BioC 3.0: CHECK report for PGSEA on oaxaca

Package: PGSEA

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.40.0.tar.gz

StartedAt: 2015-04-10 02:06:24 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:09:39 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 195.2 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PGSEA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PGSEA’ can be installed ... [13s/13s] 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.
'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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/68s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
go2smc 55.071  1.462  57.275
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/PGSEA.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GOLUBmcs	0.094	0.008	0.110
PGSEA	0.842	0.027	0.875
VAIgsc	1.378	0.025	1.414
VAImcs	0.305	0.017	0.340
aggregateExprs	0.475	0.023	0.535
convertSmc	0.001	0.000	0.001
editSmc	0.034	0.002	0.036
go2smc	55.071	1.462	57.275
kegg2smc	0.549	0.016	0.566
nbEset	0.116	0.007	0.123
readGmt	0.054	0.003	0.057
readSmc	0.047	0.002	0.050
scanSmc	0.021	0.002	0.023
smcPlot	0.588	0.046	0.634
writeGmt	0.049	0.006	0.055
writeSmc	0.048	0.002	0.050