Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:05:41 -0500 (Fri, 26 Nov 2021).

CHECK results for alpine on machv2

To the developers/maintainers of the alpine package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alpine.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 44/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.20.0  (landing page)
Michael Love
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/alpine
git_branch: RELEASE_3_14
git_last_commit: 9348ef1
git_last_commit_date: 2021-10-26 12:29:39 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: alpine
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alpine.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alpine_1.20.0.tar.gz
StartedAt: 2021-11-25 13:41:56 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 13:50:08 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 491.8 seconds
RetCode: 0
Status:   OK  
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alpine.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alpine_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/alpine.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alpine/DESCRIPTION’ ... OK
* this is package ‘alpine’ version ‘1.20.0’
* 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 ‘alpine’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
fitBiasModels     22.299  0.785  24.038
estimateAbundance 19.144  1.269  22.774
predictCoverage   12.709  0.632  14.024
getFragmentWidths  8.824  0.203   9.664
getReadLength      7.018  0.179   7.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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


Installation output

alpine.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL alpine
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘alpine’ ...
** 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 (alpine)

Tests output

alpine.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alpine)
> test_check("alpine")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 73.959   3.361  78.692 

Example timings

alpine.Rcheck/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes3.4790.1673.655
estimateAbundance19.144 1.26922.774
extractAlpine0.0320.0020.034
fitBiasModels22.299 0.78524.038
getFragmentWidths8.8240.2039.664
getReadLength7.0180.1797.846
mergeGenes0.5180.0140.536
normalizeDESeq0.0010.0010.001
plotFragLen0.0320.0060.038
plotGC0.1260.0140.141
plotGRL0.3010.0100.312
plotOrder00.0810.0080.090
plotRelPos0.0370.0050.042
predictCoverage12.709 0.63214.024
splitGenesAcrossChroms0.5820.0080.590
splitLongGenes0.7740.0090.784