Package: AnnotationDbi

Version: 1.16.10

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.16.10.tar.gz

StartedAt: 2012-01-09 01:07:53 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:15:05 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 431.5 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationDbi.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/AnnotationDbi.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.16.10'
* 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 whether package 'AnnotationDbi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   4.0Mb
    extdata              3.2Mb
* checking package directory ... OK
* checking for portable file names ... 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 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
File 'AnnotationDbi/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

.getSubNodeInfo: no visible global function definition for 'Stop'
.valid.metadata.table: no visible binding for global variable
  'DB_TYPE_NAME'
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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'AnnotationDbi_unit_tests.R'
 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
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	1.61	0.14	2.09
AnnDbObj-class	0.5	0.0	0.5
AnnDbPkg-checker	172.17	7.25	196.22
AnnDbPkg-maker	0.06	0.00	0.07
AnnotationDb-class	2.22	0.05	2.27
Bimap-direction	8.48	1.19	9.67
Bimap-keys	2.77	0.24	3.00
Bimap-toTable	4.39	0.00	5.30
Bimap	4.82	0.36	5.18
BimapFiltering	0.86	0.01	0.88
BimapFormatting	2.22	0.00	2.21
GOFrame	7.69	5.21	12.92
GOTerms-class	0	0	0
KEGGFrame	1.26	0.04	1.31
NCBI_getters	0	0	0
available.db0pkgs	0.08	0.03	0.10
createSimpleBimap	0.68	0.04	0.72
getProbeDataAffy	0	0	0
getProbeData_1lq	0	0	0
inpIDMapper	0	0	0
makeOrgPackage	0	0	0
makeProbePackage	8.26	0.03	10.27
make_eg_to_go_map	0.74	0.00	0.73
print.probetable	1.77	0.00	1.77
sqlForge-makeCHIPDB	0.00	0.01	0.01
sqlForge-popDB	0	0	0
sqlForge-wrapDBPackages	0	0	0
toSQLStringSet	0	0	0
unlist2	0.68	0.02	0.70