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 |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [7s/7s] OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
AnnDbPkg-templates 1.7Mb
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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘MakingNewAnnotationPackages.Rnw’, ‘SQLForge.Rnw’,
‘makeProbePackage.Rnw’, ‘MakingNewOrganismPackages.Rmd’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘AnnotationForge_unit_tests.R’ [8s/8s]
[8s/8s] 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
‘/home/biocbuild/bbs-2.13-bioc/meat/AnnotationForge.Rcheck/00check.log’
for details.