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BioC 3.0: CHECK report for PGSEA on moscato1

This page was generated on 2015-04-10 09:44:41 -0700 (Fri, 10 Apr 2015).

Package 655/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGSEA 1.40.0
Karl Dykema
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PGSEA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: PGSEA
Version: 1.40.0
Command: rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.40.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.40.0.tar.gz
StartedAt: 2015-04-10 04:06:31 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:11:23 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 291.6 seconds
RetCode: 0
Status:  OK  
CheckDir: PGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.40.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/PGSEA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.40.0'
* 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 'PGSEA' 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'GO.db' 'KEGG.db'
  Please remove these calls from your code.
'library' or 'require' call to 'org.Hs.eg.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GO.db' 'KEGG.db' 'annaffy' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
  partial argument match of 'env' to 'envir'
go2smc: no visible binding for global variable 'GOTERM'
go2smc: no visible binding for global variable 'org.Hs.egGO2ALLEGS'
kegg2smc: no visible binding for global variable 'KEGGPATHNAME2ID'
kegg2smc: no visible binding for global variable 'KEGGPATHID2EXTID'
* 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' ... [59s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
go2smc 47.18   0.68   47.87
** running examples for arch 'x64' ... [69s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
go2smc 56.28   0.79   57.08
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/PGSEA.Rcheck/00check.log'
for details.

PGSEA.Rcheck/00install.out:


install for i386

* installing *source* package 'PGSEA' ...
** 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 'PGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGSEA' as PGSEA_1.40.0.zip
* DONE (PGSEA)

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

nameusersystemelapsed
GOLUBmcs0.090.000.09
PGSEA0.780.030.81
VAIgsc1.120.071.19
VAImcs0.240.000.23
aggregateExprs0.390.001.39
convertSmc000
editSmc0.030.000.03
go2smc47.18 0.6847.87
kegg2smc0.750.000.75
nbEset0.140.030.18
readGmt0.060.000.06
readSmc0.050.020.06
scanSmc0.030.000.03
smcPlot0.760.000.77
writeGmt0.060.000.06
writeSmc0.070.000.06

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

nameusersystemelapsed
GOLUBmcs0.090.000.09
PGSEA1.000.011.02
VAIgsc1.210.051.26
VAImcs0.270.000.27
aggregateExprs0.390.050.43
convertSmc0.020.000.02
editSmc0.030.000.03
go2smc56.28 0.7957.08
kegg2smc0.520.020.53
nbEset0.120.000.13
readGmt0.050.000.04
readSmc0.040.000.05
scanSmc0.020.000.02
smcPlot0.470.000.46
writeGmt0.080.000.08
writeSmc0.060.000.06