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BioC 3.5: CHECK report for splatter on tokay2

This page was generated on 2017-10-18 14:26:50 -0400 (Wed, 18 Oct 2017).

Package 1255/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.0.3
Luke Zappia
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/splatter
Branch: RELEASE_3_5
Last Commit: f7e6ec1
Last Changed Date: 2017-05-25 19:27:23 -0400 (Thu, 25 May 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: splatter
Version: 1.0.3
Command: rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.0.3.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.0.3.tar.gz
StartedAt: 2017-10-18 03:12:21 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:20:07 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 465.8 seconds
RetCode: 0
Status:  OK  
CheckDir: splatter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.0.3.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/splatter.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'splatter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'splatter' version '1.0.3'
* 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 'splatter' 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
** running examples for arch 'x64' ... OK
* 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

splatter.Rcheck/00install.out:


install for i386

* installing *source* package 'splatter' ...
** 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 'splatter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'splatter' as splatter_1.0.3.zip
* DONE (splatter)

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

nameusersystemelapsed
addGeneLengths1.950.031.98
compareSCESets2.450.032.48
diffSCESets1.990.001.98
getParam000
getParams000
listSims000
lun2Estimate000
lun2Simulate2.500.162.65
lunEstimate0.080.000.08
lunSimulate1.150.041.20
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
newParams000
scDDEstimate1.220.131.61
scDDSimulate000
setParam0.010.000.01
setParams0.020.000.02
simpleEstimate0.020.030.09
simpleSimulate1.080.011.09
splatEstimate3.110.083.19
splatSimulate000
summariseDiff2.190.002.19

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

nameusersystemelapsed
addGeneLengths1.710.041.75
compareSCESets3.070.003.13
diffSCESets2.050.002.05
getParam000
getParams000
listSims000
lun2Estimate0.020.000.01
lun2Simulate2.010.102.11
lunEstimate0.060.000.06
lunSimulate1.130.031.16
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
newParams000
scDDEstimate1.060.051.10
scDDSimulate000
setParam000
setParams000
simpleEstimate0.020.030.05
simpleSimulate1.390.061.45
splatEstimate2.620.062.69
splatSimulate000
summariseDiff2.440.002.47