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BioC 3.1: CHECK report for goProfiles on moscato2

This page was generated on 2015-10-09 09:28:16 -0700 (Fri, 09 Oct 2015).

Package 422/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.30.0
Alex Sanchez
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/goProfiles
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goProfiles
Version: 1.30.0
Command: rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.30.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.30.0.tar.gz
StartedAt: 2015-10-09 02:26:21 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:31:30 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 309.0 seconds
RetCode: 0
Status:  OK  
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.30.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/goProfiles.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.30.0'
* 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' ... [112s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
compareGeneLists     29.94   0.18   31.82
fisherGOProfiles      6.37   0.06    6.43
compSummary           5.95   0.06    8.94
mergeProfilesLists    5.94   0.03    5.98
printProfiles         5.61   0.05    5.66
basicProfile          5.53   0.11   27.67
equivalentGOProfiles  5.16   0.08    5.24
plotProfiles          5.15   0.06    5.21
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
compareGeneLists   24.01   0.23   24.26
fisherGOProfiles    7.92   0.08    8.01
plotProfiles        7.10   0.04    7.13
printProfiles       6.01   0.10    6.11
mergeProfilesLists  5.68   0.05    5.72
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/goProfiles.Rcheck/00check.log'
for details.


goProfiles.Rcheck/00install.out:


install for i386

* installing *source* package 'goProfiles' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'goProfiles' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'goProfiles' as goProfiles_1.30.0.zip
* DONE (goProfiles)

goProfiles.Rcheck/examples_i386/goProfiles-Ex.timings:

nameusersystemelapsed
CD4ids0.030.000.03
GOTermsList000
basicProfile 5.53 0.1127.67
compSummary5.950.068.94
compareGOProfiles4.290.004.29
compareGeneLists29.94 0.1831.82
compareProfilesLists000
contractedProfile2.320.042.37
conversionFunctions0.040.000.03
drosophila000
equivSummary000
equivalentGOProfiles5.160.085.24
expandedLevel1.010.011.03
expandedProfile0.950.020.97
fisherGOProfiles6.370.066.43
fitGOProfile000
hugoIds0.020.000.01
mergeProfilesLists5.940.035.98
ngenes2.010.052.05
omimIds0.020.000.02
plotProfiles5.150.065.21
printProfiles5.610.055.66
prostateIds0.020.000.02

goProfiles.Rcheck/examples_x64/goProfiles-Ex.timings:

nameusersystemelapsed
CD4ids0.020.000.02
GOTermsList000
basicProfile4.640.144.78
compSummary4.480.054.53
compareGOProfiles4.760.054.80
compareGeneLists24.01 0.2324.26
compareProfilesLists000
contractedProfile2.260.002.26
conversionFunctions0.030.000.03
drosophila0.000.020.02
equivSummary000
equivalentGOProfiles4.180.014.20
expandedLevel1.050.001.04
expandedProfile0.920.000.92
fisherGOProfiles7.920.088.01
fitGOProfile000
hugoIds0.030.000.03
mergeProfilesLists5.680.055.72
ngenes2.110.012.12
omimIds0.010.000.02
plotProfiles7.100.047.13
printProfiles6.010.106.11
prostateIds000