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BioC 2.13: CHECK report for lpNet on zin1

This page was generated on 2014-04-05 09:48:34 -0700 (Sat, 05 Apr 2014).

Package 405/750HostnameOS / ArchBUILDCHECKBUILD BIN
lpNet 1.2.0
Bettina Knapp
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/lpNet
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: lpNet
Version: 1.2.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings lpNet_1.2.0.tar.gz
StartedAt: 2014-04-05 02:11:10 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:11:56 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 45.9 seconds
RetCode: 0
Status:  OK 
CheckDir: lpNet.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/lpNet.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lpNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lpNet’ version ‘1.2.0’
* 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 ‘lpNet’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... NOTE
prepare_Rd: CV.Rd:79-81: Dropping empty section \details
prepare_Rd: CV.Rd:93-95: Dropping empty section \note
prepare_Rd: CV.Rd:90-92: Dropping empty section \author
prepare_Rd: CV.Rd:87-89: Dropping empty section \references
prepare_Rd: CV.Rd:99-101: Dropping empty section \seealso
prepare_Rd: calcActivation.Rd:28-30: Dropping empty section \details
prepare_Rd: calcActivation.Rd:40-42: Dropping empty section \note
prepare_Rd: calcActivation.Rd:37-39: Dropping empty section \author
prepare_Rd: calcActivation.Rd:34-36: Dropping empty section \references
prepare_Rd: calcActivation.Rd:46-48: Dropping empty section \seealso
prepare_Rd: calcPrediction.Rd:59-61: Dropping empty section \details
prepare_Rd: calcPrediction.Rd:71-73: Dropping empty section \note
prepare_Rd: calcPrediction.Rd:68-70: Dropping empty section \author
prepare_Rd: calcPrediction.Rd:65-67: Dropping empty section \references
prepare_Rd: calcRangeLambda.Rd:25-27: Dropping empty section \details
prepare_Rd: calcRangeLambda.Rd:37-39: Dropping empty section \note
prepare_Rd: calcRangeLambda.Rd:34-36: Dropping empty section \author
prepare_Rd: calcRangeLambda.Rd:31-33: Dropping empty section \references
prepare_Rd: calcRangeLambda.Rd:43-45: Dropping empty section \seealso
prepare_Rd: doILP.Rd:53-55: Dropping empty section \details
prepare_Rd: doILP.Rd:65-67: Dropping empty section \note
prepare_Rd: doILP.Rd:62-64: Dropping empty section \author
prepare_Rd: doILP.Rd:59-61: Dropping empty section \references
prepare_Rd: doILP.Rd:71-73: Dropping empty section \seealso
prepare_Rd: getAdja.Rd:22-24: Dropping empty section \details
prepare_Rd: getAdja.Rd:34-36: Dropping empty section \note
prepare_Rd: getAdja.Rd:31-33: Dropping empty section \author
prepare_Rd: getAdja.Rd:28-30: Dropping empty section \references
prepare_Rd: getEdgeAnnot.Rd:22-24: Dropping empty section \details
prepare_Rd: getEdgeAnnot.Rd:34-36: Dropping empty section \note
prepare_Rd: getEdgeAnnot.Rd:31-33: Dropping empty section \author
prepare_Rd: getEdgeAnnot.Rd:28-30: Dropping empty section \references
prepare_Rd: getEdgeAnnot.Rd:40-42: Dropping empty section \seealso
prepare_Rd: getObsMat.Rd:31-33: Dropping empty section \details
prepare_Rd: getObsMat.Rd:43-45: Dropping empty section \note
prepare_Rd: getObsMat.Rd:40-42: Dropping empty section \author
prepare_Rd: getObsMat.Rd:37-39: Dropping empty section \references
prepare_Rd: getSampleAdja.Rd:37-39: Dropping empty section \details
prepare_Rd: getSampleAdja.Rd:49-51: Dropping empty section \note
prepare_Rd: getSampleAdja.Rd:46-48: Dropping empty section \author
prepare_Rd: getSampleAdja.Rd:43-45: Dropping empty section \references
prepare_Rd: lpNet-package.Rd:22-25: Dropping empty section \author
prepare_Rd: lpNet-package.Rd:34-37: Dropping empty section \seealso
prepare_Rd: lpNet-package.Rd:38-40: Dropping empty section \examples
prepare_Rd: summarizeRepl.Rd:22-24: Dropping empty section \details
prepare_Rd: summarizeRepl.Rd:34-36: Dropping empty section \note
prepare_Rd: summarizeRepl.Rd:31-33: Dropping empty section \author
prepare_Rd: summarizeRepl.Rd:28-30: Dropping empty section \references
prepare_Rd: summarizeRepl.Rd:40-41: Dropping empty section \seealso
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘vignette_lpNet.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/4s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/lpNet.Rcheck/00check.log’
for details.

lpNet.Rcheck/00install.out:

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

lpNet.Rcheck/lpNet-Ex.timings:

nameusersystemelapsed
CV1.3320.0281.359
calcActivation0.0120.0000.010
calcPrediction0.0160.0000.016
calcRangeLambda0.0040.0000.004
doILP0.0080.0040.013
getAdja0.0040.0080.012
getEdgeAnnot0.0040.0000.002
getObsMat0.0120.0000.012
getSampleAdja0.0040.0040.008
summarizeRepl0.0120.0000.021