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CHECK results for alpine on machv2

This page was generated on 2021-06-14 14:05:33 -0400 (Mon, 14 Jun 2021).

Package 46/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.18.0  (landing page)
Michael Love
Snapshot Date: 2021-06-13 06:50:09 -0400 (Sun, 13 Jun 2021)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_13
Last Commit: 06257d2
Last Changed Date: 2021-05-19 12:22:33 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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
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.

Summary

Package: alpine
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2021-06-13 15:50:28 -0400 (Sun, 13 Jun 2021)
EndedAt: 2021-06-13 15:57:37 -0400 (Sun, 13 Jun 2021)
EllapsedTime: 428.4 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/alpine.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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     19.953  0.795  21.294
estimateAbundance 16.941  1.087  18.866
predictCoverage   10.575  0.543  11.499
getFragmentWidths  6.870  0.185   7.538
getReadLength      5.419  0.139   6.065
* 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-3.13-bioc/meat/alpine.Rcheck/00check.log’
for details.



Installation output

alpine.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
 61.990   2.720  65.548 

Example timings

alpine.Rcheck/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes3.2460.1313.381
estimateAbundance16.941 1.08718.866
extractAlpine0.0360.0030.039
fitBiasModels19.953 0.79521.294
getFragmentWidths6.8700.1857.538
getReadLength5.4190.1396.065
mergeGenes0.4050.0070.415
normalizeDESeq0.0020.0000.002
plotFragLen0.0250.0100.034
plotGC0.0420.0110.053
plotGRL0.2440.0090.253
plotOrder00.0580.0140.074
plotRelPos0.0300.0110.042
predictCoverage10.575 0.54311.499
splitGenesAcrossChroms0.5700.0070.579
splitLongGenes0.6940.0100.705