BioC 3.3: CHECK report for ABSSeq on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:34 -0400 (Tue, 27 Oct 2015).
ABSSeq 1.7.0 Wentao Yang
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ABSSeq | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: ABSSeq |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ABSSeq_1.7.0.tar.gz |
StartedAt: 2015-10-27 01:29:45 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 01:30:31 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 46.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ABSSeq.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ABSSeq_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ABSSeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ABSSeq’ can be installed ... [1s/1s] 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 ... [26s/26s] 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:
name | user | system | elapsed
|
ABSDataSet | 0.034 | 0.001 | 0.034 |
|
ABSSeq | 3.279 | 0.019 | 3.300 |
|
LevelstoNormFC | 0.053 | 0.004 | 0.057 |
|
ReplaceOutliersByMAD | 2.721 | 0.004 | 2.725 |
|
callDEs | 3.295 | 0.000 | 3.295 |
|
callParameter | 3.046 | 0.003 | 3.050 |
|
callParameterwithoutReplicates | 1.093 | 0.000 | 1.093 |
|
counts | 0.033 | 0.000 | 0.033 |
|
estimateSizeFactorsForMatrix | 0.051 | 0.003 | 0.055 |
|
excounts | 3.119 | 0.004 | 3.125 |
|
groups | 0.057 | 0.000 | 0.057 |
|
maxRates | 0.051 | 0.004 | 0.055 |
|
minRates | 0.058 | 0.000 | 0.058 |
|
minimalDispersion | 0.057 | 0.000 | 0.057 |
|
normMethod | 0.056 | 0.000 | 0.056 |
|
normalFactors | 0.086 | 0.000 | 0.086 |
|
plotDifftoBase | 3.949 | 0.000 | 3.950 |
|
results | 4.006 | 0.008 | 4.017 |
|
sFactors | 0.094 | 0.000 | 0.094 |
|
simuN5 | 0.040 | 0.004 | 0.044 |
|