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BioC 3.5: CHECK report for MCbiclust on oaxaca

This page was generated on 2017-03-04 16:53:52 -0500 (Sat, 04 Mar 2017).

Package 742/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MCbiclust 0.99.44
Robert Bentham
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MCbiclust
Last Changed Rev: 127045 / Revision: 127142
Last Changed Date: 2017-03-01 05:47:28 -0500 (Wed, 01 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  TIMEOUT  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  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 

Summary

Package: MCbiclust
Version: 0.99.44
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MCbiclust_0.99.44.tar.gz
StartedAt: 2017-03-04 05:21:02 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 05:27:39 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 397.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MCbiclust.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 MCbiclust_0.99.44.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MCbiclust.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MCbiclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MCbiclust’ version ‘0.99.44’
* 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 ‘MCbiclust’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    5.6Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SilhouetteClustGroups 34.965  0.219  53.474
CVPlot                21.206  0.220  21.429
ThresholdBic           8.644  0.146  28.190
SampleSort             7.293  0.117  22.625
CVEval                 6.810  0.149  22.513
GOEnrichmentAnalysis   6.548  0.042   6.591
PC1VecFun              6.430  0.099  21.150
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MCbiclust.Rcheck/00check.log’
for details.


MCbiclust.Rcheck/00install.out:

* installing *source* package ‘MCbiclust’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MCbiclust)

MCbiclust.Rcheck/MCbiclust-Ex.timings:

nameusersystemelapsed
CVEval 6.810 0.14922.513
CVPlot21.206 0.22021.429
CorScoreCalc3.1210.0303.153
FindSeed2.9610.0413.004
GOEnrichmentAnalysis6.5480.0426.591
HclustGenesHiCor3.0430.0523.097
PC1VecFun 6.430 0.09921.150
SampleSort 7.293 0.11722.625
SilhouetteClustGroups34.965 0.21953.474
ThresholdBic 8.644 0.14628.190