BioC 3.5: CHECK report for goProfiles on malbec2

Package: goProfiles

Version: 1.38.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.38.0.tar.gz

StartedAt: 2017-10-17 23:41:42 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:44:14 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 152.0 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/goProfiles.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.38.0’
* 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 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     19.520  0.024  19.638
equivalentGOProfiles 16.968  0.088  21.935
fisherGOProfiles      6.428  0.020   6.453
printProfiles         6.012  0.008   6.030
plotProfiles          5.732  0.008   5.743
basicProfile          5.144  0.088   6.035
mergeProfilesLists    5.188  0.008   5.201
* 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
  ‘/home/biocbuild/bbs-3.5-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	0.012	0.000	0.013
GOTermsList	0.000	0.000	0.001
basicProfile	5.144	0.088	6.035
compSummary	0	0	0
compareGOProfiles	4.112	0.028	4.403
compareGeneLists	19.520	0.024	19.638
compareProfilesLists	0.000	0.000	0.001
contractedProfile	1.644	0.008	1.654
conversionFunctions	0.024	0.000	0.027
drosophila	0.000	0.000	0.002
equivSummary	0.000	0.000	0.001
equivalentGOProfiles	16.968	0.088	21.935
expandedLevel	0.992	0.000	0.989
expandedProfile	0.800	0.000	0.801
fisherGOProfiles	6.428	0.020	6.453
fitGOProfile	0.004	0.000	0.000
hugoIds	0.008	0.004	0.015
mergeProfilesLists	5.188	0.008	5.201
ngenes	1.820	0.000	1.822
omimIds	0.004	0.000	0.006
plotProfiles	5.732	0.008	5.743
printProfiles	6.012	0.008	6.030
prostateIds	0.008	0.000	0.008