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: 2017-10-18 03:26:33 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:38:25 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 711.9 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/transcriptR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 9.97   0.66   10.74
predictStrand-methods           7.48   0.25    7.74
peaksToBed-methods              6.38   0.25    6.65
plotFeatures-methods            5.36   0.00    5.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 14.86   0.34   15.22
peaksToBed-methods               7.78   0.31    8.09
predictStrand-methods            7.14   0.37    7.52
* 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	0.74	0.00	0.74
annotateTranscripts-methods	3.53	0.07	3.61
breakTranscriptsByPeaks-methods	9.97	0.66	10.74
constructCDS	0	0	0
constructTDS	0.49	0.00	0.48
detectTranscripts-methods	1.64	0.09	1.73
estimateBackground-methods	0.56	0.02	0.58
estimateGapDistance-methods	1.27	0.03	1.30
exportCoverage-methods	0.29	0.02	0.31
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.02	0.00	0.02
getPeaks-methods	0.03	0.01	0.04
getPredictorSignificance-methods	0.01	0.00	0.02
getProbTreshold-methods	0.02	0.00	0.02
getQuadProb-methods	0.41	0.02	0.42
getTestedGapDistances-methods	0.37	0.03	0.40
getTranscripts-methods	0.42	0.00	0.43
peaksToBed-methods	6.38	0.25	6.65
plotErrorRate-methods	0.94	0.05	0.98
plotFeatures-methods	5.36	0.00	5.36
plotGenomicAnnot-methods	1.52	0.01	1.53
plotROC-methods	1.59	0.02	1.61
predictStrand-methods	7.48	0.25	7.74
predictTssOverlap-methods	1.35	0.03	1.37
show	0.28	0.00	0.28
transcriptsToBed-methods	2.27	0.05	2.31

name	user	system	elapsed
addFeature-methods	1.08	0.01	1.10
annotateTranscripts-methods	4.14	0.05	4.19
breakTranscriptsByPeaks-methods	14.86	0.34	15.22
constructCDS	0	0	0
constructTDS	0.36	0.04	0.39
detectTranscripts-methods	1.50	0.03	1.53
estimateBackground-methods	0.50	0.03	0.53
estimateGapDistance-methods	2.14	0.01	2.16
exportCoverage-methods	0.39	0.02	0.40
getConfusionMatrix-methods	0.00	0.01	0.02
getGenomicAnnot-methods	0.00	0.02	0.01
getPeaks-methods	0.04	0.00	0.05
getPredictorSignificance-methods	0.00	0.02	0.02
getProbTreshold-methods	0.02	0.00	0.01
getQuadProb-methods	0.25	0.03	0.28
getTestedGapDistances-methods	0.3	0.0	0.3
getTranscripts-methods	0.33	0.00	0.33
peaksToBed-methods	7.78	0.31	8.09
plotErrorRate-methods	1.30	0.03	1.32
plotFeatures-methods	4.62	0.02	4.65
plotGenomicAnnot-methods	1.50	0.01	1.51
plotROC-methods	1.69	0.02	1.70
predictStrand-methods	7.14	0.37	7.52
predictTssOverlap-methods	1.94	0.00	1.94
show	0.23	0.02	0.25
transcriptsToBed-methods	1.32	0.03	1.34