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BioC 3.2: CHECK report for ABSSeq on zin1

This page was generated on 2016-04-23 10:13:43 -0700 (Sat, 23 Apr 2016).

Package 9/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.6.1
Wentao Yang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ABSSeq
Last Changed Rev: 114100 / Revision: 116712
Last Changed Date: 2016-02-29 06:15:09 -0800 (Mon, 29 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ABSSeq
Version: 1.6.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ABSSeq_1.6.1.tar.gz
StartedAt: 2016-04-22 21:54:37 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 21:55:22 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 45.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ABSSeq_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ABSSeq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABSSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ABSSeq’ version ‘1.6.1’
* 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 ‘ABSSeq’ can be installed ... [2s/2s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] 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

ABSSeq.Rcheck/00install.out:

* installing *source* package ‘ABSSeq’ ...
** 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 (ABSSeq)

ABSSeq.Rcheck/ABSSeq-Ex.timings:

nameusersystemelapsed
ABSDataSet0.0140.0000.015
ABSSeq3.8710.0073.905
LevelstoNormFC0.0400.0080.047
ReplaceOutliersByMAD2.3110.0042.314
callDEs3.6720.0053.673
callParameter3.4570.0043.471
callParameterwithoutReplicates1.3380.0001.337
counts0.0420.0000.042
estimateSizeFactorsForMatrix0.0710.0000.070
excounts2.3850.0042.388
groups0.0430.0000.043
maxRates0.0440.0000.044
minRates0.0780.0000.078
minimalDispersion0.040.000.04
normMethod0.0420.0000.042
normalFactors0.0640.0000.065
paired0.0370.0040.040
plotDifftoBase3.4780.0083.486
results3.5070.0003.507
sFactors0.0780.0000.078
simuN50.0350.0000.034