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BioC 3.2: CHECK report for goProfiles on linux1.bioconductor.org

This page was generated on 2015-10-27 17:24:15 -0400 (Tue, 27 Oct 2015).

Package 449/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.32.0
Alex Sanchez
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/goProfiles
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goProfiles
Version: 1.32.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.32.0.tar.gz
StartedAt: 2015-10-27 04:12:27 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:14:29 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 122.7 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/goProfiles.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.32.0’
* 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 ... [7s/7s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
compareGeneLists 18.735  0.027  18.769
fisherGOProfiles  5.318  0.024   5.342
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/goProfiles.Rcheck/00check.log’
for details.


goProfiles.Rcheck/00install.out:

* 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)

goProfiles.Rcheck/goProfiles-Ex.timings:

nameusersystemelapsed
CD4ids0.0120.0000.012
GOTermsList0.0010.0000.001
basicProfile4.8140.0724.887
compSummary4.6390.0164.656
compareGOProfiles3.9210.0083.929
compareGeneLists18.735 0.02718.769
compareProfilesLists0.0010.0000.000
contractedProfile1.6410.0041.648
conversionFunctions0.0250.0000.025
drosophila0.0020.0000.002
equivSummary0.0010.0000.000
equivalentGOProfiles3.0760.0003.080
expandedLevel0.7870.0000.788
expandedProfile0.6990.0000.698
fisherGOProfiles5.3180.0245.342
fitGOProfile0.0000.0000.001
hugoIds0.0140.0000.013
mergeProfilesLists4.7290.0204.749
ngenes1.5930.0041.597
omimIds0.0050.0000.005
plotProfiles4.4780.0124.490
printProfiles4.5840.0044.588
prostateIds0.0040.0000.004