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BioC 2.12: CHECK report for BioSeqClass on petty

This page was generated on 2013-10-09 09:39:49 -0700 (Wed, 09 Oct 2013).

Package 80/671HostnameOS / ArchBUILDCHECKBUILD BIN
BioSeqClass 1.18.0
Li Hong
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/BioSeqClass
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  WARNINGS 
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: BioSeqClass
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioSeqClass_1.18.0.tar.gz
StartedAt: 2013-10-08 21:44:47 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:50:17 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 330.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BioSeqClass.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioSeqClass.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 'BioSeqClass/DESCRIPTION' ... OK
* this is package 'BioSeqClass' version '1.18.0'
* 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 'BioSeqClass' can be installed ... [23s/23s] OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    scripts   3.0Mb
* 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 ... [40s/39s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
classify 14.639  0.578  14.425
* 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.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BioSeqClass.Rcheck/00check.log'
for details.

BioSeqClass.Rcheck/00install.out:

* installing *source* package 'BioSeqClass' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BioSeqClass)

BioSeqClass.Rcheck/BioSeqClass-Ex.timings:

nameusersystemelapsed
basic2.7530.0842.868
classify14.639 0.57814.425
featureAAindex0.0120.0070.021
featureBDNAVIDEO0.0110.0070.019
featureBinary0.0030.0040.008
featureCKSAAP0.0030.0040.008
featureCTD0.0040.0050.010
featureDIPRODB0.0040.0040.009
featureDOMAIN0.0020.0040.007
featureEvaluate0.0610.0250.086
featureFragmentComposition0.0120.0070.018
featureGapPairComposition0.0040.0060.009
featureHydro0.0040.0050.011
featurePSSM0.0120.0070.017
featurePseudoAAComp0.0030.0040.008
featureSSC0.0080.0080.016
hr0.0180.0130.031
model2.6790.0942.822
performance2.5150.0792.604
selectFFS1.4660.0401.510