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

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DAMEfinder_1.6.0.tar.gz

StartedAt: 2022-04-12 18:12:34 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 18:21:03 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 509.5 seconds

RetCode: 0

Status: OK

CheckDir: DAMEfinder.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:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DAMEfinder_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DAMEfinder.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 'DAMEfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DAMEfinder' version '1.6.0'
* 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 'DAMEfinder' 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
extract_bams       31.68   1.20   32.95
methyl_circle_plot  5.14   0.22    5.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
extract_bams       39.14   1.16   40.30
methyl_circle_plot  5.75   0.15    5.92
* 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/DAMEfinder_1.6.0.tar.gz && rm -rf DAMEfinder.buildbin-libdir && mkdir DAMEfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAMEfinder.buildbin-libdir DAMEfinder_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DAMEfinder_1.6.0.zip && rm DAMEfinder_1.6.0.tar.gz DAMEfinder_1.6.0.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
  4 2643k    4  118k    0     0   447k      0  0:00:05 --:--:--  0:00:05  446k
 48 2643k   48 1275k    0     0  1011k      0  0:00:02  0:00:01  0:00:01 1011k
100 2643k  100 2643k    0     0  1346k      0  0:00:01  0:00:01 --:--:-- 1346k

install for i386

* installing *source* package 'DAMEfinder' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DAMEfinder'
    finding HTML links ... done
    DAMEfinder                              html  
    calc_asm                                html  
    calc_derivedasm                         html  
    finding level-2 HTML links ... done

    calc_logodds                            html  
    calc_score                              html  
    calc_weight                             html  
    dame_track                              html  
    dame_track_mean                         html  
    empirical_pval                          html  
    extract_bams                            html  
    extractbams_output                      html  
    find_dames                              html  
    getMD                                   html  
    get_tstats                              html  
    methyl_MDS_plot                         html  
    methyl_circle_plot                      html  
    methyl_circle_plotCpG                   html  
    modulus_sqrt                            html  
    read_tuples                             html  
    readtuples_output                       html  
    simes_pval                              html  
    splitReads                              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 'DAMEfinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAMEfinder' as DAMEfinder_1.6.0.zip
* DONE (DAMEfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DAMEfinder' 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(DAMEfinder)
> 
> test_check("DAMEfinder")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  75.51    3.23   78.65


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(DAMEfinder)
> 
> test_check("DAMEfinder")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  87.68    2.00   89.57

name	user	system	elapsed
calc_asm	1.28	0.13	1.30
calc_derivedasm	2.88	0.45	3.32
dame_track	1.17	0.12	1.34
dame_track_mean	0.81	0.00	0.82
extract_bams	31.68	1.20	32.95
find_dames	0.60	0.25	0.86
get_tstats	0.30	0.02	0.31
methyl_MDS_plot	0.37	0.00	0.37
methyl_circle_plot	5.14	0.22	5.69
methyl_circle_plotCpG	3.14	0.09	3.23
read_tuples	0.22	0.06	0.18

name	user	system	elapsed
calc_asm	1.55	0.09	1.63
calc_derivedasm	3.28	0.02	3.30
dame_track	1.28	0.03	2.21
dame_track_mean	0.84	0.01	0.85
extract_bams	39.14	1.16	40.30
find_dames	0.64	0.00	0.64
get_tstats	0.28	0.00	0.28
methyl_MDS_plot	0.36	0.00	0.36
methyl_circle_plot	5.75	0.15	5.92
methyl_circle_plotCpG	4.19	0.08	4.27
read_tuples	0.16	0.05	0.13

CHECK results for DAMEfinder on tokay2

Summary

Command output

Installation output

Tests output

Example timings