BioC 3.5: CHECK report for segmentSeq on malbec2
This page was generated on 2017-10-18 14:13:41 -0400 (Wed, 18 Oct 2017).
segmentSeq 2.10.0 Thomas J. Hardcastle
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/segmentSeq | Branch: RELEASE_3_5 | Last Commit: d645674 | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: segmentSeq |
Version: 2.10.0 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.10.0.tar.gz |
StartedAt: 2017-10-18 02:23:23 -0400 (Wed, 18 Oct 2017) |
EndedAt: 2017-10-18 02:28:12 -0400 (Wed, 18 Oct 2017) |
EllapsedTime: 288.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: segmentSeq.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/segmentSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.10.0’
* 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 ‘segmentSeq’ 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
classifySeg 27.800 0.028 27.879
heuristicSeg 10.948 0.000 10.954
lociLikelihoods 10.368 0.000 10.375
normaliseNC 6.572 0.080 6.656
* 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
segmentSeq.Rcheck/00install.out:
* installing *source* package ‘segmentSeq’ ...
** 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 (segmentSeq)
segmentSeq.Rcheck/segmentSeq-Ex.timings:
name | user | system | elapsed
|
alignmentData-class | 2.756 | 0.020 | 2.774 |
|
classifySeg | 27.800 | 0.028 | 27.879 |
|
findChunks | 2.508 | 0.000 | 2.512 |
|
getCounts | 3.792 | 0.004 | 3.800 |
|
heuristicSeg | 10.948 | 0.000 | 10.954 |
|
lociLikelihoods | 10.368 | 0.000 | 10.375 |
|
normaliseNC | 6.572 | 0.080 | 6.656 |
|
plotGenome | 4.616 | 0.004 | 4.624 |
|
processAD | 3.140 | 0.000 | 3.148 |
|
readMethods | 2.520 | 0.000 | 2.526 |
|
readMeths | 4.844 | 0.044 | 4.897 |
|
segData-class | 3.064 | 0.008 | 3.074 |
|
segmentSeq-package | 2.736 | 0.000 | 2.736 |
|
thresholdFinder | 4.452 | 0.028 | 4.484 |
|