Multiple platform build/check report for BioC 3.14 - CHECK results for spatzie on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: spatzie

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spatzie.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings spatzie_1.0.1.tar.gz

StartedAt: 2022-04-13 03:20:44 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:29:21 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 516.5 seconds

RetCode: 0

Status: OK

CheckDir: spatzie.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spatzie.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings spatzie_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/spatzie.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spatzie/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spatzie' version '1.0.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'spatzie' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
scan_motifs 4.76   0.68    5.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
scan_motifs 4.89    0.3    5.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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-3.14-bioc/meat/spatzie.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/spatzie_1.0.1.tar.gz && rm -rf spatzie.buildbin-libdir && mkdir spatzie.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=spatzie.buildbin-libdir spatzie_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL spatzie_1.0.1.zip && rm spatzie_1.0.1.tar.gz spatzie_1.0.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 12 4302k   12  558k    0     0  1065k      0  0:00:04 --:--:--  0:00:04 1066k
 59 4302k   59 2558k    0     0  1681k      0  0:00:02  0:00:01  0:00:01 1681k
100 4302k  100 4302k    0     0  2026k      0  0:00:02  0:00:02 --:--:-- 2027k

install for i386

* installing *source* package 'spatzie' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatzie'
    finding HTML links ... done
    anchor_pair_enrich                      html  
    anchor_pair_example_count               html  
    anchor_pair_example_match               html  
    anchor_pair_example_score               html  
    compare_motif_pairs                     html  
    compare_pairs_example                   html  
    filter_motifs                           html  
    filter_pair_motifs                      html  
    filter_pairs_example                    html  
    find_ep_coenrichment                    html  
    get_specific_interactions               html  
    int_data_k562                           html  
    int_data_mslcl                          html  
    int_data_yy1                            html  
    interactions_yy1                        html  
    interactions_yy1_enhancer               html  
    interactions_yy1_ep                     html  
    interactions_yy1_promoter               html  
    plot_motif_occurrence                   html  
    scan_interactions_example               html  
    scan_interactions_example_filtered      html  
    scan_motifs                             html  
    spatzie                                 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

install for x64

* installing *source* package 'spatzie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spatzie' as spatzie_1.0.1.zip
* DONE (spatzie)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'spatzie' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(spatzie)

> 
> test_check("spatzie")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  22.09    3.39   25.46


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(spatzie)

> 
> test_check("spatzie")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  24.89    1.29   26.15

name	user	system	elapsed
anchor_pair_enrich	0.49	0.20	0.69
compare_motif_pairs	0.11	0.06	0.17
filter_motifs	0.02	0.01	0.03
filter_pair_motifs	0	0	0
find_ep_coenrichment	0	0	0
get_specific_interactions	0.12	0.00	0.13
plot_motif_occurrence	0.41	0.00	0.41
scan_motifs	4.76	0.68	5.43

name	user	system	elapsed
anchor_pair_enrich	0.46	0.00	0.45
compare_motif_pairs	0.12	0.02	0.14
filter_motifs	0.01	0.00	0.01
filter_pair_motifs	0	0	0
find_ep_coenrichment	0	0	0
get_specific_interactions	0.07	0.03	0.10
plot_motif_occurrence	0.37	0.05	0.42
scan_motifs	4.89	0.30	5.19

CHECK results for spatzie on tokay2

Summary

Command output

Installation output

Tests output

Example timings