Multiple platform build/check report for BioC 3.14 - CHECK results for cageminer 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: cageminer

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cageminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cageminer_1.0.0.tar.gz

StartedAt: 2022-04-12 16:44:37 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 16:55:44 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 667.2 seconds

RetCode: 0

Status: OK

CheckDir: cageminer.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cageminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cageminer_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cageminer.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 'cageminer/DESCRIPTION' ... OK
* this is package 'cageminer' 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 ... OK
* checking for portable file names ... OK
* checking whether package 'cageminer' 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_snp_circos 7.78   1.52    9.30
mine_step2      2.05   0.02   25.76
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_snp_circos 6.45   0.19    6.64
mine_step2      2.59   0.08   26.47
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cageminer_1.0.0.tar.gz && rm -rf cageminer.buildbin-libdir && mkdir cageminer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cageminer.buildbin-libdir cageminer_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cageminer_1.0.0.zip && rm cageminer_1.0.0.tar.gz cageminer_1.0.0.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
100  408k  100  408k    0     0   432k      0 --:--:-- --:--:-- --:--:--  432k
100  408k  100  408k    0     0   432k      0 --:--:-- --:--:-- --:--:--  432k

install for i386

* installing *source* package 'cageminer' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cageminer'
    finding HTML links ... done
    chr_length                              html  
    gcn                                     html  
    gene_ranges                             html  
    guides                                  html  
    hubs                                    html  
    mine2                                   html  
    mine_candidates                         html  
    mine_step1                              html  
    mine_step2                              html  
    mine_step3                              html  
    mined_candidates                        html  
    pepper_se                               html  
    plot_snp_circos                         html  
    plot_snp_distribution                   html  
    score_genes                             html  
    simulate_windows                        html  
    snp_pos                                 html  
    tfs                                     html  
*** copying figures
** 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 'cageminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cageminer' as cageminer_1.0.0.zip
* DONE (cageminer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cageminer' 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cageminer)

> 
> test_check("cageminer")
Enrichment analysis for module cyan...


Number of genes < 'pick_top'. Picking all genes.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  31.32    3.21   72.79


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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cageminer)

> 
> test_check("cageminer")
Enrichment analysis for module cyan...


Number of genes < 'pick_top'. Picking all genes.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  34.84    0.95   72.29

name	user	system	elapsed
chr_length	0	0	0
gcn	0	0	0
gene_ranges	0.05	0.00	0.05
guides	0.05	0.00	0.04
hubs	0.01	0.00	0.02
mine2	0	0	0
mine_candidates	0	0	0
mine_step1	0.14	0.04	0.19
mine_step2	2.05	0.02	25.76
mine_step3	0.53	0.08	0.61
mined_candidates	0	0	0
pepper_se	0.05	0.00	0.05
plot_snp_circos	7.78	1.52	9.30
plot_snp_distribution	0.02	0.00	0.01
score_genes	0.00	0.01	0.02
simulate_windows	1.47	0.02	1.48
snp_pos	0.01	0.00	0.02
tfs	0	0	0

name	user	system	elapsed
chr_length	0	0	0
gcn	0	0	0
gene_ranges	0.04	0.01	0.06
guides	0.02	0.02	0.04
hubs	0	0	0
mine2	0	0	0
mine_candidates	0	0	0
mine_step1	0.19	0.01	0.20
mine_step2	2.59	0.08	26.47
mine_step3	0.47	0.03	0.50
mined_candidates	0	0	0
pepper_se	0.03	0.00	0.03
plot_snp_circos	6.45	0.19	6.64
plot_snp_distribution	0.02	0.00	0.02
score_genes	0.00	0.02	0.01
simulate_windows	1.16	0.00	1.16
snp_pos	0	0	0
tfs	0.01	0.00	0.01

CHECK results for cageminer on tokay2

Summary

Command output

Installation output

Tests output

Example timings