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BioC 3.5: CHECK report for OmicsMarkeR on malbec2

This page was generated on 2017-08-16 13:16:34 -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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
StartedAt: 2017-08-16 01:04:04 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:07:21 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 197.6 seconds
RetCode: 0
Status:  OK 
CheckDir: OmicsMarkeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/OmicsMarkeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 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       11.596  0.012  11.901
perm.class          10.328  0.000  10.336
fs.stability         9.036  0.000   9.063
perm.features        8.868  0.012   8.887
predictNewClasses    8.684  0.008   8.698
performance.metrics  8.636  0.008   8.652
* 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
RPT0.0240.0040.036
aggregation0.0080.0000.007
canberra0.0040.0000.003
canberra_stability0.0040.0000.002
create.corr.matrix0.0440.0000.042
create.discr.matrix0.1240.0000.130
create.random.matrix0.0040.0000.004
denovo.grid0.0120.0000.009
feature.table11.596 0.01211.901
fit.only.model3.5560.0043.558
fs.ensembl.stability0.0040.0000.000
fs.stability9.0360.0009.063
jaccard0.0000.0000.002
kuncheva0.0000.0000.001
modelList0.0000.0000.001
ochiai0.0000.0000.001
pairwise.model.stability0.0200.0000.021
pairwise.stability0.0080.0000.005
params0.0000.0000.002
performance.metrics8.6360.0088.652
perm.class10.328 0.00010.336
perm.features8.8680.0128.887
pof0.0040.0000.001
predictNewClasses8.6840.0088.698
sorensen0.0000.0000.001
spearman0.0040.0000.000
svmrfeFeatureRanking0.2880.0000.290
svmrfeFeatureRankingForMulticlass0.1360.0000.134