BioC 2.12: CHECK report for AnnotationForge on petty

Package: AnnotationForge

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationForge_1.2.2.tar.gz

StartedAt: 2013-10-08 21:33:39 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:37:01 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 202.5 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationForge.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AnnotationForge.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'AnnotationForge' can be installed ... [16s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.3Mb
    extdata              3.1Mb
* 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/22s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
makeProbePackage 12.552  0.299  13.049
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.

* 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
* DONE (AnnotationForge)

name	user	system	elapsed
AnnDbPkg-maker	0.093	0.015	0.110
available.db0pkgs	0.216	0.011	0.328
createSimpleBimap	0.296	0.015	0.311
generateSeqnames_db	0.013	0.000	0.014
getProbeDataAffy	0.017	0.000	0.018
getProbeData_1lq	0.015	0.000	0.016
makeOrgPackage	0.030	0.001	0.031
makeProbePackage	12.552	0.299	13.049
sqlForge-makeCHIPDB	0.032	0.006	0.037
sqlForge-popDB	0.095	0.013	0.111
sqlForge-wrapDBPackages	0.035	0.004	0.039