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BioC 2.14: CHECK report for PGSEA on morelia

This page was generated on 2014-10-08 09:03:07 -0700 (Wed, 08 Oct 2014).

Package 578/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGSEA 1.38.0
Karl Dykema
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PGSEA
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: PGSEA
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.38.0.tar.gz
StartedAt: 2014-10-08 00:38:21 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:41:04 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 163.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PGSEA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGSEA’ version ‘1.38.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PGSEA’ can be installed ... [10s/10s] 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
* 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.
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
go2smc 49.449  1.252  50.974
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/PGSEA.Rcheck/00check.log’
for details.

PGSEA.Rcheck/00install.out:

* 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
* DONE (PGSEA)

PGSEA.Rcheck/PGSEA-Ex.timings:

nameusersystemelapsed
GOLUBmcs0.1020.0050.107
PGSEA0.8360.0250.869
VAIgsc1.3210.0261.365
VAImcs0.2580.0130.284
aggregateExprs0.4240.0180.450
convertSmc0.0000.0000.001
editSmc0.0340.0020.036
go2smc49.449 1.25250.974
kegg2smc0.5550.0140.569
nbEset0.1100.0050.117
readGmt0.0440.0030.047
readSmc0.0520.0030.054
scanSmc0.0220.0010.023
smcPlot0.5450.0260.576
writeGmt0.0470.0020.050
writeSmc0.0860.0190.105