BioC 3.3: CHECK report for GOstats on oaxaca

Package: GOstats

Version: 2.38.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOstats_2.38.1.tar.gz

StartedAt: 2016-10-13 02:23:26 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:27:25 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 238.9 seconds

RetCode: 0

Status:  OK

CheckDir: GOstats.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 GOstats_2.38.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GOstats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOstats/DESCRIPTION’ ... OK
* this is package ‘GOstats’ version ‘2.38.1’
* 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
Examples with CPU or elapsed time > 5s
                 user system elapsed
probeSetSummary 2.758   0.15    5.78
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/GOstats.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Ndists	0.057	0.016	0.073
compCorrGraph	0.218	0.005	1.035
compGdist	0.117	0.003	0.130
idx2dimnames	0.028	0.008	0.035
makeGOGraph	1.743	0.066	3.163
notConn	0.031	0.008	0.039
oneGOGraph	0.515	0.015	1.620
probeSetSummary	2.758	0.150	5.780
shortestPath	3.905	0.069	4.091
simLL	0.925	0.033	1.151
triadCensus	0.001	0.000	0.001