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BioC 2.13: CHECK report for IdMappingRetrieval on moscato1

This page was generated on 2014-04-05 09:50:23 -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: rm -rf IdMappingRetrieval.buildbin-libdir && mkdir IdMappingRetrieval.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IdMappingRetrieval.buildbin-libdir IdMappingRetrieval_1.8.0.tar.gz >IdMappingRetrieval-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=IdMappingRetrieval.buildbin-libdir --install="check:IdMappingRetrieval-install.out" --force-multiarch --no-vignettes --timings IdMappingRetrieval_1.8.0.tar.gz && mv IdMappingRetrieval.buildbin-libdir/* IdMappingRetrieval.Rcheck/ && rmdir IdMappingRetrieval.buildbin-libdir
StartedAt: 2014-04-05 04:40:20 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:44:03 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 223.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IdMappingRetrieval.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/IdMappingRetrieval.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'IdMappingRetrieval' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [9s] 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
  'D:/biocbld/bbs-2.13-bioc/meat/IdMappingRetrieval.Rcheck/00check.log'
for details.

IdMappingRetrieval.Rcheck/00install.out:


install for i386

* 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 

install for x64

* installing *source* package 'IdMappingRetrieval' ...
** testing if installed package can be loaded
This is  ENVISIONQuery   1.10.0   2013-08-20 
* MD5 sums
packaged installation of 'IdMappingRetrieval' as IdMappingRetrieval_1.8.0.zip
* DONE (IdMappingRetrieval)

IdMappingRetrieval.Rcheck/examples_i386/IdMappingRetrieval-Ex.timings:

nameusersystemelapsed
AnnotationDavid0.010.000.01
AnnotationEnsembl000
AnnotationEnsemblCsv000
AnnotationEnvision000
addServices.ServiceManager0.070.000.06
createSubmission.AnnotationNetAffx0.010.000.02
getArrayType.Annotation000
getArrayTypes.Annotation000
getCredentials.Annotation0.010.000.01
getDataFrame.Annotation0.020.000.02
getDataFrameList.ServiceManager000
getDefaultServices.ServiceManager0.020.000.02
getIdMap.Annotation0.010.000.01
getIdMapList.ServiceManager000
getProbesetList.AnnotationAffx000
getRoot.Annotation0.020.000.01
getServiceRoot.Annotation0.010.000.02
getServices.ServiceManager0.030.000.03
init.Annotation000
setCredentials.Annotation0.020.000.02
setCredentials.AnnotationAffx000
setOptions.Annotation0.170.000.17
setServices.ServiceManager0.040.000.05
subsetByColumn000

IdMappingRetrieval.Rcheck/examples_x64/IdMappingRetrieval-Ex.timings:

nameusersystemelapsed
AnnotationDavid000
AnnotationEnsembl0.010.000.02
AnnotationEnsemblCsv000
AnnotationEnvision000
addServices.ServiceManager0.050.000.05
createSubmission.AnnotationNetAffx0.010.000.01
getArrayType.Annotation0.020.000.02
getArrayTypes.Annotation000
getCredentials.Annotation0.010.000.01
getDataFrame.Annotation000
getDataFrameList.ServiceManager0.020.000.02
getDefaultServices.ServiceManager0.220.000.22
getIdMap.Annotation000
getIdMapList.ServiceManager000
getProbesetList.AnnotationAffx000
getRoot.Annotation000
getServiceRoot.Annotation000
getServices.ServiceManager0.010.000.02
init.Annotation000
setCredentials.Annotation000
setCredentials.AnnotationAffx000
setOptions.Annotation000
setServices.ServiceManager0.030.000.03
subsetByColumn000