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BioC 3.2: CHECK report for plgem on moscato1

This page was generated on 2015-08-20 13:18:05 -0700 (Thu, 20 Aug 2015).

Package 757/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plgem 1.41.0
Norman Pavelka
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/plgem
Last Changed Rev: 102594 / Revision: 107602
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plgem
Version: 1.41.0
Command: rm -rf plgem.buildbin-libdir plgem.Rcheck && mkdir plgem.buildbin-libdir plgem.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plgem.buildbin-libdir plgem_1.41.0.tar.gz >plgem.Rcheck\00install.out 2>&1 && cp plgem.Rcheck\00install.out plgem-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=plgem.buildbin-libdir --install="check:plgem-install.out" --force-multiarch --no-vignettes --timings plgem_1.41.0.tar.gz
StartedAt: 2015-08-20 08:42:36 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 08:44:40 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 123.8 seconds
RetCode: 0
Status:  OK  
CheckDir: plgem.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf plgem.buildbin-libdir plgem.Rcheck && mkdir plgem.buildbin-libdir plgem.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plgem.buildbin-libdir plgem_1.41.0.tar.gz >plgem.Rcheck\00install.out 2>&1 && cp plgem.Rcheck\00install.out plgem-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=plgem.buildbin-libdir --install="check:plgem-install.out" --force-multiarch --no-vignettes --timings plgem_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/plgem.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plgem/DESCRIPTION' ... OK
* this is package 'plgem' version '1.41.0'
* 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 'plgem' 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' ... [35s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plgem.pValue       8.55   0.14    8.69
plgem.deg          8.13   0.32    8.44
run.plgem          7.51   0.11    7.63
plgem.resampledStn 5.23   0.11    5.34
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plgem.deg          10.25   0.19   10.43
plgem.pValue        9.09   0.19    9.55
run.plgem           8.30   0.16    8.46
plgem.resampledStn  5.56   0.06    5.61
* 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

plgem.Rcheck/00install.out:


install for i386

* installing *source* package 'plgem' ...
** 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 'plgem' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plgem' as plgem_1.41.0.zip
* DONE (plgem)

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

nameusersystemelapsed
LPSeset0.150.030.19
plgem.deg8.130.328.44
plgem.fit1.970.042.07
plgem.obsStn0.960.000.97
plgem.pValue8.550.148.69
plgem.resampledStn5.230.115.34
plgem.write.summary000
run.plgem7.510.117.63
setGpar000

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

nameusersystemelapsed
LPSeset0.150.000.16
plgem.deg10.25 0.1910.43
plgem.fit1.920.031.95
plgem.obsStn1.250.001.25
plgem.pValue9.090.199.55
plgem.resampledStn5.560.065.61
plgem.write.summary000
run.plgem8.300.168.46
setGpar000