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BioC 3.4: CHECK report for AnnotationDbi on moscato1

This page was generated on 2016-09-16 03:42:05 -0700 (Fri, 16 Sep 2016).

Package 47/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationDbi 1.35.4
Bioconductor Package Maintainer
Snapshot Date: 2016-09-14 19:15:30 -0700 (Wed, 14 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi
Last Changed Rev: 119165 / Revision: 120967
Last Changed Date: 2016-07-06 02:58:16 -0700 (Wed, 06 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationDbi
Version: 1.35.4
Command: rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.35.4.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out && D:\biocbld\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_1.35.4.tar.gz
StartedAt: 2016-09-15 04:08:00 -0700 (Thu, 15 Sep 2016)
EndedAt: 2016-09-15 04:24:47 -0700 (Thu, 15 Sep 2016)
EllapsedTime: 1007.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AnnotationDbi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.35.4.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out  && D:\biocbld\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_1.35.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/AnnotationDbi.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.35.4'
* 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.
* 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          30.09   0.42  102.48
Bimap-direction            9.78   1.39   11.20
GOFrame                    5.19   0.70    9.19
Bimap                      4.90   0.77    5.70
print.probetable           5.29   0.06    5.35
InparanoidColsAndKeytypes  4.42   0.07  150.36
Bimap-toTable              4.12   0.09    9.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          36.77   0.35   37.11
Bimap-direction            9.17   1.37   10.56
Bimap                      5.38   0.97    6.35
GOFrame                    5.28   0.49    5.80
InparanoidColsAndKeytypes  5.41   0.21    5.63
print.probetable           5.42   0.05    5.48
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.


AnnotationDbi.Rcheck/00install.out:


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_1.35.4.zip
* DONE (AnnotationDbi)

AnnotationDbi.Rcheck/examples_i386/AnnotationDbi-Ex.timings:

nameusersystemelapsed
AnnDbObj-class0.400.010.42
AnnDbPkg-checker 30.09 0.42102.48
AnnotationDb-class0.600.050.81
Bimap-direction 9.78 1.3911.20
Bimap-envirAPI0.830.120.95
Bimap-keys1.790.242.03
Bimap-toTable4.120.099.98
Bimap4.900.775.70
BimapFiltering0.230.000.23
BimapFormatting0.390.000.39
GOColsAndKeytypes0.160.010.17
GOFrame5.190.709.19
GOTerms-class000
InparanoidColsAndKeytypes 4.42 0.07150.36
KEGGFrame0.220.000.21
colsAndKeytypes0.180.001.28
createSimpleBimap0.110.000.11
inpIDMapper000
makeGOGraph0.430.020.46
make_eg_to_go_map0.220.000.22
print.probetable5.290.065.35
toSQLStringSet000
unlist20.150.000.16

AnnotationDbi.Rcheck/examples_x64/AnnotationDbi-Ex.timings:

nameusersystemelapsed
AnnDbObj-class0.460.040.51
AnnDbPkg-checker36.77 0.3537.11
AnnotationDb-class0.700.030.73
Bimap-direction 9.17 1.3710.56
Bimap-envirAPI0.720.130.84
Bimap-keys1.980.232.22
Bimap-toTable4.230.004.23
Bimap5.380.976.35
BimapFiltering0.270.000.27
BimapFormatting0.50.00.5
GOColsAndKeytypes0.180.010.20
GOFrame5.280.495.80
GOTerms-class000
InparanoidColsAndKeytypes5.410.215.63
KEGGFrame0.230.000.24
colsAndKeytypes0.250.000.25
createSimpleBimap0.140.000.14
inpIDMapper000
makeGOGraph0.50.00.5
make_eg_to_go_map0.280.020.30
print.probetable5.420.055.48
toSQLStringSet000
unlist20.190.000.19