BioC 2.12: CHECK report for IdMappingRetrieval on petty

Package: IdMappingRetrieval

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingRetrieval_1.6.0.tar.gz

StartedAt: 2013-10-08 22:49:17 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:53:35 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 258.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IdMappingRetrieval.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingRetrieval.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (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 '1.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'IdMappingRetrieval' can be installed ... [27s/27s] OK
* checking installed package size ... OK
* checking package 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 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 ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... WARNING
checkRd: (3) createSubmission.AnnotationNetAffx.Rd:18: \synopsis will be removed in R 3.1.0
checkRd: (3) getArrayType.Annotation.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) getArrayTypes.Annotation.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) getColumns1.AnnotationEnsembl.Rd:23: \synopsis will be removed in R 3.1.0
checkRd: (3) getColumns2.AnnotationEnsembl.Rd:23: \synopsis will be removed in R 3.1.0
checkRd: (3) getCredentials.Annotation.Rd:23: \synopsis will be removed in R 3.1.0
checkRd: (3) getDefaultServices.ServiceManager.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) getProbesetList.AnnotationAffx.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) getRoot.Annotation.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) init.Annotation.Rd:24: \synopsis will be removed in R 3.1.0
checkRd: (3) setCredentials.Annotation.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) setCredentials.AnnotationAffx.Rd:20: \synopsis will be removed in R 3.1.0
* 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 ... [14s/14s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingRetrieval.Rcheck/00check.log'
for details.

* installing *source* package 'IdMappingRetrieval' ...
** R
** demo
** inst
** preparing package for lazy loading
This is  ENVISIONQuery   1.8.1   2013-08-20 
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
** testing if installed package can be loaded
This is  ENVISIONQuery   1.8.1   2013-08-20 
* DONE (IdMappingRetrieval)

name	user	system	elapsed
AnnotationDavid	0.005	0.002	0.007
AnnotationEnsembl	0.005	0.002	0.007
AnnotationEnsemblCsv	0.006	0.002	0.008
AnnotationEnvision	0.007	0.002	0.008
addServices.ServiceManager	0.104	0.003	0.107
createSubmission.AnnotationNetAffx	0.010	0.001	0.011
getArrayType.Annotation	0.016	0.001	0.019
getArrayTypes.Annotation	0.013	0.001	0.015
getCredentials.Annotation	0.011	0.002	0.014
getDataFrame.Annotation	0.016	0.004	0.020
getDataFrameList.ServiceManager	0.016	0.004	0.020
getDefaultServices.ServiceManager	0.043	0.002	0.046
getIdMap.Annotation	0.015	0.002	0.017
getIdMapList.ServiceManager	0.016	0.002	0.017
getProbesetList.AnnotationAffx	0.296	0.001	0.298
getRoot.Annotation	0.008	0.002	0.011
getServiceRoot.Annotation	0.010	0.002	0.012
getServices.ServiceManager	0.043	0.003	0.046
init.Annotation	0.006	0.001	0.007
setCredentials.Annotation	0.009	0.001	0.010
setCredentials.AnnotationAffx	0.015	0.001	0.016
setOptions.Annotation	0.009	0.003	0.012
setServices.ServiceManager	0.064	0.004	0.067
subsetByColumn	0.005	0.001	0.006