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BioC 3.5: CHECK report for InPAS on tokay2

This page was generated on 2017-08-16 13:24:20 -0400 (Wed, 16 Aug 2017).

Package 671/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 1.8.0
Jianhong Ou
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/InPAS
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: InPAS
Version: 1.8.0
Command: rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.8.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.8.0.tar.gz
StartedAt: 2017-08-16 00:38:13 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:47:13 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 540.1 seconds
RetCode: 0
Status:  OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf InPAS.buildbin-libdir InPAS.Rcheck && mkdir InPAS.buildbin-libdir InPAS.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InPAS.buildbin-libdir InPAS_1.8.0.tar.gz >InPAS.Rcheck\00install.out 2>&1 && cp InPAS.Rcheck\00install.out InPAS-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=InPAS.buildbin-libdir --install="check:InPAS-install.out" --force-multiarch --no-vignettes --timings InPAS_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/InPAS.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 'InPAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'InPAS' version '1.8.0'
* 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 'InPAS' 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
filterRes   5.73   0.21    5.94
testUsage   5.83   0.02    5.84
getUTR3eSet 5.28   0.01    5.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
filterRes   8.61   0.07    8.69
testUsage   7.22   0.03    7.25
getUTR3eSet 6.96   0.00    6.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

InPAS.Rcheck/00install.out:


install for i386

* installing *source* package 'InPAS' ...
** 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 'InPAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InPAS' as InPAS_1.8.0.zip
* DONE (InPAS)

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

nameusersystemelapsed
CPsites000
coverageFromBedGraph000
coverageRate000
filterRes5.730.215.94
fisher.exact.test0.050.000.05
getUTR3eSet5.280.015.29
inPAS000
limmaAnalyze0.050.020.07
prepare4GSEA0.140.010.15
singleGroupAnalyze0.430.000.44
singleSampleAnalyze000
testUsage5.830.025.84
usage4plot2.190.082.50
utr3.hg190.730.010.75
utr3.mm100.590.040.62
utr3Annotation000
utr3UsageEstimation000

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

nameusersystemelapsed
CPsites000
coverageFromBedGraph000
coverageRate000
filterRes8.610.078.69
fisher.exact.test0.060.020.08
getUTR3eSet6.960.006.95
inPAS000
limmaAnalyze0.030.020.05
prepare4GSEA0.120.010.14
singleGroupAnalyze0.80.00.8
singleSampleAnalyze000
testUsage7.220.037.25
usage4plot1.920.021.94
utr3.hg190.610.010.62
utr3.mm100.730.000.73
utr3Annotation000
utr3UsageEstimation0.020.000.02