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BioC 3.5: CHECK report for alpine on tokay2

This page was generated on 2017-10-18 14:26:23 -0400 (Wed, 18 Oct 2017).

Package 36/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.2.0
Michael Love
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_5
Last Commit: 896872e
Last Changed Date: 2017-04-24 15:45:44 -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: alpine
Version: 1.2.0
Command: rm -rf alpine.buildbin-libdir alpine.Rcheck && mkdir alpine.buildbin-libdir alpine.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.2.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.2.0.tar.gz
StartedAt: 2017-10-17 21:58:44 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:07:06 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 502.1 seconds
RetCode: 0
Status:  OK  
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf alpine.buildbin-libdir alpine.Rcheck && mkdir alpine.buildbin-libdir alpine.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.2.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/alpine.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 'alpine/DESCRIPTION' ... OK
* this is package 'alpine' version '1.2.0'
* 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 'alpine' 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
fitBiasModels     14.72   0.88   18.54
estimateAbundance 11.27   0.94   17.73
predictCoverage    6.03   0.38    6.58
buildFragtypes     3.64   0.27    7.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fitBiasModels     15.25   1.00   16.33
estimateAbundance 12.16   0.80   13.15
predictCoverage    5.61   0.26    5.91
* 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

alpine.Rcheck/00install.out:


install for i386

* installing *source* package 'alpine' ...
** 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 'alpine' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alpine' as alpine_1.2.0.zip
* DONE (alpine)

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

nameusersystemelapsed
buildFragtypes3.640.277.36
estimateAbundance11.27 0.9417.73
extractAlpine0.020.010.03
fitBiasModels14.72 0.8818.54
getFragmentWidths2.120.182.38
getReadLength1.160.111.30
mergeGenes0.190.000.18
normalizeDESeq000
plotFragLen0.020.000.01
plotGC0.030.000.04
plotGRL0.110.000.11
plotOrder00.040.000.04
plotRelPos0.020.000.02
predictCoverage6.030.386.58
splitGenesAcrossChroms0.330.000.32
splitLongGenes0.410.000.43

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

nameusersystemelapsed
buildFragtypes3.610.113.72
estimateAbundance12.16 0.8013.15
extractAlpine0.030.000.03
fitBiasModels15.25 1.0016.33
getFragmentWidths2.220.092.39
getReadLength1.530.071.63
mergeGenes0.210.030.23
normalizeDESeq000
plotFragLen0.010.000.02
plotGC0.030.000.03
plotGRL0.160.000.16
plotOrder00.050.000.05
plotRelPos0.020.000.01
predictCoverage5.610.265.91
splitGenesAcrossChroms0.360.000.36
splitLongGenes0.340.000.34