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CHECK report for alpine on malbec2

This page was generated on 2019-10-16 12:09:31 -0400 (Wed, 16 Oct 2019).

Package 44/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.10.0
Michael Love
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_9
Last Commit: bf22597
Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alpine
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:alpine.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings alpine_1.10.0.tar.gz
StartedAt: 2019-10-15 23:42:10 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:47:45 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 334.1 seconds
RetCode: 0
Status:  OK 
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:alpine.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings alpine_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/alpine.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 or elapsed time > 5s
                    user system elapsed
fitBiasModels     17.200  0.589  18.002
estimateAbundance 14.958  0.579  16.110
predictCoverage    9.881  0.204  10.223
getFragmentWidths  5.681  0.040   5.923
getReadLength      4.985  0.048   5.175
* 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-3.9-bioc/meat/alpine.Rcheck/00check.log’
for details.



Installation output

alpine.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL alpine
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 53.365   2.407  56.216 

Example timings

alpine.Rcheck/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes2.6910.1003.058
estimateAbundance14.958 0.57916.110
extractAlpine0.0230.0000.023
fitBiasModels17.200 0.58918.002
getFragmentWidths5.6810.0405.923
getReadLength4.9850.0485.175
mergeGenes0.3710.0160.386
normalizeDESeq0.0020.0000.002
plotFragLen0.0350.0000.035
plotGC0.0570.0000.057
plotGRL0.2160.0040.219
plotOrder00.0660.0040.070
plotRelPos0.0350.0000.035
predictCoverage 9.881 0.20410.223
splitGenesAcrossChroms0.4810.0000.481
splitLongGenes0.5500.0000.551