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BioC 2.12: CHECK report for IdMappingRetrieval on george2

This page was generated on 2013-10-09 09:37:46 -0700 (Wed, 09 Oct 2013).

Package 335/671HostnameOS / ArchBUILDCHECKBUILD BIN
IdMappingRetrieval 1.6.0
Alex Lisovich , Roger Day
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/IdMappingRetrieval
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: IdMappingRetrieval
Version: 1.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingRetrieval_1.6.0.tar.gz
StartedAt: 2013-10-09 02:40:31 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:44:59 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 268.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IdMappingRetrieval.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/IdMappingRetrieval.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.6.0’
* 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/28s] 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 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 ... [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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-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   1.8.1   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)

IdMappingRetrieval.Rcheck/IdMappingRetrieval-Ex.timings:

nameusersystemelapsed
AnnotationDavid0.0160.0000.016
AnnotationEnsembl0.0160.0000.014
AnnotationEnsemblCsv0.0120.0000.015
AnnotationEnvision0.0080.0040.014
addServices.ServiceManager0.0880.0040.091
createSubmission.AnnotationNetAffx0.0080.0000.006
getArrayType.Annotation0.0200.0000.018
getArrayTypes.Annotation0.0200.0000.019
getCredentials.Annotation0.0160.0040.020
getDataFrame.Annotation0.0240.0080.030
getDataFrameList.ServiceManager0.0240.0000.023
getDefaultServices.ServiceManager0.0400.0000.037
getIdMap.Annotation0.0200.0000.019
getIdMapList.ServiceManager0.0200.0000.021
getProbesetList.AnnotationAffx0.0160.0000.016
getRoot.Annotation0.0120.0040.017
getServiceRoot.Annotation0.0160.0040.019
getServices.ServiceManager0.0400.0040.042
init.Annotation0.0040.0000.006
setCredentials.Annotation0.0080.0000.012
setCredentials.AnnotationAffx0.0160.0000.014
setOptions.Annotation0.0000.0080.010
setServices.ServiceManager0.0560.0000.054
subsetByColumn0.0080.0000.007