BioC 3.2: CHECK report for AnnotationDbi on moscato1

Package: AnnotationDbi

Version: 1.32.3

Command: rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.32.3.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.32.3.tar.gz

StartedAt: 2016-04-22 23:31:18 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-23 00:04:36 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 1997.9 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.32.3.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.32.3.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/AnnotationDbi.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.32.3'
* 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.
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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [14m] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          36.05   0.43  498.12
Bimap-direction           10.95   1.76   15.37
print.probetable           7.21   0.08    7.29
Bimap                      6.28   0.72    7.02
InparanoidColsAndKeytypes  6.66   0.09  172.45
GOFrame                    5.90   0.72   41.72
Bimap-toTable              5.04   0.08   78.67
** running examples for arch 'x64' ... [111s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          46.55   0.33   46.88
Bimap-direction           10.59   1.96   12.57
InparanoidColsAndKeytypes  8.84   0.25    9.10
GOFrame                    7.84   0.77    9.46
print.probetable           7.72   0.11    7.83
Bimap                      6.00   0.87    6.88
* 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' [11m]
 [11m] OK
** running tests for arch 'x64' ...
  Running 'AnnotationDbi_unit_tests.R' [166s]
 [166s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'AnnotationDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationDbi' as AnnotationDbi_1.32.3.zip
* DONE (AnnotationDbi)

name	user	system	elapsed
AnnDbObj-class	0.56	0.00	4.21
AnnDbPkg-checker	36.05	0.43	498.12
AnnotationDb-class	0.70	0.02	1.82
Bimap-direction	10.95	1.76	15.37
Bimap-envirAPI	0.76	0.11	0.87
Bimap-keys	1.94	0.20	2.14
Bimap-toTable	5.04	0.08	78.67
Bimap	6.28	0.72	7.02
BimapFiltering	0.38	0.02	1.51
BimapFormatting	0.65	0.00	0.66
GOColsAndKeytypes	0.30	0.01	0.31
GOFrame	5.90	0.72	41.72
GOTerms-class	0	0	0
InparanoidColsAndKeytypes	6.66	0.09	172.45
KEGGFrame	0.22	0.00	0.22
colsAndKeytypes	0.19	0.02	0.28
createSimpleBimap	0.12	0.00	0.13
inpIDMapper	0	0	0
makeGOGraph	0.64	0.03	0.68
make_eg_to_go_map	0.23	0.00	0.23
print.probetable	7.21	0.08	7.29
toSQLStringSet	0	0	0
unlist2	0.28	0.00	0.28

name	user	system	elapsed
AnnDbObj-class	0.97	0.03	0.99
AnnDbPkg-checker	46.55	0.33	46.88
AnnotationDb-class	0.84	0.02	0.86
Bimap-direction	10.59	1.96	12.57
Bimap-envirAPI	0.67	0.13	0.79
Bimap-keys	1.94	0.26	2.20
Bimap-toTable	4.82	0.11	4.93
Bimap	6.00	0.87	6.88
BimapFiltering	0.35	0.00	0.34
BimapFormatting	0.60	0.00	0.59
GOColsAndKeytypes	0.31	0.03	0.34
GOFrame	7.84	0.77	9.46
GOTerms-class	0.02	0.00	0.01
InparanoidColsAndKeytypes	8.84	0.25	9.10
KEGGFrame	0.33	0.01	0.34
colsAndKeytypes	0.38	0.00	0.37
createSimpleBimap	0.17	0.04	0.21
inpIDMapper	0	0	0
makeGOGraph	0.76	0.01	0.78
make_eg_to_go_map	0.36	0.00	0.36
print.probetable	7.72	0.11	7.83
toSQLStringSet	0.01	0.00	0.02
unlist2	0.29	0.00	0.28