BioC 3.4: CHECK report for AnnotationDbi on tokay1

Package: AnnotationDbi

Version: 1.36.2

Command: rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.36.2.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.36.2.tar.gz

StartedAt: 2017-04-14 20:57:40 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:11:27 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 826.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationDbi.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.36.2.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.36.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/AnnotationDbi.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.36.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          30.20   0.63  116.29
Bimap-direction            6.38   1.34    7.72
print.probetable           5.53   0.23    5.76
InparanoidColsAndKeytypes  3.87   0.07  127.81
Bimap-toTable              3.61   0.11    6.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          34.16   0.41   34.77
Bimap-direction            5.72   1.31    7.03
InparanoidColsAndKeytypes  5.57   0.14    5.71
* checking for unstated dependencies in 'tests' ... WARNING
'library' or 'require' call not declared from: 'org.testing.db'
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationDbi_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'AnnotationDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationDbi' as AnnotationDbi_1.36.2.zip
* DONE (AnnotationDbi)

name	user	system	elapsed
AnnDbObj-class	0.41	0.00	0.41
AnnDbPkg-checker	30.20	0.63	116.29
AnnotationDb-class	1.01	0.00	1.27
Bimap-direction	6.38	1.34	7.72
Bimap-envirAPI	0.64	0.18	0.81
Bimap-keys	1.47	0.32	1.79
Bimap-toTable	3.61	0.11	6.40
Bimap	3.15	0.67	3.82
BimapFiltering	0.25	0.02	0.27
BimapFormatting	0.46	0.02	0.47
GOColsAndKeytypes	0.20	0.01	0.22
GOFrame	2.37	0.78	3.72
GOTerms-class	0	0	0
InparanoidColsAndKeytypes	3.87	0.07	127.81
KEGGFrame	0.17	0.00	0.17
colsAndKeytypes	0.24	0.00	0.41
createSimpleBimap	0.14	0.00	0.14
inpIDMapper	0	0	0
makeGOGraph	0.56	0.02	0.58
make_eg_to_go_map	0.24	0.03	0.27
print.probetable	5.53	0.23	5.76
toSQLStringSet	0	0	0
unlist2	0.22	0.00	0.22

name	user	system	elapsed
AnnDbObj-class	0.44	0.02	0.46
AnnDbPkg-checker	34.16	0.41	34.77
AnnotationDb-class	1.00	0.01	1.02
Bimap-direction	5.72	1.31	7.03
Bimap-envirAPI	0.63	0.18	0.80
Bimap-keys	1.73	0.34	2.08
Bimap-toTable	2.92	0.14	3.08
Bimap	2.70	0.61	3.31
BimapFiltering	0.27	0.00	0.27
BimapFormatting	0.48	0.00	0.48
GOColsAndKeytypes	0.28	0.03	0.31
GOFrame	2.54	0.75	3.29
GOTerms-class	0	0	0
InparanoidColsAndKeytypes	5.57	0.14	5.71
KEGGFrame	0.18	0.02	0.19
colsAndKeytypes	0.23	0.01	0.25
createSimpleBimap	0.16	0.00	0.16
inpIDMapper	0	0	0
makeGOGraph	0.48	0.00	0.48
make_eg_to_go_map	0.22	0.00	0.22
print.probetable	4.16	0.13	4.28
toSQLStringSet	0	0	0
unlist2	0.21	0.00	0.22