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BioC 3.5: CHECK report for IVAS on toluca2

This page was generated on 2017-04-23 14:39:35 -0400 (Sun, 23 Apr 2017).

Package 692/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 1.95.6
Seonggyun Han
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IVAS
Last Changed Rev: 128250 / Revision: 129046
Last Changed Date: 2017-04-07 00:53:57 -0400 (Fri, 07 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
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: 1.95.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IVAS_1.95.6.tar.gz
StartedAt: 2017-04-23 05:42:55 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 05:48:04 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 309.4 seconds
RetCode: 0
Status:  OK 
CheckDir: IVAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IVAS_1.95.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IVAS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IVAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IVAS’ version ‘1.95.6’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ASdb-class    15.905  0.130  16.272
saveBplot     11.431  0.086  11.588
sQTLsFinder   10.313  0.061  10.489
CalSigSNP      7.865  0.096   8.027
RatioFromFPKM  6.072  0.044   6.151
* 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:

* 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
* DONE (IVAS)

IVAS.Rcheck/IVAS-Ex.timings:

nameusersystemelapsed
ASdb-class15.905 0.13016.272
CalSigSNP7.8650.0968.027
RatioFromFPKM6.0720.0446.151
Splicingfinder4.1930.0264.238
chrseparate0.0940.0030.096
findAlternative0.7260.0070.737
findOversnp0.6520.0070.663
sQTLsFinder10.313 0.06110.489
sampleexp0.0050.0010.006
samplesnp0.0030.0010.002
samplesnplocus0.0020.0010.002
saveBplot11.431 0.08611.588