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CHECK report for alpine on nebbiolo1

This page was generated on 2020-11-24 11:55:21 -0500 (Tue, 24 Nov 2020).

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
Michael Love
Snapshot Date: 2020-11-23 14:42:42 -0500 (Mon, 23 Nov 2020)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_12
Last Commit: aee3977
Last Changed Date: 2020-10-27 11:17:10 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:alpine.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings alpine_1.16.0.tar.gz
StartedAt: 2020-11-23 19:55:42 -0500 (Mon, 23 Nov 2020)
EndedAt: 2020-11-23 20:01:28 -0500 (Mon, 23 Nov 2020)
EllapsedTime: 345.8 seconds
RetCode: 0
Status:  OK 
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:alpine.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings alpine_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/alpine.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 ‘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     17.704  1.087  19.209
estimateAbundance 14.903  0.858  16.441
predictCoverage    9.186  1.648  11.240
getFragmentWidths  5.569  0.112   6.085
getReadLength      4.698  0.148   5.868
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/alpine.Rcheck/00check.log’
for details.



Installation output

alpine.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL alpine
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
── Warning (test_alpine.R:51:3): alpine works ──────────────────────────────────
'optional' argument was ignored

── Warning (test_alpine.R:64:3): alpine works ──────────────────────────────────
'optional' argument was ignored

── Warning (test_alpine.R:73:3): alpine works ──────────────────────────────────
'optional' argument was ignored

── Warning (test_alpine.R:81:3): alpine works ──────────────────────────────────
'optional' argument was ignored

══ testthat results  ═══════════════════════════════════════════════════════════
Warning (test_alpine.R:51:3): alpine works
Warning (test_alpine.R:64:3): alpine works
Warning (test_alpine.R:73:3): alpine works
Warning (test_alpine.R:81:3): alpine works

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 50.405   3.136  54.903 

Example timings

alpine.Rcheck/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes3.0800.1363.225
estimateAbundance14.903 0.85816.441
extractAlpine0.0230.0000.024
fitBiasModels17.704 1.08719.209
getFragmentWidths5.5690.1126.085
getReadLength4.6980.1485.868
mergeGenes0.3540.0040.357
normalizeDESeq0.0020.0000.001
plotFragLen0.0210.0040.024
plotGC0.0520.0000.052
plotGRL0.2230.0040.227
plotOrder00.0430.0120.054
plotRelPos0.0260.0000.026
predictCoverage 9.186 1.64811.240
splitGenesAcrossChroms0.3430.0200.363
splitLongGenes0.4290.0000.429