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BioC 3.4: CHECK report for GOstats on zin1

This page was generated on 2016-09-21 03:35:47 -0700 (Wed, 21 Sep 2016).

Package 531/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.39.1
Bioconductor Package Maintainer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOstats
Last Changed Rev: 118908 / Revision: 121152
Last Changed Date: 2016-06-23 08:38:14 -0700 (Thu, 23 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOstats
Version: 2.39.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOstats_2.39.1.tar.gz
StartedAt: 2016-09-20 07:29:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:32:18 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 141.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GOstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOstats_2.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GOstats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.39.1’
* 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 ... 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’
Undefined global functions or variables:
  as.matrix.csr 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.4-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
Ndists0.0480.0000.048
compCorrGraph0.1440.0000.142
compGdist0.1000.0000.098
idx2dimnames0.0240.0000.023
makeGOGraph1.3120.0161.338
notConn0.020.000.02
oneGOGraph0.3920.0040.404
probeSetSummary2.2560.0362.295
shortestPath3.2280.0323.261
simLL0.6200.0120.631
triadCensus000