BioC 2.13: CHECK report for AnnotationForge on moscato1

Package: AnnotationForge

Version: 1.4.4

Command: rm -rf AnnotationForge.buildbin-libdir && mkdir AnnotationForge.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationForge.buildbin-libdir AnnotationForge_1.4.4.tar.gz >AnnotationForge-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=AnnotationForge.buildbin-libdir --install="check:AnnotationForge-install.out" --force-multiarch --no-vignettes --timings AnnotationForge_1.4.4.tar.gz && mv AnnotationForge.buildbin-libdir/* AnnotationForge.Rcheck/ && rmdir AnnotationForge.buildbin-libdir

StartedAt: 2014-04-05 02:10:05 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:13:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 223.8 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationForge.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/AnnotationForge.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationForge/DESCRIPTION' ... OK
* this is package 'AnnotationForge' version '1.4.4'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/ProbePkg-template/data/.dummy.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'AnnotationForge' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.3Mb
    extdata              3.3Mb
* 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' 'BiocGenerics' 'Biobase' '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
Namespaces in Imports field not imported from:
  'methods' 'utils'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'AnnotationDbi' 'methods' 'org.Hs.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.addEssentialMetadata' '.addMeta' '.createMetadataTables'
  '.makeARABIDOPSISCHIP_DB' '.makeBOVINECHIP_DB' '.makeCANINECHIP_DB'
  '.makeCHICKENCHIP_DB' '.makeECOLICHIP_DB' '.makeFLYCHIP_DB'
  '.makeGenesTable' '.makeHUMANCHIP_DB' '.makeMOUSECHIP_DB'
  '.makePIGCHIP_DB' '.makeRATCHIP_DB' '.makeRHESUSCHIP_DB'
  '.makeWORMCHIP_DB' '.makeXENOPUSCHIP_DB' '.makeYEASTCHIP_DB'
  '.makeZEBRAFISHCHIP_DB' 'popANOPHELESDB' 'popARABIDOPSISCHIPDB'
  'popARABIDOPSISDB' 'popBOVINECHIPDB' 'popBOVINEDB' 'popCANINECHIPDB'
  'popCANINEDB' 'popCHICKENCHIPDB' 'popCHICKENDB' 'popCHIMPDB'
  'popECOLICHIPDB' 'popECOLIDB' 'popFLYCHIPDB' 'popFLYDB'
  'popHUMANCHIPDB' 'popHUMANDB' 'popMALARIADB' 'popMOUSECHIPDB'
  'popMOUSEDB' 'popPIGCHIPDB' 'popPIGDB' 'popRATCHIPDB' 'popRATDB'
  'popRHESUSCHIPDB' 'popRHESUSDB' 'popWORMCHIPDB' 'popWORMDB'
  'popXENOPUSCHIPDB' 'popXENOPUSDB' 'popYEASTCHIPDB' 'popYEASTDB'
  'popZEBRAFISHCHIPDB' 'popZEBRAFISHDB'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.getSubNodeInfo: no visible global function definition for 'Stop'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'MakingNewAnnotationPackages.Rnw', 'SQLForge.Rnw',
  'makeProbePackage.Rnw', 'MakingNewOrganismPackages.Rmd'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [17s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 5.25   0.05    8.18
** running examples for arch 'x64' ... [14s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 4.48   0.03    7.57
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'AnnotationForge_unit_tests.R' [11s]
 [12s] OK
** running tests for arch 'x64'
  Running 'AnnotationForge_unit_tests.R' [10s]
 [10s] 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

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'AnnotationForge' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AnnotationForge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationForge' as AnnotationForge_1.4.4.zip
* DONE (AnnotationForge)

name	user	system	elapsed
AnnDbPkg-maker	0.43	0.01	0.44
available.db0pkgs	1.50	0.01	2.40
createSimpleBimap	0.22	0.03	0.25
generateSeqnames_db	0	0	0
getProbeDataAffy	0	0	0
getProbeData_1lq	0	0	0
makeOrgPackage	0	0	0
makeOrgPackageFromDataFrames	0.02	0.00	0.01
makeProbePackage	5.25	0.05	8.18
sqlForge-makeCHIPDB	0.16	0.00	0.15
sqlForge-popDB	0.01	0.00	0.01
sqlForge-wrapDBPackages	0	0	0

name	user	system	elapsed
AnnDbPkg-maker	0.41	0.02	0.42
available.db0pkgs	1.39	0.04	1.45
createSimpleBimap	0.14	0.02	0.16
generateSeqnames_db	0	0	0
getProbeDataAffy	0	0	0
getProbeData_1lq	0.02	0.00	0.02
makeOrgPackage	0	0	0
makeOrgPackageFromDataFrames	0.14	0.00	0.14
makeProbePackage	4.48	0.03	7.57
sqlForge-makeCHIPDB	0.02	0.00	0.02
sqlForge-popDB	0.03	0.00	0.03
sqlForge-wrapDBPackages	0.02	0.00	0.01