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BioC 3.5: CHECK report for OmicsMarkeR on veracruz2

This page was generated on 2017-08-16 13:33:06 -0400 (Wed, 16 Aug 2017).

Package 921/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsMarkeR 1.8.0
Charles E. Determan Jr.
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/OmicsMarkeR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: OmicsMarkeR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
StartedAt: 2017-08-16 06:06:36 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:10:50 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 254.5 seconds
RetCode: 0
Status:  OK 
CheckDir: OmicsMarkeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.8.0’
* 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 ‘OmicsMarkeR’ can be installed ... 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
feature.table       14.590  0.282  15.818
perm.class          13.025  0.275  13.730
fs.stability        12.358  0.285  13.772
perm.features       11.968  0.373  12.742
predictNewClasses   11.708  0.332  12.558
performance.metrics 11.318  0.284  12.526
fit.only.model       4.841  0.155   6.168
* 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: OK

OmicsMarkeR.Rcheck/00install.out:

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

OmicsMarkeR.Rcheck/OmicsMarkeR-Ex.timings:

nameusersystemelapsed
RPT0.1890.0010.198
aggregation0.0060.0010.006
canberra0.0010.0000.002
canberra_stability0.0020.0010.003
create.corr.matrix0.0330.0010.042
create.discr.matrix0.1190.0140.135
create.random.matrix0.0070.0010.008
denovo.grid0.0120.0020.014
feature.table14.590 0.28215.818
fit.only.model4.8410.1556.168
fs.ensembl.stability0.0010.0000.001
fs.stability12.358 0.28513.772
jaccard0.0010.0000.002
kuncheva0.0020.0000.002
modelList0.0020.0010.002
ochiai0.0010.0000.002
pairwise.model.stability0.0330.0000.035
pairwise.stability0.0070.0010.007
params0.0030.0000.003
performance.metrics11.318 0.28412.526
perm.class13.025 0.27513.730
perm.features11.968 0.37312.742
pof0.0020.0000.001
predictNewClasses11.708 0.33212.558
sorensen0.0010.0000.001
spearman0.0010.0000.001
svmrfeFeatureRanking0.4150.0010.423
svmrfeFeatureRankingForMulticlass0.1680.0010.171