BioC 3.1: CHECK report for goProfiles on morelia
This page was generated on 2015-10-09 09:38:48 -0700 (Fri, 09 Oct 2015).
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 UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Package: goProfiles |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goProfiles_1.30.0.tar.gz |
StartedAt: 2015-10-09 02:33:07 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 02:35:35 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 148.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: goProfiles.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goProfiles_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/goProfiles.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘goProfiles’ can be installed ... [7s/8s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [70s/70s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
compareGeneLists 20.847 0.958 21.859
fisherGOProfiles 5.881 0.316 6.201
mergeProfilesLists 4.942 0.279 5.222
plotProfiles 4.633 0.459 5.093
compareGOProfiles 4.739 0.287 5.030
* 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/goProfiles.Rcheck/00check.log’
for details.
goProfiles.Rcheck/00install.out:
* 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’
* DONE (goProfiles)
goProfiles.Rcheck/goProfiles-Ex.timings:
name | user | system | elapsed
|
CD4ids | 0.022 | 0.003 | 0.025 |
|
GOTermsList | 0.001 | 0.000 | 0.001 |
|
basicProfile | 4.482 | 0.443 | 4.969 |
|
compSummary | 4.332 | 0.290 | 4.647 |
|
compareGOProfiles | 4.739 | 0.287 | 5.030 |
|
compareGeneLists | 20.847 | 0.958 | 21.859 |
|
compareProfilesLists | 0.000 | 0.000 | 0.001 |
|
contractedProfile | 1.753 | 0.021 | 1.774 |
|
conversionFunctions | 0.031 | 0.002 | 0.033 |
|
drosophila | 0.003 | 0.000 | 0.003 |
|
equivSummary | 0.001 | 0.001 | 0.001 |
|
equivalentGOProfiles | 3.067 | 0.043 | 3.110 |
|
expandedLevel | 0.878 | 0.093 | 0.995 |
|
expandedProfile | 0.834 | 0.029 | 0.863 |
|
fisherGOProfiles | 5.881 | 0.316 | 6.201 |
|
fitGOProfile | 0 | 0 | 0 |
|
hugoIds | 0.014 | 0.004 | 0.018 |
|
mergeProfilesLists | 4.942 | 0.279 | 5.222 |
|
ngenes | 1.809 | 0.151 | 1.960 |
|
omimIds | 0.005 | 0.002 | 0.006 |
|
plotProfiles | 4.633 | 0.459 | 5.093 |
|
printProfiles | 4.543 | 0.324 | 4.868 |
|
prostateIds | 0.004 | 0.000 | 0.004 |
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