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BioC 3.0: CHECK report for lpNet on oaxaca

This page was generated on 2015-04-10 10:06:53 -0700 (Fri, 10 Apr 2015).

Package 493/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lpNet 1.6.0
Bettina Knapp
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/lpNet
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: lpNet
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lpNet_1.6.0.tar.gz
StartedAt: 2015-04-10 00:53:03 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:54:17 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 74.2 seconds
RetCode: 0
Status:  OK 
CheckDir: lpNet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lpNet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/lpNet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.6.0’
* 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 ... [6s/7s] 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/5s] 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
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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
CV1.2970.0251.407
calcActivation0.0050.0000.006
calcPrediction0.010.000.01
calcRangeLambda0.0020.0010.001
doILP0.0070.0000.007
getAdja0.0060.0010.006
getEdgeAnnot0.0010.0000.000
getObsMat0.0040.0000.005
getSampleAdja0.0040.0000.005
summarizeRepl0.0130.0010.034