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CHECK report for segmentSeq on malbec2

This page was generated on 2020-10-17 11:55:43 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE segmentSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1618/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.22.0
Thomas J. Hardcastle
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/segmentSeq
Branch: RELEASE_3_11
Last Commit: 4bb4854
Last Changed Date: 2020-04-27 14:21:25 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: segmentSeq
Version: 2.22.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings segmentSeq_2.22.0.tar.gz
StartedAt: 2020-10-17 05:20:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:26:53 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 373.3 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings segmentSeq_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.22.0’
* 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 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 ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
  ‘sDP’
Undefined global functions or variables:
  sDP
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
classifySeg     38.617  0.147  38.765
lociLikelihoods 15.972  0.012  16.103
heuristicSeg    14.545  0.016  14.560
plotGenome       8.482  0.008   8.490
getCounts        6.270  0.000   6.270
normaliseNC      4.913  0.076   5.005
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.



Installation output

segmentSeq.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL segmentSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘segmentSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (segmentSeq)

Tests output


Example timings

segmentSeq.Rcheck/segmentSeq-Ex.timings

nameusersystemelapsed
alignmentData-class3.9630.0004.093
classifySeg38.617 0.14738.765
findChunks3.8770.0003.959
getCounts6.270.006.27
getOverlaps4.2540.0004.255
heuristicSeg14.545 0.01614.560
lociLikelihoods15.972 0.01216.103
normaliseNC4.9130.0765.005
plotGenome8.4820.0088.490
processAD4.6790.0004.679
readMethods3.3960.0043.401
readMeths2.730.042.77
segData-class4.2590.0044.286
segmentSeq-package4.3240.0004.325
thresholdFinder2.9120.0522.963