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BioC 2.12: CHECK report for annaffy on petty

This page was generated on 2013-10-09 09:39:22 -0700 (Wed, 09 Oct 2013).

Package 33/671HostnameOS / ArchBUILDCHECKBUILD BIN
annaffy 1.32.0
Colin A. Smith
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/annaffy
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

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

Command output

* 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.

annaffy.Rcheck/00install.out:

* 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)

annaffy.Rcheck/annaffy-Ex.timings:

nameusersystemelapsed
aafChromLoc0.8940.0430.938
aafChromosome0.1560.0120.168
aafCytoband0.1730.0140.199
aafDescription0.1360.0110.148
aafGO0.7190.0790.801
aafGenBank0.1490.0160.209
aafLocusLink0.1510.0100.161
aafPathway1.8800.0341.938
aafProbe0.1110.0080.120
aafPubMed0.3420.0510.751
aafSearchText2.3970.0392.452
aafSymbol0.1450.0110.156
aafUniGene0.1570.0110.179
is.annpkg 8.733 0.76910.011