BioC 2.12: CHECK report for AnnotationForge on moscato2

Package: AnnotationForge

Version: 1.2.2

Command: rm -rf AnnotationForge.buildbin-libdir && mkdir AnnotationForge.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationForge.buildbin-libdir AnnotationForge_1.2.2.tar.gz >AnnotationForge-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=AnnotationForge.buildbin-libdir --install="check:AnnotationForge-install.out" --force-multiarch --no-vignettes --timings AnnotationForge_1.2.2.tar.gz && mv AnnotationForge.buildbin-libdir/* AnnotationForge.Rcheck/ && rmdir AnnotationForge.buildbin-libdir

StartedAt: 2013-10-09 00:58:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:01:59 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 204.3 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationForge.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/AnnotationForge.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.2.2'
* 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  5.6Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.2Mb
    extdata              3.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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 examples ...
** running examples for arch 'i386' ... [16s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 6.28   0.03   10.64
** running examples for arch 'x64' ... [18s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 7.88   0.09   11.28
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'Biostrings'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.12-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_1.2.2.zip
* DONE (AnnotationForge)