Package: AnnotationDbi

Version: 1.15.9

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.15.9.tar.gz

StartedAt: 2011-07-07 01:23:23 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:35:59 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 755.6 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationDbi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/AnnotationDbi.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.15.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'AnnotationDbi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   4.2Mb
    extdata              3.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
.getSubNodeInfo: no visible global function definition for 'Stop'
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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'org.Hs.eg.db'
* 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

* installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

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 "colnames" from package "base" in package "AnnotationDbi"
Creating a generic function for "subset" from package "base" in package "AnnotationDbi"
Creating a generic function for "as.data.frame" 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 "nrow" from package "base" in package "AnnotationDbi"
Creating a generic function for "ncol" from package "base" 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 "mget" from package "base" in package "AnnotationDbi"
Creating a generic function for "eapply" from package "base" in package "AnnotationDbi"
Creating a generic function for "get" 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 ...
*** tangling vignette sources ...
   'AnnotationDbi.Rnw' 
   'NewSchema.Rnw' 
   'SQLForge.Rnw' 
   'makeProbePackage.Rnw' 
** testing if installed package can be loaded

* DONE (AnnotationDbi)

name	user	system	elapsed
AnnDbBimap-envirAPI	1.978	0.681	2.691
AnnDbObj-class	37.647	32.903	334.161
AnnDbPkg-checker	205.326	10.752	224.371
AnnDbPkg-maker	0.072	0.014	0.088
Bimap-direction	15.495	0.185	15.818
Bimap-keys	4.612	0.078	4.820
Bimap-toTable	5.822	0.182	6.187
Bimap	8.175	0.057	9.355
BimapFiltering	0.889	0.015	1.008
BimapFormatting	2.535	0.049	2.831
GOFrame	9.461	0.877	11.059
GOTerms-class	0.003	0.001	0.004
KEGGFrame	1.037	0.019	1.070
NCBI_getters	0.001	0.000	0.001
available.db0pkgs	0.135	0.009	0.160
createSimpleBimap	0.577	0.012	0.596
getProbeDataAffy	0.000	0.000	0.001
getProbeData_1lq	0.000	0.000	0.001
inpIDMapper	0.002	0.001	0.002
makeOrgPackage	0.001	0.000	0.001
makeProbePackage	16.205	0.500	17.404
make_eg_to_go_map	1.545	0.156	1.798
print.probetable	1.998	0.079	2.106
sqlForge-makeCHIPDB	0.001	0.000	0.002
sqlForge-popDB	0.002	0.001	0.002
sqlForge-wrapDBPackages	0.001	0.000	0.001
toSQLStringSet	0.002	0.000	0.002
unlist2	0.728	0.021	0.759