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BioC 3.2: CHECK report for lpNet on oaxaca

This page was generated on 2016-04-23 10:26:29 -0700 (Sat, 23 Apr 2016).

Package 576/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lpNet 2.2.0
Lars Kaderali
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/lpNet
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: lpNet
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lpNet_2.2.0.tar.gz
StartedAt: 2016-04-23 01:38:27 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:39:24 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 56.5 seconds
RetCode: 0
Status:  OK 
CheckDir: lpNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lpNet_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/lpNet.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.2.0’
* 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runitCalcActivation.R’ [0s/0s]
  Running ‘runitCalcPredictionKfoldCV.R’ [0s/0s]
  Running ‘runitCalcPredictionKfoldCV_timeSeries.R’ [0s/0s]
  Running ‘runitCalcPredictionLOOCV.R’ [0s/0s]
  Running ‘runitCalcPredictionLOOCV_timeSeries.R’ [0s/0s]
  Running ‘runitCalcRangeLambda.R’ [0s/0s]
  Running ‘runitDoILP.R’ [0s/0s]
  Running ‘runitDoILP_timeSeries.R’ [0s/0s]
  Running ‘runitGenerateTimeSeriesNetStates.R’ [0s/0s]
  Running ‘runitGetAdja.R’ [0s/0s]
  Running ‘runitGetBaseline.R’ [0s/0s]
  Running ‘runitGetEdgeAnnot.R’ [0s/0s]
  Running ‘runitGetObsMat.R’ [0s/0s]
  Running ‘runitGetSampleAdja.R’ [0s/0s]
  Running ‘runitGetSampleAdjaMAD.R’ [0s/0s]
  Running ‘runitKfoldCV.R’ [0s/0s]
  Running ‘runitKfoldCV_timeSeries.R’ [0s/0s]
  Running ‘runitLOOCV.R’ [0s/0s]
  Running ‘runitLOOCV_timeSeries.R’ [0s/0s]
 [7s/7s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘KEGGgraph’
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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
CV0.6660.0210.855
calcActivation0.0060.0000.006
calcPrediction0.0040.0000.005
calcRangeLambda0.0010.0000.001
doILP0.0040.0000.005
generateTimeSeriesNetStates0.0030.0010.004
getAdja0.0060.0000.007
getBaseline0.0060.0000.007
getEdgeAnnot0.0010.0000.001
getObsMat0.0060.0000.007
getSampleAdja0.0030.0010.004
summarizeRepl0.0130.0010.037