59 1.42 47.47
isoformSwitchAnalysisCombined 28.94 2.52 31.46
prepareSalmonFilesDataFrame 11.00 0.55 16.97
analyzeORF 9.97 0.01 9.99
extractSequence 9.72 0.00 9.72
extractSwitchSummary 8.72 0.00 8.72
extractTopSwitches 8.25 0.02 8.27
isoformSwitchAnalysisPart1 7.82 0.03 7.86
analyzeAlternativSplicing 7.29 0.02 7.33
IsoformSwitchTestDRIMSeq 5.61 0.23 10.89
importRdata 1.95 0.38 7.30
isoformToGeneExp 2.08 0.25 10.09
switchAnalyzeRlist 1.54 0.25 6.88
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'IsoformSwitchAnalyzeR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils.c -o utils.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'IsoformSwitchAnalyzeR'
finding HTML links ... done
CDSSet html
IsoformSwitchTestDEXSeq html
IsoformSwitchTestDRIMSeq html
finding level-2 HTML links ... done
addORFfromGTF html
analyzeAlternativSplicing html
analyzeCPAT html
analyzeCPC2 html
analyzeIUPred2A html
analyzeNetSurf2 html
analyzeNovelIsoformORF html
analyzeORF html
analyzePFAM html
analyzeSignalP html
analyzeSwitchConsequences html
expressionAnalysisPlots html
extractConsequenceEnrichment html
extractConsequenceEnrichmentComparison
html
extractConsequenceSummary html
extractGeneExpression html
extractGenomeWideAnalysis html
extractGenomeWideSplicingAnalysis html
extractSequence html
extractSplicingEnrichment html
extractSplicingEnrichmentComparison html
extractSplicingSummary html
extractSwitchOverlap html
extractSwitchSummary html
extractTopSwitches html
getCDS html
importCufflinksGalaxyData html
importGTF html
importIsoformExpression html
importRdata html
importSalmonData html
isoformSwitchAnalysisCombined html
isoformSwitchAnalysisPart1 html
isoformSwitchAnalysisPart2 html
isoformToGeneExp html
isoformToIsoformFraction html
preFilter html
prepareSalmonFilesDataFrame html
subsetSwitchAnalyzeRlist html
switchAnalyzeRlist html
switchPlot html
switchPlotTopSwitches html
switchPlotTranscript html
testData html
** 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)
Making 'packages.html' ... done
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
| name | user | system | elapsed | |
| IsoformSwitchTestDEXSeq | 37.59 | 0.39 | 43.22 | |
| IsoformSwitchTestDRIMSeq | 5.61 | 0.23 | 10.89 | |
| addORFfromGTF | 0.75 | 0.02 | 3.37 | |
| analyzeAlternativSplicing | 7.29 | 0.02 | 7.33 | |
| analyzeCPAT | 0.07 | 0.01 | 0.08 | |
| analyzeCPC2 | 0.06 | 0.02 | 0.08 | |
| analyzeIUPred2A | 2.70 | 0.03 | 2.73 | |
| analyzeNovelIsoformORF | 0.67 | 0.00 | 0.67 | |
| analyzeORF | 9.97 | 0.01 | 9.99 | |
| analyzePFAM | 0.33 | 0.03 | 0.36 | |
| analyzeSignalP | 0.11 | 0.00 | 0.11 | |
| analyzeSwitchConsequences | 1.09 | 0.04 | 1.13 | |
| expressionAnalysisPlots | 1.06 | 0.01 | 1.08 | |
| extractConsequenceEnrichment | 0.47 | 0.02 | 0.48 | |
| extractConsequenceEnrichmentComparison | 0.77 | 0.00 | 0.77 | |
| extractConsequenceSummary | 0.86 | 0.00 | 0.85 | |
| extractGeneExpression | 0.04 | 0.01 | 0.07 | |
| extractGenomeWideAnalysis | 2.52 | 0.07 | 2.58 | |
| extractGenomeWideSplicingAnalysis | 2.33 | 0.01 | 2.34 | |
| extractSequence | 9.72 | 0.00 | 9.72 | |
| extractSplicingEnrichment | 1.07 | 0.02 | 1.09 | |
| extractSplicingEnrichmentComparison | 1.61 | 0.00 | 1.61 | |
| extractSplicingSummary | 1.06 | 0.00 | 1.06 | |
| extractSwitchOverlap | 0.58 | 0.01 | 0.59 | |
| extractSwitchSummary | 8.72 | 0.00 | 8.72 | |
| extractTopSwitches | 8.25 | 0.02 | 8.27 | |
| getCDS | 0 | 0 | 0 | |
| importCufflinksGalaxyData | 0 | 0 | 0 | |
| importGTF | 0.65 | 0.01 | 3.29 | |
| importIsoformExpression | 1.40 | 0.28 | 4.36 | |
| importRdata | 1.95 | 0.38 | 7.30 | |
| importSalmonData | 32.59 | 1.42 | 47.47 | |
| isoformSwitchAnalysisCombined | 28.94 | 2.52 | 31.46 | |
| isoformSwitchAnalysisPart1 | 7.82 | 0.03 | 7.86 | |
| isoformSwitchAnalysisPart2 | 2.97 | 0.14 | 3.11 | |
| isoformToGeneExp | 2.08 | 0.25 | 10.09 | |
| isoformToIsoformFraction | 0.63 | 0.16 | 0.66 | |
| preFilter | 0.03 | 0.01 | 0.04 | |
| prepareSalmonFilesDataFrame | 11.00 | 0.55 | 16.97 | |
| subsetSwitchAnalyzeRlist | 0.03 | 0.00 | 0.03 | |
| switchAnalyzeRlist | 1.54 | 0.25 | 6.88 | |
| switchPlot | 2.52 | 0.01 | 2.53 | |
| switchPlotTranscript | 1.75 | 0.02 | 1.77 | |
| testData | 0.00 | 0.01 | 0.01 | |