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BioC 2.12: CHECK report for AnnotationDbi on george2

This page was generated on 2013-10-09 09:37:21 -0700 (Wed, 09 Oct 2013).

Package 36/671HostnameOS / ArchBUILDCHECKBUILD BIN
AnnotationDbi 1.22.6
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/AnnotationDbi
Last Changed Rev: 77176 / Revision: 81334
Last Changed Date: 2013-06-04 13:22:47 -0700 (Tue, 04 Jun 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 

Summary

Package: AnnotationDbi
Version: 1.22.6
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.22.6.tar.gz
StartedAt: 2013-10-09 00:05:37 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:20:02 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 865.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationDbi.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/AnnotationDbi.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.22.6’
* 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 ... [17s/18s] 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 ... [500s/511s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnDbPkg-checker          333.037  4.172 343.143
supportedSeqnameStyles     49.259  0.348  50.894
InparanoidColsAndKeytypes  22.410  0.696  24.805
Bimap-direction            15.561  0.048  15.615
print.probetable           10.781  0.260  11.091
GOFrame                     8.280  0.584   9.125
Bimap-toTable               7.520  0.024   7.647
Bimap                       6.688  0.008   6.697
Bimap-envirAPI              5.244  0.324   5.717
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.R’ [156s/167s]
 [156s/167s] 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
  ‘/home/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-class1.4960.0441.544
AnnDbPkg-checker333.037 4.172343.143
AnnotationDb-class2.5920.0162.728
Bimap-direction15.561 0.04815.615
Bimap-envirAPI5.2440.3245.717
Bimap-keys4.5490.0084.602
Bimap-toTable7.5200.0247.647
Bimap6.6880.0086.697
BimapFiltering1.7490.0161.764
BimapFormatting4.0360.0044.041
GOColsAndKeytypes1.2960.0121.316
GOFrame8.2800.5849.125
GOTerms-class0.0240.0000.024
InparanoidColsAndKeytypes22.410 0.69624.805
KEGGFrame2.4560.0202.699
colsAndKeytypes1.9040.0161.947
inpIDMapper0.0240.0000.022
makeGOGraph3.3800.0283.494
make_eg_to_go_map1.7760.0202.200
print.probetable10.781 0.26011.091
supportedSeqnameStyles49.259 0.34850.894
toSQLStringSet0.0120.0000.009
unlist21.5400.0121.553