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BioC 3.5: CHECK report for coseq on tokay2

This page was generated on 2017-08-16 13:26:33 -0400 (Wed, 16 Aug 2017).

Package 284/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coseq 1.0.1
Andrea Rau
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/coseq
Last Changed Rev: 129183 / Revision: 131943
Last Changed Date: 2017-04-26 05:06:31 -0400 (Wed, 26 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: coseq
Version: 1.0.1
Command: rm -rf coseq.buildbin-libdir coseq.Rcheck && mkdir coseq.buildbin-libdir coseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coseq.buildbin-libdir coseq_1.0.1.tar.gz >coseq.Rcheck\00install.out 2>&1 && cp coseq.Rcheck\00install.out coseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coseq.buildbin-libdir --install="check:coseq-install.out" --force-multiarch --no-vignettes --timings coseq_1.0.1.tar.gz
StartedAt: 2017-08-15 22:59:11 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:05:36 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 385.0 seconds
RetCode: 0
Status:  OK  
CheckDir: coseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf coseq.buildbin-libdir coseq.Rcheck && mkdir coseq.buildbin-libdir coseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coseq.buildbin-libdir coseq_1.0.1.tar.gz >coseq.Rcheck\00install.out 2>&1 && cp coseq.Rcheck\00install.out coseq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coseq.buildbin-libdir --install="check:coseq-install.out" --force-multiarch --no-vignettes --timings coseq_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/coseq.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 'coseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coseq' version '1.0.1'
* 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 'coseq' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
compareARI 8.22   0.03    8.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
compareARI 8.91      0     8.9
* 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

coseq.Rcheck/00install.out:


install for i386

* installing *source* package 'coseq' ...
** R
** data
** 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 'coseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coseq' as coseq_1.0.1.zip
* DONE (coseq)

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

nameusersystemelapsed
NormMixClus1.030.051.08
NormMixClusK0.810.000.81
NormMixParam0.220.000.22
clusterEntropy000
clusterInertia0.670.010.69
compareARI8.220.038.25
compareICL4.920.085.00
coseq-package3.330.023.34
coseq3.970.013.99
coseqHelpers4.230.024.25
coseqRun1.20.01.2
kmeansProbaPost0.050.000.05
matchContTable000
plot3.630.003.62
summary3.680.003.69
transformRNAseq000

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

nameusersystemelapsed
NormMixClus1.380.001.40
NormMixClusK0.730.000.74
NormMixParam0.140.000.15
clusterEntropy000
clusterInertia0.610.010.63
compareARI8.910.008.90
compareICL4.360.004.36
coseq-package3.920.023.94
coseq3.690.003.69
coseqHelpers3.840.013.86
coseqRun1.140.001.14
kmeansProbaPost0.030.000.03
matchContTable0.020.000.02
plot3.680.003.69
summary3.630.023.64
transformRNAseq000