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CHECK report for alpine on merida1

This page was generated on 2021-05-06 12:34:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the alpine package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 46/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.16.0  (landing page)
Michael Love
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_12
Last Commit: aee3977
Last Changed Date: 2020-10-27 11:17:10 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: alpine
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:alpine.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alpine_1.16.0.tar.gz
StartedAt: 2021-05-05 23:08:04 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:15:14 -0400 (Wed, 05 May 2021)
EllapsedTime: 429.8 seconds
RetCode: 0
Status:   OK  
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:alpine.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alpine_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/alpine.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.16.0’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::fancy_mseq’
  See the note in ?`:::` about the use of this operator.
* 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     18.411  0.719  19.601
estimateAbundance 15.873  1.009  17.630
predictCoverage   10.246  0.490  11.072
getFragmentWidths  6.297  0.172   6.843
getReadLength      5.709  0.133   6.156
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/alpine.Rcheck/00check.log’
for details.



Installation output

alpine.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
 56.751   2.438  61.016 

Example timings

alpine.Rcheck/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes3.5700.1583.745
estimateAbundance15.873 1.00917.630
extractAlpine0.0270.0020.029
fitBiasModels18.411 0.71919.601
getFragmentWidths6.2970.1726.843
getReadLength5.7090.1336.156
mergeGenes0.3290.0080.338
normalizeDESeq0.0020.0010.002
plotFragLen0.0260.0050.032
plotGC0.0440.0060.051
plotGRL0.2550.0080.289
plotOrder00.0660.0080.073
plotRelPos0.0310.0050.037
predictCoverage10.246 0.49011.072
splitGenesAcrossChroms0.5140.0080.522
splitLongGenes0.7350.0140.753