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Package 33/514HostnameOS / ArchBUILDCHECKBUILD BIN
AnnotationDbi 1.16.19
Bioconductor Package Maintainer
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/AnnotationDbi
Last Changed Rev: 63650 / Revision: 64395
Last Changed Date: 2012-03-08 16:42:31 -0800 (Thu, 08 Mar 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: AnnotationDbi
Version: 1.16.19
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.16.19.tar.gz
StartedAt: 2012-03-23 23:15:04 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:24:46 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 582.0 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationDbi.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/AnnotationDbi.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.16.19'
* 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  9.9Mb
  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 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 sizes of PDF files under '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 ... 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

AnnotationDbi.Rcheck/00install.out:

* 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)

AnnotationDbi.Rcheck/AnnotationDbi-Ex.timings:

nameusersystemelapsed
AnnDbBimap-envirAPI1.8640.6732.567
AnnDbObj-class0.4920.0350.527
AnnDbPkg-checker205.035 9.052219.948
AnnDbPkg-maker0.0640.0150.080
AnnotationDb-class3.3570.1283.492
Bimap-direction12.459 0.13212.596
Bimap-keys3.7730.0413.814
Bimap-toTable6.6340.1416.805
Bimap6.6080.0426.656
BimapFiltering0.8680.0150.883
BimapFormatting2.7060.0452.761
GOFrame18.39218.76137.852
GOTerms-class0.0030.0000.003
KEGGFrame1.0270.0161.043
NCBI_getters0.0010.0010.001
available.db0pkgs0.1290.0060.142
createSimpleBimap0.5890.0080.598
getProbeDataAffy0.0000.0000.001
getProbeData_1lq0.0010.0000.001
inpIDMapper0.0010.0000.001
makeOrgPackage0.0000.0010.001
makeProbePackage15.022 0.45515.541
make_eg_to_go_map0.8040.0460.850
print.probetable2.1410.1912.335
sqlForge-makeCHIPDB0.0010.0010.001
sqlForge-popDB0.0020.0010.001
sqlForge-wrapDBPackages0.0010.0000.001
toSQLStringSet0.0010.0000.002
unlist20.6540.0180.672