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BioC 3.5: CHECK report for segmentSeq on veracruz2

This page was generated on 2017-10-18 14:29:01 -0400 (Wed, 18 Oct 2017).

Package 1192/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: segmentSeq
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.10.0.tar.gz
StartedAt: 2017-10-18 08:51:07 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 08:57:01 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 353.3 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/segmentSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 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
classifySeg     29.218  0.217  30.313
lociLikelihoods 12.023  0.092  12.731
heuristicSeg    11.211  0.066  11.628
normaliseNC      8.449  0.541  10.112
readMeths        5.195  0.527   6.206
plotGenome       5.556  0.041   6.258
thresholdFinder  4.744  0.536   5.617
* 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:

nameusersystemelapsed
alignmentData-class3.0560.0393.215
classifySeg29.218 0.21730.313
findChunks2.2590.0132.336
getCounts3.6400.0213.791
heuristicSeg11.211 0.06611.628
lociLikelihoods12.023 0.09212.731
normaliseNC 8.449 0.54110.112
plotGenome5.5560.0416.258
processAD3.2070.0223.376
readMethods2.4140.0182.630
readMeths5.1950.5276.206
segData-class2.8480.0223.160
segmentSeq-package2.8920.0153.253
thresholdFinder4.7440.5365.617