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BioC 3.2: CHECK report for GOstats on zin1

This page was generated on 2015-08-24 10:46:56 -0700 (Mon, 24 Aug 2015).

Package 441/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.35.1
Bioconductor Package Maintainer
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOstats
Last Changed Rev: 104626 / Revision: 107696
Last Changed Date: 2015-06-05 17:40:59 -0700 (Fri, 05 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  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: GOstats
Version: 2.35.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GOstats_2.35.1.tar.gz
StartedAt: 2015-08-24 00:29:34 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:32:12 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 157.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GOstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GOstats_2.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GOstats.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOstats/DESCRIPTION’ ... OK
* this is package ‘GOstats’ version ‘2.35.1’
* 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 ‘GOstats’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘Category’ ‘graph’ ‘GO.db’ ‘annotate’
A package should be listed in only one of these fields.
* 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 in package code:
  ‘Rgraphviz’ ‘SparseM’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘Category:::XXX_getSummaryGeneric_XXX’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compCorrGraph: no visible global function definition for
  ‘as.matrix.csr’
plotGOTermGraph: no visible global function definition for
  ‘makeNodeAttrs’
* 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 ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [41s/41s]
 [41s/41s] OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GOstats.Rcheck/00check.log’
for details.


GOstats.Rcheck/00install.out:

* installing *source* package ‘GOstats’ ...
** 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 (GOstats)

GOstats.Rcheck/GOstats-Ex.timings:

nameusersystemelapsed
Ndists0.0430.0000.042
compCorrGraph0.1840.0000.183
compGdist0.1230.0000.123
idx2dimnames0.0230.0000.023
makeGOGraph1.5270.0241.550
notConn0.0200.0000.021
oneGOGraph0.4020.0040.413
probeSetSummary2.2370.0642.300
shortestPath2.5060.0042.508
simLL0.6860.0120.697
triadCensus000