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BioC 2.13: CHECK report for goProfiles on zin1

This page was generated on 2014-04-05 09:47:38 -0700 (Sat, 05 Apr 2014).

Package 316/750HostnameOS / ArchBUILDCHECKBUILD BIN
goProfiles 1.24.0
Alex Sanchez
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/goProfiles
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: goProfiles
Version: 1.24.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.24.0.tar.gz
StartedAt: 2014-04-05 01:36:03 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:38:30 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 147.1 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/goProfiles.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.24.0’
* 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 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
* 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’ ... NOTE
The following files should probably not be installed:
  ‘fancyhdr.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘goProfiles.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
compareGeneLists   24.153  0.064  24.258
fisherGOProfiles    7.500  0.032   7.556
mergeProfilesLists  6.709  0.036   6.770
plotProfiles        6.576  0.008   6.611
printProfiles       5.797  0.008   5.814
basicProfile        5.484  0.052   5.553
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
CD4ids0.0200.0000.019
GOTermsList0.0040.0000.004
basicProfile5.4840.0525.553
compSummary4.5960.0364.645
compareGOProfiles4.5570.0524.614
compareGeneLists24.153 0.06424.258
compareProfilesLists0.0080.0000.009
contractedProfile2.3040.0082.347
conversionFunctions0.0560.0000.057
drosophila0.0080.0000.009
equivSummary0.0040.0000.007
equivalentGOProfiles4.8450.0164.922
expandedLevel1.4400.0001.441
expandedProfile0.9160.0080.925
fisherGOProfiles7.5000.0327.556
fitGOProfile0.0120.0000.012
hugoIds0.0160.0000.015
mergeProfilesLists6.7090.0366.770
ngenes2.4120.0122.491
omimIds0.0040.0000.010
plotProfiles6.5760.0086.611
printProfiles5.7970.0085.814
prostateIds0.0040.0000.006