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BioC 3.5: CHECK report for transcriptR on tokay2

This page was generated on 2017-08-16 13:25:12 -0400 (Wed, 16 Aug 2017).

Package 1328/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.4.0
Armen R. Karapetyan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/transcriptR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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 3.4.1 (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

transcriptR.Rcheck/00install.out:


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)

transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings:

nameusersystemelapsed
addFeature-methods0.490.020.50
annotateTranscripts-methods5.280.275.54
breakTranscriptsByPeaks-methods13.99 0.4614.56
constructCDS0.000.020.02
constructTDS0.280.000.28
detectTranscripts-methods1.670.121.79
estimateBackground-methods0.890.040.93
estimateGapDistance-methods1.660.061.72
exportCoverage-methods0.280.010.29
getConfusionMatrix-methods000
getGenomicAnnot-methods0.010.000.02
getPeaks-methods0.040.000.03
getPredictorSignificance-methods0.000.020.01
getProbTreshold-methods0.010.000.02
getQuadProb-methods0.280.020.30
getTestedGapDistances-methods0.270.030.29
getTranscripts-methods0.300.010.32
peaksToBed-methods8.350.308.97
plotErrorRate-methods1.520.061.68
plotFeatures-methods4.390.004.39
plotGenomicAnnot-methods1.630.001.63
plotROC-methods1.340.021.36
predictStrand-methods5.610.426.03
predictTssOverlap-methods1.350.001.35
show0.360.000.36
transcriptsToBed-methods1.590.081.67

transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings:

nameusersystemelapsed
addFeature-methods0.260.000.26
annotateTranscripts-methods5.140.125.27
breakTranscriptsByPeaks-methods12.56 0.3612.94
constructCDS0.000.020.02
constructTDS0.250.000.25
detectTranscripts-methods1.190.061.25
estimateBackground-methods0.390.060.46
estimateGapDistance-methods1.070.021.09
exportCoverage-methods0.440.030.47
getConfusionMatrix-methods000
getGenomicAnnot-methods000
getPeaks-methods0.060.000.07
getPredictorSignificance-methods0.000.000.01
getProbTreshold-methods0.020.000.02
getQuadProb-methods0.40.00.4
getTestedGapDistances-methods0.280.100.38
getTranscripts-methods0.280.010.29
peaksToBed-methods7.280.337.61
plotErrorRate-methods0.970.031.00
plotFeatures-methods3.980.003.99
plotGenomicAnnot-methods1.610.001.61
plotROC-methods1.340.021.36
predictStrand-methods4.520.144.66
predictTssOverlap-methods1.260.011.28
show0.240.000.23
transcriptsToBed-methods1.120.031.16