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CHECK report for DAMEfinder on tokay1

This page was generated on 2021-05-06 12:30:35 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the DAMEfinder package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 423/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAMEfinder 1.2.0  (landing page)
Stephany Orjuela
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/DAMEfinder
Branch: RELEASE_3_12
Last Commit: 99d17c3
Last Changed Date: 2020-10-27 11:52:56 -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: DAMEfinder
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DAMEfinder_1.2.0.tar.gz
StartedAt: 2021-05-06 01:58:13 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:08:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 608.7 seconds
RetCode: 0
Status:   OK   
CheckDir: DAMEfinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DAMEfinder_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DAMEfinder.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 'DAMEfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DAMEfinder' version '1.2.0'
* 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          40.97   1.66   44.35
methyl_circle_plot     8.29   0.20    8.52
methyl_circle_plotCpG  5.41   0.08    5.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
extract_bams       38.05   0.83   40.53
methyl_circle_plot  7.54   0.09    7.65
* 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


Installation output

DAMEfinder.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DAMEfinder_1.2.0.tar.gz && rm -rf DAMEfinder.buildbin-libdir && mkdir DAMEfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAMEfinder.buildbin-libdir DAMEfinder_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DAMEfinder_1.2.0.zip && rm DAMEfinder_1.2.0.tar.gz DAMEfinder_1.2.0.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 2642k  100 2642k    0     0  19.9M      0 --:--:-- --:--:-- --:--:-- 20.1M

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_1.2.0.zip
* DONE (DAMEfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DAMEfinder' successfully unpacked and MD5 sums checked

Tests output

DAMEfinder.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 3 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  98.57    3.43  103.56 

DAMEfinder.Rcheck/tests_x64/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(DAMEfinder)
> 
> test_check("DAMEfinder")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 110.20    2.25  116.25 

Example timings

DAMEfinder.Rcheck/examples_i386/DAMEfinder-Ex.timings

nameusersystemelapsed
calc_asm0.510.270.79
calc_derivedasm3.300.253.54
dame_track0.890.151.05
dame_track_mean0.780.010.80
extract_bams40.97 1.6644.35
find_dames0.780.471.25
get_tstats0.330.170.50
methyl_MDS_plot0.580.090.67
methyl_circle_plot8.290.208.52
methyl_circle_plotCpG5.410.085.48
read_tuples0.050.020.07

DAMEfinder.Rcheck/examples_x64/DAMEfinder-Ex.timings

nameusersystemelapsed
calc_asm1.270.011.28
calc_derivedasm2.690.032.72
dame_track0.780.080.86
dame_track_mean0.680.000.69
extract_bams38.05 0.8340.53
find_dames0.590.030.63
get_tstats0.240.000.23
methyl_MDS_plot0.350.020.38
methyl_circle_plot7.540.097.65
methyl_circle_plotCpG3.920.084.00
read_tuples0.030.010.05