BioC 3.6: CHECK report for transcriptR on tokay1

Package: transcriptR

Version: 1.5.0

Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.5.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.5.0.tar.gz

StartedAt: 2017-08-16 02:53:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:04:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 629.9 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.5.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.5.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/transcriptR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'transcriptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptR' version '1.5.0'
* 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 'transcriptR' can be installed ... OK
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 11.68   0.55   12.33
peaksToBed-methods              11.44   0.48   11.94
predictStrand-methods            8.00   0.35    8.34
plotFeatures-methods             6.12   0.02    6.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 16.81   0.44   17.50
peaksToBed-methods               9.23   0.34    9.58
predictStrand-methods            7.23   0.28    7.52
plotFeatures-methods             6.39   0.01    6.41
annotateTranscripts-methods      6.25   0.09    6.37
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: OK

install for i386

* installing *source* package 'transcriptR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.5.0.zip
* DONE (transcriptR)

name	user	system	elapsed
addFeature-methods	0.23	0.01	0.25
annotateTranscripts-methods	3.77	0.11	3.87
breakTranscriptsByPeaks-methods	11.68	0.55	12.33
constructCDS	0	0	0
constructTDS	0.30	0.02	0.31
detectTranscripts-methods	1.77	0.09	1.86
estimateBackground-methods	0.83	0.02	0.84
estimateGapDistance-methods	1.97	0.00	1.97
exportCoverage-methods	0.31	0.02	0.33
getConfusionMatrix-methods	0.02	0.00	0.01
getGenomicAnnot-methods	0.01	0.00	0.02
getPeaks-methods	0.05	0.00	0.05
getPredictorSignificance-methods	0.00	0.01	0.01
getProbTreshold-methods	0.00	0.02	0.02
getQuadProb-methods	0.39	0.03	0.42
getTestedGapDistances-methods	0.42	0.00	0.42
getTranscripts-methods	0.39	0.03	0.42
peaksToBed-methods	11.44	0.48	11.94
plotErrorRate-methods	1.33	0.08	1.81
plotFeatures-methods	6.12	0.02	6.71
plotGenomicAnnot-methods	1.64	0.01	1.65
plotROC-methods	1.82	0.00	1.82
predictStrand-methods	8.00	0.35	8.34
predictTssOverlap-methods	1.82	0.03	1.86
show	0.34	0.01	0.36
transcriptsToBed-methods	1.71	0.03	1.74

name	user	system	elapsed
addFeature-methods	0.28	0.02	0.30
annotateTranscripts-methods	6.25	0.09	6.37
breakTranscriptsByPeaks-methods	16.81	0.44	17.50
constructCDS	0	0	0
constructTDS	0.24	0.03	0.26
detectTranscripts-methods	1.48	0.06	1.55
estimateBackground-methods	0.64	0.02	0.66
estimateGapDistance-methods	1.54	0.03	1.56
exportCoverage-methods	0.34	0.01	0.36
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.00	0.02	0.01
getPeaks-methods	0.06	0.00	0.07
getPredictorSignificance-methods	0.02	0.00	0.01
getProbTreshold-methods	0.01	0.00	0.02
getQuadProb-methods	0.35	0.03	0.37
getTestedGapDistances-methods	0.39	0.00	0.39
getTranscripts-methods	0.36	0.02	0.38
peaksToBed-methods	9.23	0.34	9.58
plotErrorRate-methods	1.61	0.05	1.65
plotFeatures-methods	6.39	0.01	6.41
plotGenomicAnnot-methods	2.41	0.00	2.45
plotROC-methods	2.20	0.05	2.25
predictStrand-methods	7.23	0.28	7.52
predictTssOverlap-methods	1.97	0.02	2.00
show	0.25	0.00	0.25
transcriptsToBed-methods	1.33	0.00	1.32