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Package 36/671HostnameOS / ArchBUILDCHECKBUILD BIN
AnnotationDbi 1.22.3
Bioconductor Package Maintainer
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/AnnotationDbi
Last Changed Rev: 76032 / Revision: 76155
Last Changed Date: 2013-04-25 10:27:40 -0700 (Thu, 25 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: AnnotationDbi
Version: 1.22.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.22.3.tar.gz
StartedAt: 2013-05-01 02:12:47 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:29:04 -0700 (Wed, 01 May 2013)
EllapsedTime: 976.9 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationDbi.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AnnotationDbi.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.22.3'
* 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 ... [15s/19s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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'
* 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 examples ... [548s/577s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnDbPkg-checker          373.708 15.382 410.329
supportedSeqnameStyles     25.945  0.384  26.501
Bimap-direction            25.731  0.262  26.043
InparanoidColsAndKeytypes  22.966  2.634  31.502
GOFrame                    15.932  1.266  17.578
Bimap                      13.322  0.080  13.468
Bimap-toTable               8.896  0.172   9.122
print.probetable            5.993  0.558   6.560
Bimap-keys                  6.419  0.047   6.473
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'AnnotationDbi_unit_tests.R' [219s/232s]
 [219s/232s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.

AnnotationDbi.Rcheck/00install.out:

* 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)

AnnotationDbi.Rcheck/AnnotationDbi-Ex.timings:

nameusersystemelapsed
AnnDbObj-class1.2180.0941.373
AnnDbPkg-checker373.708 15.382410.329
AnnotationDb-class2.3610.0642.462
Bimap-direction25.731 0.26226.043
Bimap-envirAPI3.7600.6244.384
Bimap-keys6.4190.0476.473
Bimap-toTable8.8960.1729.122
Bimap13.322 0.08013.468
BimapFiltering1.3500.0371.566
BimapFormatting3.4150.0403.544
GOColsAndKeytypes1.0230.0331.067
GOFrame15.932 1.26617.578
GOTerms-class0.0110.0120.024
InparanoidColsAndKeytypes22.966 2.63431.502
KEGGFrame1.4680.0291.496
colsAndKeytypes1.2470.0301.279
inpIDMapper0.1400.0200.161
makeGOGraph2.1450.0262.172
make_eg_to_go_map1.3330.0321.364
print.probetable5.9930.5586.560
supportedSeqnameStyles25.945 0.38426.501
toSQLStringSet0.0050.0050.010
unlist21.0330.0261.059