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BioC 3.0: CHECK report for GSEABase on oaxaca

This page was generated on 2015-04-10 10:02:35 -0700 (Fri, 10 Apr 2015).

Package 408/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEABase 1.28.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GSEABase
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: GSEABase
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.28.0.tar.gz
StartedAt: 2015-04-10 00:21:27 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:25:01 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 213.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GSEABase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GSEABase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.28.0’
* 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 ‘GSEABase’ can be installed ... [14s/15s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GSC_Pfam_helper: no visible global function definition for ‘select’
.GSC_genes_helper: no visible global function definition for
  ‘mappedLkeys’
.GSC_genes_helper: no visible global function definition for
  ‘mappedRkeys’
GeneSetCollection,GOAllFrame-missing-GOCollection: no visible global
  function definition for ‘getGOFrameData’
GeneSetCollection,KEGGFrame-missing-KEGGCollection: no visible global
  function definition for ‘getKEGGFrameData’
GeneSetCollection,character-AnnotationIdentifier-GOCollection: no
  visible global function definition for ‘mappedLkeys’
GeneSetCollection,character-AnnotationIdentifier-GOCollection: no
  visible global function definition for ‘toTable’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/21s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GeneSetCollection-methods 9.389  0.191   9.631
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘unitTests.R’ [46s/48s]
 [47s/48s] OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GSEABase.Rcheck/00check.log’
for details.

GSEABase.Rcheck/00install.out:

* installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSEABase)

GSEABase.Rcheck/GSEABase-Ex.timings:

nameusersystemelapsed
CollectionType-class0.8680.0430.914
CollectionType-constructors0.420.010.43
GSEABase-package0.2050.0120.219
GeneColorSet-class0.2270.0090.237
GeneIdentifierType-class0.1610.0090.170
GeneIdentifierType-constructors0.4910.0110.514
GeneSet-class0.3330.0140.347
GeneSet-methods0.3110.0080.324
GeneSetCollection-class0.0200.0010.021
GeneSetCollection-methods9.3890.1919.631
OBOCollection-class0.1620.0030.165
getOBOCollection0.1520.0060.158
getObjects0.0640.0020.067
goSlim-methods0.7780.0380.861
incidence-methods0.0410.0010.043