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BioC 3.5: CHECK report for IVAS on tokay2

This page was generated on 2017-10-18 14:24:24 -0400 (Wed, 18 Oct 2017).

Package 694/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 1.96.0
Seonggyun Han
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/IVAS
Branch: RELEASE_3_5
Last Commit: 59fe33c
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IVAS
Version: 1.96.0
Command: rm -rf IVAS.buildbin-libdir IVAS.Rcheck && mkdir IVAS.buildbin-libdir IVAS.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IVAS.buildbin-libdir IVAS_1.96.0.tar.gz >IVAS.Rcheck\00install.out 2>&1 && cp IVAS.Rcheck\00install.out IVAS-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=IVAS.buildbin-libdir --install="check:IVAS-install.out" --force-multiarch --no-vignettes --timings IVAS_1.96.0.tar.gz
StartedAt: 2017-10-18 00:50:23 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:56:44 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 381.8 seconds
RetCode: 0
Status:  OK  
CheckDir: IVAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IVAS.buildbin-libdir IVAS.Rcheck && mkdir IVAS.buildbin-libdir IVAS.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IVAS.buildbin-libdir IVAS_1.96.0.tar.gz >IVAS.Rcheck\00install.out 2>&1 && cp IVAS.Rcheck\00install.out IVAS-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=IVAS.buildbin-libdir --install="check:IVAS-install.out" --force-multiarch --no-vignettes --timings IVAS_1.96.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/IVAS.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 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '1.96.0'
* 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 'IVAS' 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
* 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 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
ASdb-class  9.18   0.16    9.35
saveBplot   6.77   0.06    6.89
sQTLsFinder 5.91   0.10    6.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ASdb-class  11.54   0.06   11.61
saveBplot    8.37   0.08   10.54
sQTLsFinder  7.70   0.02    7.72
CalSigSNP    5.50   0.08    5.57
* 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

IVAS.Rcheck/00install.out:


install for i386

* installing *source* package 'IVAS' ...
** 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 'IVAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IVAS' as IVAS_1.96.0.zip
* DONE (IVAS)

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

nameusersystemelapsed
ASdb-class9.180.169.35
CalSigSNP4.580.064.64
RatioFromFPKM3.360.003.36
Splicingfinder2.310.022.33
chrseparate0.050.000.04
findAlternative0.450.000.46
findOversnp0.390.010.40
sQTLsFinder5.910.106.00
sampleexp000
samplesnp0.010.000.01
samplesnplocus000
saveBplot6.770.066.89

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

nameusersystemelapsed
ASdb-class11.54 0.0611.61
CalSigSNP5.500.085.57
RatioFromFPKM4.450.024.47
Splicingfinder2.770.012.78
chrseparate0.060.000.06
findAlternative0.670.000.67
findOversnp0.470.030.50
sQTLsFinder7.700.027.72
sampleexp000
samplesnp000
samplesnplocus000
saveBplot 8.37 0.0810.54