AnnotationDbi 1.26.1
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/AnnotationDbi | | Last Changed Rev: 94803 / Revision: 95116 | | Last Changed Date: 2014-10-01 12:44:53 -0700 (Wed, 01 Oct 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.26.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/AnnotationDbi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.26.1’
* 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 ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/inst/extdata/org.TguttataTestingSubset.eg.sqlite
AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/man/org.TguttataTestingSubset.eg_dbconn.Rd
AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/man/org.TguttataTestingSubset.egORGANISM.Rd
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... [18s/19s] OK
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
extdata 6.0Mb
* 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.keys’ ‘createAnnObjs.AFFYHUEX_DB’ ‘createAnnObjs.ANOPHELES_DB’
‘createAnnObjs.ANOPHELESCHIP_DB’ ‘createAnnObjs.ARABIDOPSIS_DB’
‘createAnnObjs.ARABIDOPSISCHIP_DB’ ‘createAnnObjs.BOVINE_DB’
‘createAnnObjs.BOVINECHIP_DB’ ‘createAnnObjs.CANINE_DB’
‘createAnnObjs.CANINECHIP_DB’ ‘createAnnObjs.CHICKEN_DB’
‘createAnnObjs.CHICKENCHIP_DB’ ‘createAnnObjs.CHIMP_DB’
‘createAnnObjs.CHIMPCHIP_DB’ ‘createAnnObjs.COELICOLOR_DB’
‘createAnnObjs.COELICOLORCHIP_DB’ ‘createAnnObjs.ECOLI_DB’
‘createAnnObjs.ECOLICHIP_DB’ ‘createAnnObjs.FLY_DB’
‘createAnnObjs.FLYCHIP_DB’ ‘createAnnObjs.GO_DB’
‘createAnnObjs.HUMAN_DB’ ‘createAnnObjs.HUMANCHIP_DB’
‘createAnnObjs.HUMANCROSSCHIP_DB’ ‘createAnnObjs.INPARANOID_DB’
‘createAnnObjs.KEGG_DB’ ‘createAnnObjs.MALARIA_DB’
‘createAnnObjs.MALARIACHIP_DB’ ‘createAnnObjs.MOUSE_DB’
‘createAnnObjs.MOUSECHIP_DB’ ‘createAnnObjs.ORGANISM_DB’
‘createAnnObjs.PFAM_DB’ ‘createAnnObjs.PIG_DB’
‘createAnnObjs.PIGCHIP_DB’ ‘createAnnObjs.RAT_DB’
‘createAnnObjs.RATCHIP_DB’ ‘createAnnObjs.RHESUS_DB’
‘createAnnObjs.RHESUSCHIP_DB’ ‘createAnnObjs.WORM_DB’
‘createAnnObjs.WORMCHIP_DB’ ‘createAnnObjs.XENOPUS_DB’
‘createAnnObjs.XENOPUSCHIP_DB’ ‘createAnnObjs.YEAST_DB’
‘createAnnObjs.YEASTCHIP_DB’ ‘createAnnObjs.ZEBRAFISH_DB’
‘createAnnObjs.ZEBRAFISHCHIP_DB’ ‘dbConn’ ‘Go3tablenames’
‘packageName’
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
.selectWarnJT: no visible binding for global variable ‘jointype’
annotMessage: no visible binding for global variable ‘pkgName’
createORGANISMSeeds: no visible global function definition for
‘makeAnnDbMapSeeds’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [431s/459s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AnnDbPkg-checker 297.728 11.761 330.474
InparanoidColsAndKeytypes 20.550 2.482 28.417
Bimap-direction 17.867 0.163 18.045
GOFrame 11.671 1.350 14.191
print.probetable 12.390 0.521 12.950
Bimap 10.373 0.032 10.433
Bimap-toTable 9.070 0.095 9.204
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘AnnotationDbi_unit_tests.R’ [10m/10m]
[10m/10m] 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 5 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘subset’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘AnnotationDbi’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘AnnotationDbi’
Creating a generic function for ‘as.list’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)