Package: IdMappingRetrieval

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R --arch x86_64 CMD check --no-vignettes --timings --no-multiarch IdMappingRetrieval_1.2.0.tar.gz

StartedAt: 2012-09-24 00:37:53 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:41:05 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 192.2 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingRetrieval.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/IdMappingRetrieval.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IdMappingRetrieval/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingRetrieval' version '1.2.0'
* 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 whether package 'IdMappingRetrieval' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* 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' ... NOTE
The following files should probably not be installed:
  'IdMappingRetrieval.lyx'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/IdMappingRetrieval.Rcheck/00check.log'
for details.

* installing *source* package 'IdMappingRetrieval' ...
** R
** demo
** inst
** preparing package for lazy loading
This is  ENVISIONQuery   1.4.0   2011-07-17 
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getServices to getServices.default, which was defined in environment ENVISIONQuery.
** help
*** installing help indices
** building package indices
** installing vignettes
   'IdMappingRetrieval.Rnw' using 'latin-9' 
** testing if installed package can be loaded
This is  ENVISIONQuery   1.4.0   2011-07-17 

* DONE (IdMappingRetrieval)

name	user	system	elapsed
AnnotationDavid	0	0	0
AnnotationEnsembl	0.000	0.000	0.001
AnnotationEnsemblCsv	0.000	0.000	0.001
AnnotationEnvision	0	0	0
addServices.ServiceManager	0.039	0.007	0.046
createSubmission.AnnotationNetAffx	0.001	0.000	0.000
getArrayType.Annotation	0	0	0
getArrayTypes.Annotation	0.000	0.000	0.001
getCredentials.Annotation	0.001	0.000	0.000
getDataFrame.Annotation	0	0	0
getDataFrameList.ServiceManager	0	0	0
getDefaultServices.ServiceManager	0.013	0.002	0.015
getIdMap.Annotation	0	0	0
getIdMapList.ServiceManager	0.001	0.000	0.000
getProbesetList.AnnotationAffx	0	0	0
getRoot.Annotation	0.000	0.001	0.000
getServiceRoot.Annotation	0.001	0.000	0.000
getServices.ServiceManager	0.014	0.003	0.017
init.Annotation	0	0	0
setCredentials.Annotation	0.001	0.001	0.001
setCredentials.AnnotationAffx	0.000	0.000	0.001
setOptions.Annotation	0.000	0.000	0.001
setServices.ServiceManager	0.019	0.004	0.023
subsetByColumn	0.000	0.000	0.001