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This page was generated on 2022-06-29 11:05:36 -0400 (Wed, 29 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for segmentSeq on lconway


To the developers/maintainers of the segmentSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1786/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.31.0  (landing page)
Thomas J. Hardcastle
Snapshot Date: 2022-06-28 14:00:02 -0400 (Tue, 28 Jun 2022)
git_url: https://git.bioconductor.org/packages/segmentSeq
git_branch: master
git_last_commit: 5751cb5
git_last_commit_date: 2022-04-26 11:04:22 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: segmentSeq
Version: 2.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.31.0.tar.gz
StartedAt: 2022-06-28 23:06:03 -0400 (Tue, 28 Jun 2022)
EndedAt: 2022-06-28 23:12:11 -0400 (Tue, 28 Jun 2022)
EllapsedTime: 368.0 seconds
RetCode: 0
Status:   OK  
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/segmentSeq.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.31.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
classifySeg     31.911  0.446  32.470
lociLikelihoods 14.967  0.107  15.119
heuristicSeg    14.477  0.062  14.577
plotGenome       8.004  0.075   8.101
getCounts        5.331  0.020   5.363
* 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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.



Installation output

segmentSeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL segmentSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-class3.3160.0123.332
classifySeg31.911 0.44632.470
findChunks3.5530.0163.573
getCounts5.3310.0205.363
getOverlaps3.6050.0133.627
heuristicSeg14.477 0.06214.577
lociLikelihoods14.967 0.10715.119
normaliseNC3.9890.2494.258
plotGenome8.0040.0758.101
processAD4.4980.0464.567
readMethods3.5170.0163.544
readMeths3.5340.2393.783
segData-class4.3680.0354.407
segmentSeq-package4.5890.0174.615
thresholdFinder2.8260.2083.061