Package: AnnotationDbi

Version: 1.18.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.18.0.tar.gz

StartedAt: 2012-03-31 23:33:08 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:38:59 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 350.6 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationDbi.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/AnnotationDbi.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.18.0'
* 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 whether package 'AnnotationDbi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   5.2Mb
    doc                  1.0Mb
    extdata              3.2Mb
* 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 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'
cleanSrcMap: warning in strsplit(id, split = ";", fix = T): partial
  argument match of 'fix' to 'fixed'
createORGANISMSeeds: no visible global function definition for
  'makeAnnDbMapSeeds'
makeBaseMaps: warning in strsplit(eg, split = " /// ", fix = T):
  partial argument match of 'fix' to 'fixed'
* 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'AnnotationDbi_unit_tests.R'
 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
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.

* 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 '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 '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
   'AnnotationDbi.Rnw' 
   'IntroToAnnotationPackages.Rnw' 
   'NewSchema.Rnw' 
   'SQLForge.Rnw' 
   'makeProbePackage.Rnw' 
** testing if installed package can be loaded

* DONE (AnnotationDbi)

name	user	system	elapsed
AnnDbBimap-envirAPI	1.072	0.200	1.330
AnnDbObj-class	0.388	0.016	0.472
AnnDbPkg-checker	131.864	0.836	132.800
AnnDbPkg-maker	0.040	0.000	0.042
AnnotationDb-class	2.632	0.016	2.674
Bimap-direction	7.457	0.028	7.514
Bimap-keys	2.584	0.008	2.633
Bimap-toTable	4.296	0.016	4.323
Bimap	4.096	0.016	4.140
BimapFiltering	0.620	0.012	0.654
BimapFormatting	1.628	0.004	1.651
GOFrame	4.825	2.564	7.439
GOTerms-class	0.000	0.000	0.002
KEGGFrame	0.864	0.008	0.912
NCBI_getters	0	0	0
available.db0pkgs	0.072	0.008	0.089
createSimpleBimap	0.496	0.004	0.524
getProbeDataAffy	0.000	0.000	0.001
getProbeData_1lq	0.000	0.000	0.001
inpIDMapper	0.000	0.000	0.001
makeOrgPackage	0.000	0.000	0.001
makeProbePackage	8.056	0.104	8.396
make_eg_to_go_map	0.716	0.016	0.753
print.probetable	1.624	0.068	1.694
sqlForge-makeCHIPDB	0	0	0
sqlForge-popDB	0.004	0.000	0.001
sqlForge-wrapDBPackages	0	0	0
toSQLStringSet	0.000	0.000	0.002
unlist2	0.537	0.012	0.578