BioC 3.2: CHECK report for goProfiles on perceval

Package: goProfiles

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goProfiles_1.32.0.tar.gz

StartedAt: 2015-10-27 08:28:02 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:30:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 173.3 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.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 goProfiles_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/goProfiles.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.32.0’
* 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 ‘goProfiles’ can be installed ... [9s/9s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘Biobase’ ‘GO.db’
  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
BioCprobes2Entrez: warning in mget(probeslist, env = myenvir,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
expandTerm: no visible binding for global variable ‘GOMFCHILDREN’
expandTerm: no visible binding for global variable ‘GOBPCHILDREN’
expandTerm: no visible binding for global variable ‘GOCCCHILDREN’
getGOLevel: no visible global function definition for ‘toTable’
getGOLevel: no visible binding for global variable ‘GOMFCHILDREN’
getGOLevel: no visible binding for global variable ‘GOBPCHILDREN’
getGOLevel: no visible binding for global variable ‘GOCCCHILDREN’
niceProfile: no visible global function definition for ‘toTable’
niceProfile: no visible binding for global variable ‘GOTERM’
* 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 ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     27.089  0.218  27.308
fisherGOProfiles      8.009  0.118   8.127
mergeProfilesLists    6.638  0.126   6.764
printProfiles         6.470  0.101   6.572
plotProfiles          6.207  0.098   6.306
basicProfile          5.372  0.193   5.566
compSummary           5.135  0.082   5.218
compareGOProfiles     5.067  0.042   5.109
equivalentGOProfiles  4.991  0.034   5.026
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/goProfiles.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CD4ids	0.022	0.003	0.025
GOTermsList	0	0	0
basicProfile	5.372	0.193	5.566
compSummary	5.135	0.082	5.218
compareGOProfiles	5.067	0.042	5.109
compareGeneLists	27.089	0.218	27.308
compareProfilesLists	0.001	0.000	0.001
contractedProfile	2.445	0.020	2.464
conversionFunctions	0.056	0.003	0.059
drosophila	0.003	0.001	0.003
equivSummary	0.000	0.000	0.001
equivalentGOProfiles	4.991	0.034	5.026
expandedLevel	1.193	0.027	1.219
expandedProfile	1.088	0.011	1.099
fisherGOProfiles	8.009	0.118	8.127
fitGOProfile	0.001	0.000	0.001
hugoIds	0.020	0.001	0.020
mergeProfilesLists	6.638	0.126	6.764
ngenes	2.550	0.027	2.576
omimIds	0.007	0.000	0.008
plotProfiles	6.207	0.098	6.306
printProfiles	6.470	0.101	6.572
prostateIds	0.006	0.001	0.006