Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-25 14:05:33 -0400 (Mon, 25 Oct 2021).

CHECK results for branchpointer on nebbiolo2

To the developers/maintainers of the branchpointer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/branchpointer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 213/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
branchpointer 1.19.0  (landing page)
Beth Signal
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/branchpointer
git_branch: master
git_last_commit: 6b26be6
git_last_commit_date: 2021-05-19 12:26:29 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: branchpointer
Version: 1.19.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:branchpointer.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings branchpointer_1.19.0.tar.gz
StartedAt: 2021-10-24 19:21:17 -0400 (Sun, 24 Oct 2021)
EndedAt: 2021-10-24 19:25:55 -0400 (Sun, 24 Oct 2021)
EllapsedTime: 278.0 seconds
RetCode: 0
Status:   OK  
CheckDir: branchpointer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:branchpointer.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings branchpointer_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/branchpointer.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘branchpointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘branchpointer’ version ‘1.19.0’
* 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 ‘branchpointer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         4.1Mb
    extdata   1.1Mb
* 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plotBranchpointWindow       5.116  0.156   5.273
makeBranchpointWindowForSNP 3.725  0.147  19.081
* 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-3.14-bioc/meat/branchpointer.Rcheck/00check.log’
for details.



Installation output

branchpointer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL branchpointer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘branchpointer’ ...
** using staged installation
** R
** 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 (branchpointer)

Tests output


Example timings

branchpointer.Rcheck/branchpointer-Ex.timings

nameusersystemelapsed
gtfToExons1.0570.0371.093
makeBranchpointWindowForExons1.4170.0241.441
makeBranchpointWindowForSNP 3.725 0.14719.081
plotBranchpointWindow5.1160.1565.273
predictBranchpoints3.2130.0523.265
predictionsToSummary3.4490.0483.497
readQueryFile2.1670.0122.180