AnnotationDbi 1.31.17
Bioconductor Package Maintainer
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi | | Last Changed Rev: 105101 / Revision: 107696 | | Last Changed Date: 2015-06-17 15:48:10 -0700 (Wed, 17 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.31.17.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/AnnotationDbi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.31.17’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... [7s/7s] 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’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘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
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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:
‘createAnnDbBimap’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotMessage: no visible binding for global variable ‘pkgName’
createORGANISMSeeds: no visible global function definition for
‘makeAnnDbMapSeeds’
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
* 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 ... [174s/178s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AnnDbPkg-checker 128.234 1.381 131.051
Bimap-direction 7.358 0.008 7.381
InparanoidColsAndKeytypes 5.527 0.108 6.301
Bimap-toTable 4.162 0.013 5.182
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’
* checking tests ...
Running ‘AnnotationDbi_unit_tests.R’ [75s/82s]
[75s/82s] 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
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-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 ‘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)