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BioC 2.13: CHECK report for AnnotationForge on perceval

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

Package 39/750HostnameOS / ArchBUILDCHECKBUILD BIN
AnnotationForge 1.4.4
Bioconductor Package Maintainer
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/AnnotationForge
Last Changed Rev: 83415 / Revision: 88450
Last Changed Date: 2013-11-19 11:28:11 -0800 (Tue, 19 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: AnnotationForge
Version: 1.4.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationForge_1.4.4.tar.gz
StartedAt: 2014-04-04 23:23:36 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:26:34 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 177.5 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationForge.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/AnnotationForge.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 ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ version ‘1.4.4’
* 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:
  inst/ProbePkg-template/data/.dummy.txt
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 ‘AnnotationForge’ can be installed ... [13s/14s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.3Mb
    extdata              3.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘BiocGenerics’ ‘Biobase’ ‘DBI’ ‘RSQLite’
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
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘methods’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.addEssentialMetadata’ ‘.addMeta’ ‘.createMetadataTables’
  ‘.makeARABIDOPSISCHIP_DB’ ‘.makeBOVINECHIP_DB’ ‘.makeCANINECHIP_DB’
  ‘.makeCHICKENCHIP_DB’ ‘.makeECOLICHIP_DB’ ‘.makeFLYCHIP_DB’
  ‘.makeGenesTable’ ‘.makeHUMANCHIP_DB’ ‘.makeMOUSECHIP_DB’
  ‘.makePIGCHIP_DB’ ‘.makeRATCHIP_DB’ ‘.makeRHESUSCHIP_DB’
  ‘.makeWORMCHIP_DB’ ‘.makeXENOPUSCHIP_DB’ ‘.makeYEASTCHIP_DB’
  ‘.makeZEBRAFISHCHIP_DB’ ‘popANOPHELESDB’ ‘popARABIDOPSISCHIPDB’
  ‘popARABIDOPSISDB’ ‘popBOVINECHIPDB’ ‘popBOVINEDB’ ‘popCANINECHIPDB’
  ‘popCANINEDB’ ‘popCHICKENCHIPDB’ ‘popCHICKENDB’ ‘popCHIMPDB’
  ‘popECOLICHIPDB’ ‘popECOLIDB’ ‘popFLYCHIPDB’ ‘popFLYDB’
  ‘popHUMANCHIPDB’ ‘popHUMANDB’ ‘popMALARIADB’ ‘popMOUSECHIPDB’
  ‘popMOUSEDB’ ‘popPIGCHIPDB’ ‘popPIGDB’ ‘popRATCHIPDB’ ‘popRATDB’
  ‘popRHESUSCHIPDB’ ‘popRHESUSDB’ ‘popWORMCHIPDB’ ‘popWORMDB’
  ‘popXENOPUSCHIPDB’ ‘popXENOPUSDB’ ‘popYEASTCHIPDB’ ‘popYEASTDB’
  ‘popZEBRAFISHCHIPDB’ ‘popZEBRAFISHDB’
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
.getSubNodeInfo: no visible global function definition for ‘Stop’
* 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’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘makeProbePackage.Rnw’, ‘MakingNewAnnotationPackages.Rnw’,
  ‘SQLForge.Rnw’, ‘MakingNewOrganismPackages.Rmd’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
makeProbePackage 6.842   0.33     7.3
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘AnnotationForge_unit_tests.R’ [13s/13s]
 [13s/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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

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

AnnotationForge.Rcheck/00install.out:

* installing *source* package ‘AnnotationForge’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationForge)

AnnotationForge.Rcheck/AnnotationForge-Ex.timings:

nameusersystemelapsed
AnnDbPkg-maker0.5290.0190.548
available.db0pkgs3.2460.0523.336
createSimpleBimap0.1920.0290.222
generateSeqnames_db0.0020.0030.005
getProbeDataAffy0.0020.0030.005
getProbeData_1lq0.0020.0040.006
makeOrgPackage0.0100.0110.021
makeOrgPackageFromDataFrames0.0180.0180.036
makeProbePackage6.8420.3307.300
sqlForge-makeCHIPDB0.0380.0050.043
sqlForge-popDB0.0860.0130.099
sqlForge-wrapDBPackages0.0450.0050.049