goProfiles 1.35.0
Alex Sanchez
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/goProfiles | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.35.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/goProfiles.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goProfiles/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'goProfiles' version '1.35.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
plot1Prof: no visible global function definition for 'win.graph'
plot2Prof: no visible global function definition for 'par'
plot2Prof: no visible global function definition for 'win.graph'
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 win.graph
Consider adding
importFrom("grDevices", "rainbow", "win.graph")
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareGeneLists 21.93 0.10 23.12
equivalentGOProfiles 16.52 0.12 18.23
fisherGOProfiles 6.47 0.05 6.52
plotProfiles 5.53 0.04 5.57
mergeProfilesLists 5.46 0.02 5.48
printProfiles 5.30 0.08 5.38
basicProfile 4.15 0.11 5.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareGeneLists 23.62 0.17 23.80
equivalentGOProfiles 15.71 0.08 15.79
fisherGOProfiles 6.74 0.02 6.76
printProfiles 5.62 0.06 5.68
mergeProfilesLists 5.51 0.04 5.55
plotProfiles 5.21 0.00 5.21
* 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
'D:/biocbld/bbs-3.4-bioc/meat/goProfiles.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'goProfiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goProfiles' as goProfiles_1.35.0.zip
* DONE (goProfiles)