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BioC 3.2: CHECK report for CompGO on moscato1

This page was generated on 2016-04-23 10:20:09 -0700 (Sat, 23 Apr 2016).

Package 216/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.6.0
Ashley J. Waardenberg
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CompGO
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 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 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] 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: CompGO
Version: 1.6.0
Command: rm -rf CompGO.buildbin-libdir CompGO.Rcheck && mkdir CompGO.buildbin-libdir CompGO.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CompGO.buildbin-libdir CompGO_1.6.0.tar.gz >CompGO.Rcheck\00install.out 2>&1 && cp CompGO.Rcheck\00install.out CompGO-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CompGO.buildbin-libdir --install="check:CompGO-install.out" --force-multiarch --no-vignettes --timings CompGO_1.6.0.tar.gz
StartedAt: 2016-04-23 01:03:55 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:13:35 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 580.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CompGO.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CompGO.buildbin-libdir CompGO.Rcheck && mkdir CompGO.buildbin-libdir CompGO.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CompGO.buildbin-libdir CompGO_1.6.0.tar.gz >CompGO.Rcheck\00install.out 2>&1 && cp CompGO.Rcheck\00install.out CompGO-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CompGO.buildbin-libdir --install="check:CompGO-install.out" --force-multiarch --no-vignettes --timings CompGO_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CompGO.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CompGO/DESCRIPTION' ... OK
* this is package 'CompGO' version '1.6.0'
* 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 'CompGO' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/CompGO.Rcheck/00install.out' for details.
* 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 ... NOTE
doZtrans.single: no visible binding for global variable 'Term'
doZtrans.single: no visible binding for global variable 'Z'
plotInteractive: no visible binding for global variable 'Var1'
plotInteractive: no visible binding for global variable 'Var2'
plotInteractive: no visible binding for global variable 'value'
plotTwoGODags: no visible global function definition for 'goDag'
plotTwoGODags: no visible global function definition for 'nodes'
plotTwoGODags: no visible global function definition for
  'nodeRenderInfo<-'
plotZRankedDAG: no visible global function definition for 'goDag'
plotZRankedDAG: no visible global function definition for 'nodes'
plotZRankedDAG: no visible global function definition for
  'nodeRenderInfo<-'
slidingJaccard: no visible binding for global variable 'useRawPvals'
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
plotTwoGODags 12.12   0.08   12.65
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plotTwoGODags 9.06    0.1    9.19
* 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 WARNING, 1 NOTE
See
  'D:/biocbld/bbs-3.2-bioc/meat/CompGO.Rcheck/00check.log'
for details.


CompGO.Rcheck/00install.out:


install for i386

* installing *source* package 'CompGO' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5

install for x64

* installing *source* package 'CompGO' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'CompGO' as CompGO_1.6.0.zip
* DONE (CompGO)

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

nameusersystemelapsed
annotateBedFromDb1.010.061.07
compareZscores0.090.020.25
doZtrans.single0.040.000.03
getFnAnot_genome000
plotPairwise0.650.030.70
plotTwoGODags12.12 0.0812.65
plotZRankedDAG000
plotZScores1.870.011.89
slidingJaccard0.100.000.09
viewKegg000
zTransformDirectory000

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

nameusersystemelapsed
annotateBedFromDb0.670.030.70
compareZscores0.040.020.06
doZtrans.single0.000.020.01
getFnAnot_genome000
plotPairwise0.520.000.58
plotTwoGODags9.060.109.19
plotZRankedDAG0.020.000.01
plotZScores1.900.001.91
slidingJaccard0.060.020.08
viewKegg000
zTransformDirectory0.020.000.01