BioC 3.5: CHECK report for AnnotationDbi on toluca2

Package: AnnotationDbi

Version: 1.37.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.37.4.tar.gz

StartedAt: 2017-04-23 00:21:12 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:25:41 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 269.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationDbi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.37.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationDbi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.37.4’
* 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 sizes of PDF files under ‘inst/doc’ ... 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          36.273  0.877  37.476
InparanoidColsAndKeytypes  6.281  0.772   8.005
Bimap-direction            5.494  0.728   6.225
print.probetable           5.185  0.283   5.471
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
AnnDbObj-class	0.904	0.031	0.943
AnnDbPkg-checker	36.273	0.877	37.476
AnnotationDb-class	1.128	0.013	1.142
Bimap-direction	5.494	0.728	6.225
Bimap-envirAPI	0.774	0.313	1.087
Bimap-keys	1.421	0.180	1.601
Bimap-toTable	2.929	0.076	3.012
Bimap	3.069	0.397	3.468
BimapFiltering	0.217	0.004	0.221
BimapFormatting	0.453	0.011	0.463
GOColsAndKeytypes	0.214	0.007	0.221
GOFrame	2.759	0.682	3.443
GOTerms-class	0.002	0.000	0.001
InparanoidColsAndKeytypes	6.281	0.772	8.005
KEGGFrame	0.149	0.001	0.150
colsAndKeytypes	0.213	0.003	0.216
createSimpleBimap	0.116	0.002	0.118
inpIDMapper	0.002	0.000	0.002
makeGOGraph	0.452	0.011	0.464
make_eg_to_go_map	0.221	0.005	0.226
print.probetable	5.185	0.283	5.471
toSQLStringSet	0.001	0.000	0.001
unlist2	0.683	0.005	0.690