AnnotationDbi 1.24.0
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/AnnotationDbi | | 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 | 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 ‘/Users/biocbuild/bbs-2.13-bioc/meat/AnnotationDbi.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 ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.24.0’
* 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 ... 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 ... [14s/15s] OK
* checking installed package size ... NOTE
installed size is 8.2Mb
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
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.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.COELICOLOR_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.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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘AnnotationDbi.Rnw’, ‘IntroToAnnotationPackages.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [442s/474s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AnnDbPkg-checker 292.468 12.061 314.403
supportedSeqnameStyles 33.924 0.484 34.673
InparanoidColsAndKeytypes 17.502 2.803 41.279
Bimap-direction 12.962 0.268 13.251
print.probetable 8.502 0.478 9.012
GOFrame 7.805 1.116 9.008
Bimap-toTable 7.426 0.172 7.739
Bimap 6.828 0.053 6.932
Bimap-envirAPI 4.840 0.559 5.407
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘AnnotationDbi_unit_tests.R’ [367s/404s]
[367s/404s] 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/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 ‘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)