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CHECK report for ALPS on tokay1

This page was generated on 2020-09-27 10:18:35 -0400 (Sun, 27 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ALPS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 45/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALPS 1.3.0
Venu Thatikonda
Snapshot Date: 2020-09-26 14:42:06 -0400 (Sat, 26 Sep 2020)
URL: https://git.bioconductor.org/packages/ALPS
Branch: master
Last Commit: 10e65ff
Last Changed Date: 2020-04-27 15:31:37 -0400 (Mon, 27 Apr 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ALPS
Version: 1.3.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ALPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ALPS_1.3.0.tar.gz
StartedAt: 2020-09-27 06:45:15 -0400 (Sun, 27 Sep 2020)
EndedAt: 2020-09-27 06:56:43 -0400 (Sun, 27 Sep 2020)
EllapsedTime: 688.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ALPS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ALPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ALPS_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ALPS.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ALPS/DESCRIPTION' ... OK
* this is package 'ALPS' version '1.3.0'
* package encoding: UTF-8
* 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:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ALPS' 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plot_genomic_annotations 88.28   2.11   90.39
get_genomic_annotations  69.77   3.00   72.97
plot_browser_tracks      42.66   1.12   43.80
plot_correlation          6.14   0.03   38.97
plot_enrichments          3.89   0.02   32.83
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ALPS.Rcheck/00check.log'
for details.



Installation output

ALPS.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch ALPS
###
##############################################################################
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* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'ALPS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ALPS'
    finding HTML links ... done
    ALPS-package                            html  
    get_genomic_annotations                 html  
    get_variable_regions                    html  
    merge_GR                                html  
    multiBigwig_summary                     html  
    pipe                                    html  
    plot_browser_tracks                     html  
    plot_correlation                        html  
    plot_enrichments                        html  
    plot_genomic_annotations                html  
    plot_motif_logo                         html  
    process_homer                           html  
    process_jaspar                          html  
    process_meme                            html  
    process_pfm                             html  
    process_transfac                        html  
** 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 (ALPS)
Making 'packages.html' ... done

Tests output

ALPS.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(ALPS)


> 
> test_check("ALPS")
== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  22.46    1.12   23.65 

Example timings

ALPS.Rcheck/ALPS-Ex.timings

nameusersystemelapsed
get_genomic_annotations69.77 3.0072.97
get_variable_regions0.090.020.11
merge_GR0.040.000.04
multiBigwig_summary1.080.001.11
plot_browser_tracks42.66 1.1243.80
plot_correlation 6.14 0.0338.97
plot_enrichments 3.89 0.0232.83
plot_genomic_annotations88.28 2.1190.39
plot_motif_logo0.270.000.26
process_homer0.010.000.02
process_jaspar0.020.000.01
process_meme0.000.000.02
process_pfm0.010.000.02
process_transfac0.020.000.01