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BioC 3.5: CHECK report for AnnotationDbi on malbec2

This page was generated on 2017-08-16 13:12:46 -0400 (Wed, 16 Aug 2017).

Package 48/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationDbi 1.38.2
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AnnotationDbi
Last Changed Rev: 131573 / Revision: 131943
Last Changed Date: 2017-07-25 17:39:19 -0400 (Tue, 25 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationDbi
Version: 1.38.2
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.38.2.tar.gz
StartedAt: 2017-08-15 21:08:27 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:12:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 216.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AnnotationDbi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.38.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AnnotationDbi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.38.2’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  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’ ‘IRanges’ ‘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’ ‘KEGG.db’ ‘RSQLite’ ‘graph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.selectInp8: no visible global function definition for ‘.resort’
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’
Undefined global functions or variables:
  .resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL
  makeAnnDbMapSeeds pkgName
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
AnnDbPkg-checker          30.396  0.504  40.465
InparanoidColsAndKeytypes  4.928  0.176   6.949
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.


AnnotationDbi.Rcheck/00install.out:

* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘initialize’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘toString’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘show’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘rev’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
Creating a new generic function for ‘packageName’ 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-class0.7320.0080.746
AnnDbPkg-checker30.396 0.50440.465
AnnotationDb-class0.9000.0201.013
Bimap-direction3.8680.3884.259
Bimap-envirAPI0.5440.1480.694
Bimap-keys0.9760.0681.044
Bimap-toTable2.8880.0323.201
Bimap1.9960.1882.186
BimapFiltering0.2120.0000.214
BimapFormatting0.4120.0000.414
GOColsAndKeytypes0.240.000.24
GOFrame1.8960.1482.352
GOTerms-class0.0040.0000.002
InparanoidColsAndKeytypes4.9280.1766.949
KEGGFrame0.1960.0000.196
colsAndKeytypes0.3440.0080.409
createSimpleBimap0.1800.0000.177
inpIDMapper0.0000.0000.001
makeGOGraph0.4800.0120.506
make_eg_to_go_map0.2440.0000.244
print.probetable4.5520.1524.708
toSQLStringSet0.0000.0000.001
unlist20.2160.0040.220