Package: ALPS

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ALPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ALPS_1.0.0.tar.gz

StartedAt: 2020-04-15 01:13:52 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:23:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 554.5 seconds

RetCode: 0

Status:  OK

CheckDir: ALPS.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ALPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ALPS_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ALPS.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.0.0'
* 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 or elapsed time > 5s
                          user system elapsed
get_genomic_annotations  73.49   2.63   76.73
plot_genomic_annotations 59.77   1.82   61.56
plot_browser_tracks      31.56   0.63   32.19
plot_correlation          4.13   0.05   28.83
plot_enrichments          2.04   0.00   27.11
* 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-3.10-bioc/meat/ALPS.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch ALPS
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* installing to library 'C:/Users/biocbuild/bbs-3.10-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

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 
  17.90    0.87   18.76 

name	user	system	elapsed
get_genomic_annotations	73.49	2.63	76.73
get_variable_regions	0.09	0.00	0.10
merge_GR	0.09	0.01	0.08
multiBigwig_summary	0.88	0.00	1.09
plot_browser_tracks	31.56	0.63	32.19
plot_correlation	4.13	0.05	28.83
plot_enrichments	2.04	0.00	27.11
plot_genomic_annotations	59.77	1.82	61.56
plot_motif_logo	0.19	0.00	0.19
process_homer	0.01	0.00	0.01
process_jaspar	0	0	0
process_meme	0.00	0.00	0.06
process_pfm	0	0	0
process_transfac	0	0	0