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BioC 3.0: CHECK report for AnnotationDbi on perceval

This page was generated on 2015-04-10 09:53:15 -0700 (Fri, 10 Apr 2015).

Package 40/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationDbi 1.28.2
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/AnnotationDbi
Last Changed Rev: 100825 / Revision: 102249
Last Changed Date: 2015-03-18 15:00:57 -0700 (Wed, 18 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: AnnotationDbi
Version: 1.28.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.28.2.tar.gz
StartedAt: 2015-04-09 22:39:35 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:52:43 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 788.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationDbi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationDbi_1.28.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/AnnotationDbi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.28.2’
* 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 ... NOTE
Found the following non-portable file paths:
  AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/inst/extdata/org.TguttataTestingSubset.eg.sqlite
  AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/man/org.TguttataTestingSubset.eg_dbconn.Rd
  AnnotationDbi/inst/extdata/org.TguttataTestingSubset.eg.db/man/org.TguttataTestingSubset.egORGANISM.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... [16s/31s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘DBI’ ‘RSQLite’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘graph’ ‘KEGG.db’ ‘RSQLite’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘createAnnDbBimap’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkForDeprecatedKeytype: no visible global function definition for
  ‘wmsg’
.GOid2go_synonymField: no visible global function definition for
  ‘GO_dbconn’
.GOid2go_termField: no visible global function definition for
  ‘GO_dbconn’
.selectWarnJT: no visible binding for global variable ‘jointype’
addToNamespaceAndExport : warnIfDep: no visible global function
  definition for ‘wmsg’
addToNamespaceAndExport : warnIfDef: no visible global function
  definition for ‘wmsg’
annotMessage: no visible binding for global variable ‘pkgName’
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [346s/353s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnDbPkg-checker          246.790 10.213 261.821
InparanoidColsAndKeytypes  12.455  2.334  17.188
Bimap-direction            10.012  0.168  10.181
print.probetable            8.082  0.436   8.521
GOFrame                     7.289  1.150   8.928
Bimap-toTable               7.304  0.136   7.464
Bimap                       5.502  0.015   5.518
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.R’ [245s/259s]
 [246s/260s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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 ‘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-class1.1770.0601.248
AnnDbPkg-checker246.790 10.213261.821
AnnotationDb-class2.1060.0372.142
Bimap-direction10.012 0.16810.181
Bimap-envirAPI4.2200.4964.722
Bimap-keys3.1550.0313.187
Bimap-toTable7.3040.1367.464
Bimap5.5020.0155.518
BimapFiltering1.1280.0071.135
BimapFormatting3.4120.0123.424
GOColsAndKeytypes0.9820.0251.007
GOFrame7.2891.1508.928
GOTerms-class0.0050.0010.005
InparanoidColsAndKeytypes12.455 2.33417.188
KEGGFrame1.9990.0242.023
colsAndKeytypes1.3190.0171.373
createSimpleBimap1.0360.0061.043
inpIDMapper0.0020.0000.002
makeGOGraph2.5500.0242.579
make_eg_to_go_map1.4380.0141.452
print.probetable8.0820.4368.521
toSQLStringSet0.0030.0000.002
unlist21.2160.0141.230