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BioC 2.13: CHECK report for IdMappingRetrieval on perceval

This page was generated on 2014-04-05 09:52:40 -0700 (Sat, 05 Apr 2014).

Package 366/750HostnameOS / ArchBUILDCHECKBUILD BIN
IdMappingRetrieval 1.8.0
Alex Lisovich , Roger Day
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/IdMappingRetrieval
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  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: IdMappingRetrieval
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingRetrieval_1.8.0.tar.gz
StartedAt: 2014-04-05 02:05:59 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:09:51 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 231.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IdMappingRetrieval.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/IdMappingRetrieval.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdMappingRetrieval/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingRetrieval’ version ‘1.8.0’
* 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 ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ENVISIONQuery’ ‘R.oo’
A package should be listed in only one of these fields.
* 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:
  ‘RCurl’ ‘XML’
  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
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘IdMappingRetrieval.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [13s/13s] 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

WARNING: There was 1 warning.
NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/IdMappingRetrieval.Rcheck/00check.log’
for details.

IdMappingRetrieval.Rcheck/00install.out:

* installing *source* package ‘IdMappingRetrieval’ ...
** R
** demo
** inst
** preparing package for lazy loading
This is  ENVISIONQuery   1.10.0   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   1.10.0   2013-08-20 
* DONE (IdMappingRetrieval)

IdMappingRetrieval.Rcheck/IdMappingRetrieval-Ex.timings:

nameusersystemelapsed
AnnotationDavid0.0110.0020.013
AnnotationEnsembl0.0100.0010.011
AnnotationEnsemblCsv0.0130.0010.014
AnnotationEnvision0.0110.0020.013
addServices.ServiceManager0.0890.0050.094
createSubmission.AnnotationNetAffx0.0070.0000.007
getArrayType.Annotation0.0170.0020.018
getArrayTypes.Annotation0.0080.0020.009
getCredentials.Annotation0.0140.0020.016
getDataFrame.Annotation0.0120.0050.017
getDataFrameList.ServiceManager0.0150.0060.021
getDefaultServices.ServiceManager0.0340.0040.038
getIdMap.Annotation0.0100.0030.013
getIdMapList.ServiceManager0.0140.0030.017
getProbesetList.AnnotationAffx0.0100.0020.011
getRoot.Annotation0.0070.0020.009
getServiceRoot.Annotation0.0100.0030.013
getServices.ServiceManager0.0340.0030.037
init.Annotation0.0070.0010.007
setCredentials.Annotation0.0080.0020.011
setCredentials.AnnotationAffx0.0090.0020.011
setOptions.Annotation0.0080.0030.011
setServices.ServiceManager0.0450.0050.052
subsetByColumn0.0110.0010.014