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BioC 2.12: CHECK report for LPE on petty

This page was generated on 2013-10-09 09:39:23 -0700 (Wed, 09 Oct 2013).

Package 372/671HostnameOS / ArchBUILDCHECKBUILD BIN
LPE 1.34.0
Nitin Jain
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/LPE
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  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: LPE
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LPE_1.34.0.tar.gz
StartedAt: 2013-10-08 22:57:24 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:58:16 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 51.4 seconds
RetCode: 0
Status:  OK 
CheckDir: LPE.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/LPE.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 'LPE/DESCRIPTION' ... OK
* this is package 'LPE' version '1.34.0'
* 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 'LPE' can be installed ... [2s/2s] OK
* 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' ... NOTE
The following files should probably not be installed:
  'isorot.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
resamp.adj 6.437  0.235   6.741
fdr.adjust 4.901  0.186   5.120
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/LPE.Rcheck/00check.log'
for details.

LPE.Rcheck/00install.out:

* installing *source* package 'LPE' ...
** 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 (LPE)

LPE.Rcheck/LPE-Ex.timings:

nameusersystemelapsed
am.trans0.0150.0010.015
baseOlig.error1.5060.1061.621
baseOlig.error.step10.5100.0370.547
baseOlig.error.step20.9330.0200.954
fdr.adjust4.9010.1865.120
fixbounds.predict.smooth.spline0.9450.0390.991
iqr0.0130.0020.015
lowess.normalize0.1160.0100.126
lpe2.0120.0352.096
mt.rawp2adjp1.5860.0311.723
n.genes.adaptive.int0.5910.0190.611
permute0.0190.0000.020
preprocess0.2920.0140.310
quan.norm0.0070.0020.009
quartile.normalize0.1010.0150.116
resamp.adj6.4370.2356.741