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BioC 3.5: CHECK report for PathoStat on tokay2

This page was generated on 2017-08-16 13:26:19 -0400 (Wed, 16 Aug 2017).

Package 951/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PathoStat 1.2.0
Solaiappan Manimaran
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/PathoStat
Last Changed Rev: 129482 / Revision: 131943
Last Changed Date: 2017-05-08 23:37:35 -0400 (Mon, 08 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: PathoStat
Version: 1.2.0
Command: rm -rf PathoStat.buildbin-libdir PathoStat.Rcheck && mkdir PathoStat.buildbin-libdir PathoStat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PathoStat.buildbin-libdir PathoStat_1.2.0.tar.gz >PathoStat.Rcheck\00install.out 2>&1 && cp PathoStat.Rcheck\00install.out PathoStat-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PathoStat.buildbin-libdir --install="check:PathoStat-install.out" --force-multiarch --no-vignettes --timings PathoStat_1.2.0.tar.gz
StartedAt: 2017-08-16 01:48:50 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:57:31 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 520.7 seconds
RetCode: 0
Status:  OK  
CheckDir: PathoStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PathoStat.buildbin-libdir PathoStat.Rcheck && mkdir PathoStat.buildbin-libdir PathoStat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PathoStat.buildbin-libdir PathoStat_1.2.0.tar.gz >PathoStat.Rcheck\00install.out 2>&1 && cp PathoStat.Rcheck\00install.out PathoStat-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PathoStat.buildbin-libdir --install="check:PathoStat-install.out" --force-multiarch --no-vignettes --timings PathoStat_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PathoStat.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 'PathoStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PathoStat' version '1.2.0'
* 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 'PathoStat' 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
createPathoStat 2.21   0.41   18.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
createPathoStat  2.3   0.13   17.91
* 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

PathoStat.Rcheck/00install.out:


install for i386

* installing *source* package 'PathoStat' ...
** 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 'PathoStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PathoStat' as PathoStat_1.2.0.zip
* DONE (PathoStat)

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

nameusersystemelapsed
coreOTU0.060.000.06
coreOTUModule000
coreOTUModuleUI0.230.000.23
coreOTUNormalize0.110.000.11
coreOTUQuantile0.50.00.5
createPathoStat 2.21 0.4118.64
findRAfromCount0.230.030.27
findTaxonLevel0.110.000.67
findTaxonMat0.220.013.24
findTaxonomy0.220.002.86
getShinyInput000
getShinyInputCombat0.010.000.01
getShinyInputOrig000
grepTid000
loadPathoscopeReports2.110.462.56
loadPstat000
log2CPM0.030.000.03
pathostat0.310.000.41
plotConfRegion101
readPathoscopeData0.030.000.03
runPathoStat3.590.284.35
savePstat0.000.010.01
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
sizeNormalize0.030.000.03

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

nameusersystemelapsed
coreOTU0.050.000.05
coreOTUModule0.010.000.01
coreOTUModuleUI0.780.000.78
coreOTUNormalize0.10.00.1
coreOTUQuantile0.030.000.03
createPathoStat 2.30 0.1317.91
findRAfromCount0.20.00.2
findTaxonLevel0.090.010.61
findTaxonMat0.310.003.00
findTaxonomy0.210.022.72
getShinyInput000
getShinyInputCombat000
getShinyInputOrig000
grepTid000
loadPathoscopeReports1.790.342.14
loadPstat000
log2CPM0.020.000.02
pathostat0.260.000.26
plotConfRegion1.130.001.13
readPathoscopeData0.030.000.03
runPathoStat2.810.253.34
savePstat0.000.020.02
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
sizeNormalize0.060.000.06