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BioC 3.5: CHECK report for OmicsMarkeR on tokay2

This page was generated on 2017-08-16 13:24:25 -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: rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.8.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
StartedAt: 2017-08-16 01:42:15 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:49:24 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 428.5 seconds
RetCode: 0
Status:  OK  
CheckDir: OmicsMarkeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.8.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/OmicsMarkeR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
feature.table       12.00   0.05   12.22
perm.class          10.49   0.00   10.49
fs.stability         9.93   0.01    9.95
predictNewClasses    9.49   0.07    9.56
performance.metrics  9.00   0.06    9.06
perm.features        8.46   0.07    8.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
fs.stability        13.78   0.00   14.00
feature.table       13.52   0.00   13.51
perm.class          12.94   0.02   13.05
performance.metrics 12.58   0.00   12.59
predictNewClasses   11.64   0.03   11.88
perm.features       10.93   0.04   10.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'OmicsMarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.8.0.zip
* DONE (OmicsMarkeR)

OmicsMarkeR.Rcheck/examples_i386/OmicsMarkeR-Ex.timings:

nameusersystemelapsed
RPT0.030.000.24
aggregation0.020.000.01
canberra000
canberra_stability000
create.corr.matrix0.070.000.06
create.discr.matrix0.150.000.16
create.random.matrix000
denovo.grid000
feature.table12.00 0.0512.22
fit.only.model3.840.053.89
fs.ensembl.stability000
fs.stability9.930.019.95
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.020.000.02
pairwise.stability0.010.000.01
params000
performance.metrics9.000.069.06
perm.class10.49 0.0010.49
perm.features8.460.078.55
pof000
predictNewClasses9.490.079.56
sorensen000
spearman0.010.000.01
svmrfeFeatureRanking0.270.000.27
svmrfeFeatureRankingForMulticlass0.120.000.12

OmicsMarkeR.Rcheck/examples_x64/OmicsMarkeR-Ex.timings:

nameusersystemelapsed
RPT0.030.000.04
aggregation000
canberra000
canberra_stability000
create.corr.matrix0.030.000.03
create.discr.matrix0.110.000.11
create.random.matrix0.010.000.02
denovo.grid000
feature.table13.52 0.0013.51
fit.only.model4.560.024.58
fs.ensembl.stability000
fs.stability13.78 0.0014.00
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.020.000.01
pairwise.stability000
params000
performance.metrics12.58 0.0012.59
perm.class12.94 0.0213.05
perm.features10.93 0.0410.98
pof000
predictNewClasses11.64 0.0311.88
sorensen000
spearman0.010.000.01
svmrfeFeatureRanking0.560.000.56
svmrfeFeatureRankingForMulticlass0.140.000.16