BioC 3.2: CHECK report for GSEABase on zin1

Package: GSEABase

Version: 1.31.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GSEABase_1.31.3.tar.gz

StartedAt: 2015-08-24 00:37:28 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:39:26 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 117.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GSEABase_1.31.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GSEABase.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 ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.31.3’
* 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 ... [8s/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 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
goSlim,ExpressionSet-GOCollection : .local: no visible binding for
  global variable ‘sample.ExpressionSet’
* 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 ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GeneSetCollection-methods 5.396  0.032   5.424
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unitTests.R’ [32s/33s]
 [33s/33s] 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GSEABase.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
CollectionType-class	0.588	0.016	0.613
CollectionType-constructors	0.172	0.000	0.172
GSEABase-package	0.127	0.000	0.127
GeneColorSet-class	0.143	0.004	0.146
GeneIdentifierType-class	0.115	0.000	0.115
GeneIdentifierType-constructors	0.255	0.004	0.259
GeneSet-class	0.366	0.004	0.383
GeneSet-methods	0.118	0.000	0.117
GeneSetCollection-class	0.025	0.000	0.025
GeneSetCollection-methods	5.396	0.032	5.424
OBOCollection-class	0.103	0.000	0.103
getOBOCollection	0.068	0.004	0.072
getObjects	0.037	0.000	0.037
goSlim-methods	0.545	0.012	0.568
incidence-methods	0.022	0.001	0.022