BioC 3.3: CHECK report for transcriptR on moscato2

Package: transcriptR

Version: 1.0.2

Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.0.2.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.0.2.tar.gz

StartedAt: 2016-10-13 09:41:47 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 09:54:53 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 785.8 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.0.2.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=transcriptR.buildbin-libdir --install="check:transcriptR-install.out" --force-multiarch --no-vignettes --timings transcriptR_1.0.2.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/transcriptR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.0.2'
* 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 16.13   0.53   16.78
predictStrand-methods           11.78   0.28   12.05
peaksToBed-methods              10.50   0.20   10.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 18.39   0.67   19.09
predictStrand-methods           12.51   0.35   12.85
peaksToBed-methods              11.41   0.28   11.69
annotateTranscripts-methods      5.40   0.11    5.51
* 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_1.0.2.zip
* DONE (transcriptR)

name	user	system	elapsed
addFeature-methods	0.15	0.01	0.18
annotateTranscripts-methods	4.29	0.02	4.30
breakTranscriptsByPeaks-methods	16.13	0.53	16.78
constructCDS	0	0	0
constructTDS	0.45	0.02	0.47
detectTranscripts-methods	2.40	0.03	2.43
estimateBackground-methods	0.66	0.01	0.67
estimateGapDistance-methods	1.23	0.00	1.24
exportCoverage-methods	0.27	0.03	0.29
getConfusionMatrix-methods	0.01	0.00	0.02
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.02	0.03	0.05
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0	0	0
getQuadProb-methods	0.39	0.00	0.39
getTestedGapDistances-methods	0.37	0.02	0.39
getTranscripts-methods	0.33	0.01	0.34
peaksToBed-methods	10.50	0.20	10.71
plotErrorRate-methods	1.57	0.08	1.65
plotFeatures-methods	3.34	0.00	3.33
plotGenomicAnnot-methods	0.57	0.00	0.58
plotROC-methods	1.8	0.0	1.8
predictStrand-methods	11.78	0.28	12.05
predictTssOverlap-methods	2.24	0.03	2.28
show	0.36	0.00	0.36
transcriptsToBed-methods	2.93	0.02	2.95

name	user	system	elapsed
addFeature-methods	0.22	0.01	0.23
annotateTranscripts-methods	5.40	0.11	5.51
breakTranscriptsByPeaks-methods	18.39	0.67	19.09
constructCDS	0.02	0.00	0.02
constructTDS	0.37	0.02	0.39
detectTranscripts-methods	2.79	0.06	2.85
estimateBackground-methods	0.78	0.00	0.78
estimateGapDistance-methods	1.78	0.00	1.78
exportCoverage-methods	0.39	0.02	0.40
getConfusionMatrix-methods	0.01	0.00	0.02
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.04	0.00	0.05
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.00	0.01	0.01
getQuadProb-methods	0.36	0.03	0.39
getTestedGapDistances-methods	0.37	0.02	0.39
getTranscripts-methods	0.25	0.03	0.28
peaksToBed-methods	11.41	0.28	11.69
plotErrorRate-methods	2.09	0.03	2.20
plotFeatures-methods	3.92	0.02	4.40
plotGenomicAnnot-methods	0.58	0.01	0.59
plotROC-methods	2.38	0.00	2.39
predictStrand-methods	12.51	0.35	12.85
predictTssOverlap-methods	1.95	0.01	1.96
show	0.27	0.02	0.28
transcriptsToBed-methods	2.09	0.01	2.11