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BioC 3.6: CHECK report for alpine on tokay1

This page was generated on 2017-08-16 13:36:47 -0400 (Wed, 16 Aug 2017).

Package 36/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.3.0
Michael Love
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/alpine
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alpine
Version: 1.3.0
Command: rm -rf alpine.buildbin-libdir alpine.Rcheck && mkdir alpine.buildbin-libdir alpine.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.3.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.3.0.tar.gz
StartedAt: 2017-08-15 21:41:17 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:49:18 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 481.4 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.3.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/alpine.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 'alpine/DESCRIPTION' ... OK
* this is package 'alpine' version '1.3.0'
* 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     14.39   0.95   15.99
estimateAbundance 11.67   1.03   13.50
predictCoverage    6.14   0.36    6.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fitBiasModels     13.70   0.89   14.78
estimateAbundance 11.57   0.64   12.97
predictCoverage    5.72   0.31    6.10
* 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_1.3.0.zip
* DONE (alpine)

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

nameusersystemelapsed
buildFragtypes3.880.194.84
estimateAbundance11.67 1.0313.50
extractAlpine000
fitBiasModels14.39 0.9515.99
getFragmentWidths1.780.051.99
getReadLength1.250.061.37
mergeGenes0.190.000.19
normalizeDESeq0.010.000.01
plotFragLen0.020.000.02
plotGC0.010.000.02
plotGRL0.110.020.12
plotOrder00.030.000.03
plotRelPos0.010.000.02
predictCoverage6.140.366.62
splitGenesAcrossChroms0.280.000.28
splitLongGenes0.320.000.43

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

nameusersystemelapsed
buildFragtypes4.230.194.42
estimateAbundance11.57 0.6412.97
extractAlpine0.020.000.02
fitBiasModels13.70 0.8914.78
getFragmentWidths1.770.081.98
getReadLength1.200.021.25
mergeGenes0.200.000.21
normalizeDESeq000
plotFragLen0.020.000.01
plotGC0.010.010.03
plotGRL0.140.000.14
plotOrder00.050.000.05
plotRelPos0.000.020.02
predictCoverage5.720.316.10
splitGenesAcrossChroms0.370.000.38
splitLongGenes0.390.000.39