BioC 3.5: CHECK report for transcriptR on tokay2

Package: transcriptR

Version: 1.4.0

Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.4.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.4.0.tar.gz

StartedAt: 2017-08-16 03:20:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:30:54 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 606.1 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.4.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-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 '1.4.0'
* 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 13.99   0.46   14.56
peaksToBed-methods               8.35   0.30    8.97
predictStrand-methods            5.61   0.42    6.03
annotateTranscripts-methods      5.28   0.27    5.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 12.56   0.36   12.94
peaksToBed-methods               7.28   0.33    7.61
annotateTranscripts-methods      5.14   0.12    5.27
* 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_1.4.0.zip
* DONE (transcriptR)

name	user	system	elapsed
addFeature-methods	0.49	0.02	0.50
annotateTranscripts-methods	5.28	0.27	5.54
breakTranscriptsByPeaks-methods	13.99	0.46	14.56
constructCDS	0.00	0.02	0.02
constructTDS	0.28	0.00	0.28
detectTranscripts-methods	1.67	0.12	1.79
estimateBackground-methods	0.89	0.04	0.93
estimateGapDistance-methods	1.66	0.06	1.72
exportCoverage-methods	0.28	0.01	0.29
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.01	0.00	0.02
getPeaks-methods	0.04	0.00	0.03
getPredictorSignificance-methods	0.00	0.02	0.01
getProbTreshold-methods	0.01	0.00	0.02
getQuadProb-methods	0.28	0.02	0.30
getTestedGapDistances-methods	0.27	0.03	0.29
getTranscripts-methods	0.30	0.01	0.32
peaksToBed-methods	8.35	0.30	8.97
plotErrorRate-methods	1.52	0.06	1.68
plotFeatures-methods	4.39	0.00	4.39
plotGenomicAnnot-methods	1.63	0.00	1.63
plotROC-methods	1.34	0.02	1.36
predictStrand-methods	5.61	0.42	6.03
predictTssOverlap-methods	1.35	0.00	1.35
show	0.36	0.00	0.36
transcriptsToBed-methods	1.59	0.08	1.67

name	user	system	elapsed
addFeature-methods	0.26	0.00	0.26
annotateTranscripts-methods	5.14	0.12	5.27
breakTranscriptsByPeaks-methods	12.56	0.36	12.94
constructCDS	0.00	0.02	0.02
constructTDS	0.25	0.00	0.25
detectTranscripts-methods	1.19	0.06	1.25
estimateBackground-methods	0.39	0.06	0.46
estimateGapDistance-methods	1.07	0.02	1.09
exportCoverage-methods	0.44	0.03	0.47
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.06	0.00	0.07
getPredictorSignificance-methods	0.00	0.00	0.01
getProbTreshold-methods	0.02	0.00	0.02
getQuadProb-methods	0.4	0.0	0.4
getTestedGapDistances-methods	0.28	0.10	0.38
getTranscripts-methods	0.28	0.01	0.29
peaksToBed-methods	7.28	0.33	7.61
plotErrorRate-methods	0.97	0.03	1.00
plotFeatures-methods	3.98	0.00	3.99
plotGenomicAnnot-methods	1.61	0.00	1.61
plotROC-methods	1.34	0.02	1.36
predictStrand-methods	4.52	0.14	4.66
predictTssOverlap-methods	1.26	0.01	1.28
show	0.24	0.00	0.23
transcriptsToBed-methods	1.12	0.03	1.16