BioC 3.4: CHECK report for transcriptR on moscato1

Package: transcriptR

Version: 1.1.2

Command: rm -rf transcriptR.buildbin-libdir transcriptR.Rcheck && mkdir transcriptR.buildbin-libdir transcriptR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.1.2.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out && D:\biocbld\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_1.1.2.tar.gz

StartedAt: 2016-09-20 17:48:02 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 17:57:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 569.0 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=transcriptR.buildbin-libdir transcriptR_1.1.2.tar.gz >transcriptR.Rcheck\00install.out 2>&1 && cp transcriptR.Rcheck\00install.out transcriptR-install.out  && D:\biocbld\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_1.1.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-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 '1.1.2'
* 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 11.40   0.21   11.76
predictStrand-methods            7.58   0.26    7.85
peaksToBed-methods               7.30   0.22    7.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 14.04   0.18   14.22
predictStrand-methods            8.00   0.15    8.14
peaksToBed-methods               6.88   0.33    7.21
* 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_1.1.2.zip
* DONE (transcriptR)

name	user	system	elapsed
addFeature-methods	0.10	0.00	0.11
annotateTranscripts-methods	3.36	0.06	3.41
breakTranscriptsByPeaks-methods	11.40	0.21	11.76
constructCDS	0.02	0.00	0.02
constructTDS	0.29	0.00	0.30
detectTranscripts-methods	2.13	0.04	2.16
estimateBackground-methods	0.62	0.02	0.64
estimateGapDistance-methods	1.50	0.05	1.55
exportCoverage-methods	0.26	0.01	0.28
getConfusionMatrix-methods	0.02	0.00	0.02
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.03	0.00	0.03
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.02	0.00	0.01
getQuadProb-methods	0.29	0.00	0.30
getTestedGapDistances-methods	0.28	0.00	0.28
getTranscripts-methods	0.28	0.02	0.30
peaksToBed-methods	7.30	0.22	7.51
plotErrorRate-methods	1.52	0.00	1.53
plotFeatures-methods	2.21	0.00	2.22
plotGenomicAnnot-methods	0.36	0.00	0.36
plotROC-methods	1.47	0.00	1.46
predictStrand-methods	7.58	0.26	7.85
predictTssOverlap-methods	1.50	0.02	1.51
show	0.28	0.01	0.30
transcriptsToBed-methods	1.64	0.03	1.67

name	user	system	elapsed
addFeature-methods	0.19	0.00	0.19
annotateTranscripts-methods	4.58	0.07	4.65
breakTranscriptsByPeaks-methods	14.04	0.18	14.22
constructCDS	0	0	0
constructTDS	0.26	0.02	0.28
detectTranscripts-methods	2.51	0.03	2.54
estimateBackground-methods	0.55	0.03	0.58
estimateGapDistance-methods	2.26	0.08	2.34
exportCoverage-methods	0.27	0.00	0.26
getConfusionMatrix-methods	0.01	0.00	0.02
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.05	0.00	0.05
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0	0	0
getQuadProb-methods	0.25	0.01	0.27
getTestedGapDistances-methods	0.27	0.02	0.28
getTranscripts-methods	0.23	0.03	0.26
peaksToBed-methods	6.88	0.33	7.21
plotErrorRate-methods	1.25	0.00	1.25
plotFeatures-methods	2.43	0.00	2.43
plotGenomicAnnot-methods	0.39	0.01	0.41
plotROC-methods	1.92	0.00	1.92
predictStrand-methods	8.00	0.15	8.14
predictTssOverlap-methods	1.69	0.01	1.70
show	0.26	0.00	0.27
transcriptsToBed-methods	1.74	0.02	1.74