BioC 2.12: CHECK report for annaffy on petty

Package: annaffy

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annaffy_1.32.0.tar.gz

StartedAt: 2013-10-08 21:32:25 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:35:42 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 196.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: annaffy.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/annaffy.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 'annaffy/DESCRIPTION' ... OK
* this is package 'annaffy' version '1.32.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'annaffy' can be installed ... [17s/18s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/annaffy.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [26s/27s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
is.annpkg 8.733  0.769  10.011
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/annaffy.Rcheck/00check.log'
for details.

* installing *source* package 'annaffy' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
Creating a generic function for 'colnames<-' from package 'base' in package 'annaffy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (annaffy)

name	user	system	elapsed
aafChromLoc	0.894	0.043	0.938
aafChromosome	0.156	0.012	0.168
aafCytoband	0.173	0.014	0.199
aafDescription	0.136	0.011	0.148
aafGO	0.719	0.079	0.801
aafGenBank	0.149	0.016	0.209
aafLocusLink	0.151	0.010	0.161
aafPathway	1.880	0.034	1.938
aafProbe	0.111	0.008	0.120
aafPubMed	0.342	0.051	0.751
aafSearchText	2.397	0.039	2.452
aafSymbol	0.145	0.011	0.156
aafUniGene	0.157	0.011	0.179
is.annpkg	8.733	0.769	10.011