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BioC 3.4: CHECK report for MADSEQ on zin1

This page was generated on 2016-09-21 03:40:53 -0700 (Wed, 21 Sep 2016).

Package 679/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MADSEQ 0.99.9
Yu Kong
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MADSEQ
Last Changed Rev: 118181 / Revision: 121152
Last Changed Date: 2016-06-04 11:14:00 -0700 (Sat, 04 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MADSEQ
Version: 0.99.9
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MADSEQ_0.99.9.tar.gz
StartedAt: 2016-09-20 08:46:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:50:19 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 210.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MADSEQ.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MADSEQ_0.99.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MADSEQ.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MADSEQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MADSEQ’ version ‘0.99.9’
* 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 ‘MADSEQ’ 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 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runMadSeq         19.068  0.036  19.162
normalizeCoverage  8.220  0.096   8.485
prepareHetero      7.356  0.004   7.392
* 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

MADSEQ.Rcheck/00install.out:

* installing *source* package ‘MADSEQ’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MADSEQ)

MADSEQ.Rcheck/MADSEQ-Ex.timings:

nameusersystemelapsed
aneuploidy_chr180.0240.0000.022
deltaBIC0.0080.0040.012
normalizeCoverage8.2200.0968.485
plotFraction0.0160.0000.017
plotMadSeq0.0280.0040.035
plotMixture0.0200.0000.019
posterior0.1400.1000.237
prepareCoverageGC1.4840.0081.498
prepareHetero7.3560.0047.392
runMadSeq19.068 0.03619.162
summary-method0.0160.0000.017