BioC 3.2: CHECK report for goProfiles on windows1.bioconductor.org

Package: goProfiles

Version: 1.32.0

Command: rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.32.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.32.0.tar.gz

StartedAt: 2015-10-27 02:20:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:23:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 197.6 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.32.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.32.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/goProfiles.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.32.0'
* 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 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [57s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compareGeneLists 17.78   0.15   17.94
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compareGeneLists 18.97   0.28   19.30
fisherGOProfiles  5.85   0.08    5.94
plotProfiles      5.05   0.05    5.09
* 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
  'C:/biocbld/bbs-3.2-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_1.32.0.zip
* DONE (goProfiles)

name	user	system	elapsed
CD4ids	0.02	0.00	0.02
GOTermsList	0	0	0
basicProfile	3.38	0.09	3.47
compSummary	3.55	0.07	3.61
compareGOProfiles	3.52	0.07	3.58
compareGeneLists	17.78	0.15	17.94
compareProfilesLists	0	0	0
contractedProfile	1.45	0.02	1.47
conversionFunctions	0.03	0.00	0.03
drosophila	0	0	0
equivSummary	0	0	0
equivalentGOProfiles	3.03	0.09	3.12
expandedLevel	0.96	0.03	0.99
expandedProfile	0.68	0.02	0.70
fisherGOProfiles	4.87	0.08	4.95
fitGOProfile	0	0	0
hugoIds	0.01	0.00	0.02
mergeProfilesLists	4.72	0.04	4.80
ngenes	1.66	0.03	1.68
omimIds	0	0	0
plotProfiles	4.26	0.08	4.34
printProfiles	4.24	0.06	4.30
prostateIds	0	0	0

name	user	system	elapsed
CD4ids	0.01	0.00	0.02
GOTermsList	0	0	0
basicProfile	3.80	0.07	3.86
compSummary	3.98	0.04	4.06
compareGOProfiles	3.50	0.02	3.52
compareGeneLists	18.97	0.28	19.30
compareProfilesLists	0	0	0
contractedProfile	1.62	0.02	1.64
conversionFunctions	0.02	0.01	0.03
drosophila	0	0	0
equivSummary	0	0	0
equivalentGOProfiles	3.51	0.05	3.57
expandedLevel	0.89	0.00	0.89
expandedProfile	0.74	0.03	0.76
fisherGOProfiles	5.85	0.08	5.94
fitGOProfile	0	0	0
hugoIds	0.01	0.00	0.01
mergeProfilesLists	4.77	0.01	4.78
ngenes	1.76	0.03	1.80
omimIds	0	0	0
plotProfiles	5.05	0.05	5.09
printProfiles	4.90	0.04	4.96
prostateIds	0	0	0