BioC 3.4: CHECK report for goProfiles on morelia

Package: goProfiles

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goProfiles_1.36.0.tar.gz

StartedAt: 2017-04-15 03:06:07 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:09:15 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 187.8 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_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/goProfiles.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.36.0’
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chiDisjoint: no visible global function definition for ‘var’
chiIntersect: no visible global function definition for ‘var’
chiPnP0Correct: no visible global function definition for ‘var’
chiRestrict: no visible global function definition for ‘var’
equivalentGOProfiles.GOProfileHtest: no visible global function
  definition for ‘qnorm’
equivalentGOProfiles.GOProfileHtest: no visible global function
  definition for ‘pnorm’
estimProbPrecision: no visible global function definition for ‘qnorm’
generate.multinomial: no visible global function definition for
  ‘rbinom’
internal.compareGOProf: no visible global function definition for
  ‘pchisq’
internal.compareGOProf: no visible global function definition for
  ‘qnorm’
internal.enrichProfile: no visible global function definition for
  ‘fisher.test’
internal.enrichProfile: no visible global function definition for
  ‘p.adjust’
internal.equivalentGOProf: no visible global function definition for
  ‘qnorm’
internal.equivalentGOProf: no visible global function definition for
  ‘pnorm’
internal.fitGOProf: no visible global function definition for ‘pchisq’
internal.fitGOProf: no visible global function definition for ‘qnorm’
meanICLength: no visible global function definition for ‘qnorm’
meanICLength: no visible global function definition for ‘sd’
normIntLength: no visible global function definition for ‘qnorm’
plcombChisq: no visible global function definition for ‘rchisq’
plot1Prof: no visible global function definition for ‘rainbow’
plot1Prof: no visible global function definition for ‘par’
plot2Prof: no visible global function definition for ‘par’
plotOne: no visible global function definition for ‘barplot’
plotOne: no visible global function definition for ‘text’
plotOne: no visible global function definition for ‘axis’
plotOne: no visible global function definition for ‘title’
plotProfiles: no visible global function definition for ‘rainbow’
plotTwo: no visible global function definition for ‘par’
plotTwo: no visible global function definition for ‘barplot’
plotTwo: no visible global function definition for ‘text’
plotTwo: no visible global function definition for ‘axis’
plotTwo: no visible global function definition for ‘title’
qlcombChisq: no visible global function definition for ‘quantile’
qlcombChisq: no visible global function definition for ‘rchisq’
rlcombChisq: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  axis barplot fisher.test p.adjust par pchisq pnorm qnorm quantile
  rainbow rbinom rchisq sd text title var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "barplot", "par", "text", "title")
  importFrom("stats", "fisher.test", "p.adjust", "pchisq", "pnorm",
             "qnorm", "quantile", "rbinom", "rchisq", "sd", "var")
to your NAMESPACE file.
* 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
compareGeneLists     28.319  0.189  28.636
equivalentGOProfiles 20.744  0.253  27.303
fisherGOProfiles      7.681  0.132   7.817
plotProfiles          7.585  0.096   7.693
printProfiles         7.538  0.079   7.623
mergeProfilesLists    6.260  0.090   6.353
compareGOProfiles     5.291  0.088   5.386
basicProfile          4.850  0.134   5.100
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	0.019	0.005	0.025
GOTermsList	0.001	0.000	0.001
basicProfile	4.850	0.134	5.100
compSummary	0.001	0.000	0.001
compareGOProfiles	5.291	0.088	5.386
compareGeneLists	28.319	0.189	28.636
compareProfilesLists	0.001	0.000	0.001
contractedProfile	2.419	0.014	2.436
conversionFunctions	0.038	0.003	0.040
drosophila	0.003	0.001	0.003
equivSummary	0.000	0.000	0.001
equivalentGOProfiles	20.744	0.253	27.303
expandedLevel	1.532	0.021	1.610
expandedProfile	1.195	0.016	1.211
fisherGOProfiles	7.681	0.132	7.817
fitGOProfile	0.001	0.000	0.001
hugoIds	0.020	0.002	0.022
mergeProfilesLists	6.260	0.090	6.353
ngenes	2.128	0.020	2.148
omimIds	0.008	0.001	0.008
plotProfiles	7.585	0.096	7.693
printProfiles	7.538	0.079	7.623
prostateIds	0.006	0.001	0.007