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BioC 3.2: CHECK report for graphite on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:39 -0400 (Tue, 27 Oct 2015).

Package 464/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.16.0
Gabriele Sales
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/graphite
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graphite
Version: 1.16.0
Command: rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.16.0.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.16.0.tar.gz
StartedAt: 2015-10-27 02:29:37 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:36:05 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 388.1 seconds
RetCode: 0
Status:  OK  
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.16.0.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/graphite.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.16.0'
* 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 'graphite' 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
* 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 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 ... NOTE
  Note: found 32 marked UTF-8 strings
* 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' ... [130s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
runClipperMulti 96.06   0.33   96.41
runClipper      16.09   0.31   16.41
** running examples for arch 'x64' ... [132s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
runClipperMulti 93.64   0.11   93.80
runClipper      18.08   0.25   18.36
* 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: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/graphite.Rcheck/00check.log'
for details.


graphite.Rcheck/00install.out:


install for i386

* installing *source* package 'graphite' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'graphite'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'graphite' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graphite' as graphite_1.16.0.zip
* DONE (graphite)

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

nameusersystemelapsed
as.list.DeprecatedPathwayList1.200.161.36
as.list.PathwayList0.080.010.09
convertIdentifiers0.50.00.5
cytoscapePlot000
pathwayDatabases000
pathwayGraph0.050.000.05
pathways000
runClipper16.09 0.3116.41
runClipperMulti96.06 0.3396.41
runDEGraph2.080.353.88
runDEGraphMulti0.780.010.79
runSPIA4.250.084.33
runTopologyGSA1.380.001.49
runTopologyGSAMulti0.860.001.22

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

nameusersystemelapsed
as.list.DeprecatedPathwayList1.360.181.55
as.list.PathwayList0.090.030.12
convertIdentifiers0.720.052.58
cytoscapePlot000
pathwayDatabases0.010.000.02
pathwayGraph0.080.000.07
pathways000
runClipper18.08 0.2518.36
runClipperMulti93.64 0.1193.80
runDEGraph1.490.231.72
runDEGraphMulti0.460.020.48
runSPIA4.750.034.78
runTopologyGSA1.110.061.59
runTopologyGSAMulti1.060.031.45