Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-24 15:06:07 -0400 (Fri, 24 Sep 2021).

CHECK results for DAMEfinder on tokay2

To the developers/maintainers of the DAMEfinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DAMEfinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 440/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAMEfinder 1.4.0  (landing page)
Stephany Orjuela
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/DAMEfinder
git_branch: RELEASE_3_13
git_last_commit: a0da475
git_last_commit_date: 2021-05-19 12:49:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAMEfinder
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DAMEfinder_1.4.0.tar.gz
StartedAt: 2021-09-23 21:10:50 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 21:19:04 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 493.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DAMEfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAMEfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DAMEfinder_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DAMEfinder.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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       30.00   1.03   31.80
methyl_circle_plot  4.91   0.28    5.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
extract_bams 33.86   0.92   34.78
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DAMEfinder_1.4.0.tar.gz && rm -rf DAMEfinder.buildbin-libdir && mkdir DAMEfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAMEfinder.buildbin-libdir DAMEfinder_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DAMEfinder_1.4.0.zip && rm DAMEfinder_1.4.0.tar.gz DAMEfinder_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2644k  100 2644k    0     0  3355k      0 --:--:-- --:--:-- --:--:-- 3355k

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_1.4.0.zip
* DONE (DAMEfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DAMEfinder' successfully unpacked and MD5 sums checked

Tests output

DAMEfinder.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  78.65    2.93   81.51 

DAMEfinder.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  86.21    1.78   87.84 

Example timings

DAMEfinder.Rcheck/examples_i386/DAMEfinder-Ex.timings

nameusersystemelapsed
calc_asm1.080.131.13
calc_derivedasm2.980.423.40
dame_track0.780.050.83
dame_track_mean0.640.030.67
extract_bams30.00 1.0331.80
find_dames0.630.230.86
get_tstats0.230.140.37
methyl_MDS_plot0.390.070.46
methyl_circle_plot4.910.285.18
methyl_circle_plotCpG3.500.113.61
read_tuples0.190.090.19

DAMEfinder.Rcheck/examples_x64/DAMEfinder-Ex.timings

nameusersystemelapsed
calc_asm1.100.171.13
calc_derivedasm3.330.063.39
dame_track1.060.051.11
dame_track_mean1.080.021.10
extract_bams33.86 0.9234.78
find_dames0.590.010.61
get_tstats0.270.000.26
methyl_MDS_plot0.580.020.60
methyl_circle_plot4.650.114.78
methyl_circle_plotCpG3.300.063.36
read_tuples0.170.050.14