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CHECK report for ALPS on tokay1

This page was generated on 2021-05-06 12:29:52 -0400 (Thu, 06 May 2021).

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 47/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALPS 1.4.0  (landing page)
Venu Thatikonda
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ALPS
Branch: RELEASE_3_12
Last Commit: efa0189
Last Changed Date: 2020-10-27 11:50:35 -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: ALPS
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2021-05-06 00:23:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:35:09 -0400 (Thu, 06 May 2021)
EllapsedTime: 699.0 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_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ALPS.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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
get_genomic_annotations  84.17   2.86  106.09
plot_genomic_annotations 66.95   2.64   69.61
plot_browser_tracks      44.91   0.80   45.70
plot_correlation          5.36   0.02   29.09
plot_enrichments          2.51   0.04   30.86
* 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
###
##############################################################################
##############################################################################


* 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  16.76    0.71   19.09 

Example timings

ALPS.Rcheck/ALPS-Ex.timings

nameusersystemelapsed
get_genomic_annotations 84.17 2.86106.09
get_variable_regions0.180.000.17
merge_GR0.100.000.09
multiBigwig_summary1.040.011.07
plot_browser_tracks44.91 0.8045.70
plot_correlation 5.36 0.0229.09
plot_enrichments 2.51 0.0430.86
plot_genomic_annotations66.95 2.6469.61
plot_motif_logo0.160.000.16
process_homer0.020.000.01
process_jaspar000
process_meme0.010.000.02
process_pfm000
process_transfac0.020.000.01