BioC 3.4: CHECK report for transcriptR on tokay1

Package: transcriptR

Version: 1.2.0

Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.2.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.2.0.tar.gz

StartedAt: 2017-04-15 01:11:33 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:21:10 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 577.6 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.2.0.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/transcriptR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.2.0'
* 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 12.49   0.62   13.33
predictStrand-methods            6.14   0.25    6.41
peaksToBed-methods               6.11   0.27    6.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 10.59   0.61   11.28
predictStrand-methods            7.94   0.14    8.08
peaksToBed-methods               5.89   0.41    6.30
* 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_1.2.0.zip
* DONE (transcriptR)

name	user	system	elapsed
addFeature-methods	0.08	0.03	0.10
annotateTranscripts-methods	2.72	0.13	2.85
breakTranscriptsByPeaks-methods	12.49	0.62	13.33
constructCDS	0.00	0.02	0.01
constructTDS	0.25	0.03	0.28
detectTranscripts-methods	1.71	0.05	1.77
estimateBackground-methods	0.47	0.06	0.54
estimateGapDistance-methods	1.08	0.01	1.10
exportCoverage-methods	0.27	0.02	0.28
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.00	0.02	0.01
getPeaks-methods	0.03	0.00	0.03
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.01	0.00	0.02
getQuadProb-methods	0.25	0.03	0.28
getTestedGapDistances-methods	0.30	0.01	0.31
getTranscripts-methods	0.28	0.00	0.28
peaksToBed-methods	6.11	0.27	6.38
plotErrorRate-methods	1.31	0.01	1.33
plotFeatures-methods	2.11	0.02	2.12
plotGenomicAnnot-methods	0.32	0.00	0.31
plotROC-methods	1.68	0.05	1.74
predictStrand-methods	6.14	0.25	6.41
predictTssOverlap-methods	1.38	0.01	1.39
show	0.27	0.02	0.28
transcriptsToBed-methods	1.23	0.01	1.25

name	user	system	elapsed
addFeature-methods	0.09	0.00	0.09
annotateTranscripts-methods	3.05	0.11	3.16
breakTranscriptsByPeaks-methods	10.59	0.61	11.28
constructCDS	0	0	0
constructTDS	0.36	0.02	0.38
detectTranscripts-methods	2.16	0.04	2.21
estimateBackground-methods	0.46	0.04	0.50
estimateGapDistance-methods	1.07	0.03	1.09
exportCoverage-methods	0.26	0.00	0.27
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.02	0.00	0.01
getPeaks-methods	0.04	0.01	0.06
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0	0	0
getQuadProb-methods	0.27	0.01	0.28
getTestedGapDistances-methods	0.23	0.02	0.25
getTranscripts-methods	0.22	0.03	0.25
peaksToBed-methods	5.89	0.41	6.30
plotErrorRate-methods	1.58	0.03	1.61
plotFeatures-methods	2.41	0.00	2.40
plotGenomicAnnot-methods	0.36	0.00	0.36
plotROC-methods	1.40	0.00	1.41
predictStrand-methods	7.94	0.14	8.08
predictTssOverlap-methods	1.42	0.00	1.42
show	0.24	0.00	0.23
transcriptsToBed-methods	1.33	0.01	1.35