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CHECK report for methylSig on tokay2

This page was generated on 2020-10-17 11:57:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE methylSig PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1065/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylSig 1.0.0
Raymond G. Cavalcante
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/methylSig
Branch: RELEASE_3_11
Last Commit: 006aa88
Last Changed Date: 2020-04-27 15:36:08 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylSig
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylSig.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylSig_1.0.0.tar.gz
StartedAt: 2020-10-17 05:58:55 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:06:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 484.0 seconds
RetCode: 0
Status:  OK  
CheckDir: methylSig.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylSig.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylSig_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylSig.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylSig/DESCRIPTION' ... OK
* this is package 'methylSig' 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 'methylSig' 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 R/sysdata.rda ... 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
diff_binomial           4.43   0.26    5.89
filter_loci_by_coverage 1.82   0.06   15.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
filter_loci_by_coverage 2.61   0.05   17.72
* 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

methylSig.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/methylSig_1.0.0.tar.gz && rm -rf methylSig.buildbin-libdir && mkdir methylSig.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylSig.buildbin-libdir methylSig_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methylSig_1.0.0.zip && rm methylSig_1.0.0.tar.gz methylSig_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 60338  100 60338    0     0   731k      0 --:--:-- --:--:-- --:--:--  807k

install for i386

* installing *source* package 'methylSig' ...
** 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 'methylSig'
    finding HTML links ... done
    bsseq_destranded                        html  
    bsseq_multichrom                        html  
    bsseq_stranded                          html  
    diff_binomial                           html  
    diff_dss_fit                            html  
    diff_dss_test                           html  
    diff_methylsig                          html  
    filter_loci_by_coverage                 html  
    filter_loci_by_group_coverage           html  
    filter_loci_by_location                 html  
    methylSig                               html  
    promoters_gr                            html  
    tile_by_regions                         html  
    tile_by_windows                         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 'methylSig' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylSig' as methylSig_1.0.0.zip
* DONE (methylSig)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methylSig' successfully unpacked and MD5 sums checked

Tests output

methylSig.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(methylSig)
> 
> test_check("methylSig")
Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: == testthat results  ===========================================================
[ OK: 140 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.85    2.71   30.59 

methylSig.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(methylSig)
> 
> test_check("methylSig")
Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: Fitting DML model for CpG site: == testthat results  ===========================================================
[ OK: 140 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  35.06    1.79   36.89 

Example timings

methylSig.Rcheck/examples_i386/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded000
bsseq_multichrom0.010.000.02
bsseq_stranded0.020.000.02
diff_binomial4.430.265.89
diff_dss_fit1.720.181.89
diff_dss_test2.250.292.54
diff_methylsig2.070.252.32
filter_loci_by_coverage 1.82 0.0615.28
filter_loci_by_group_coverage2.350.212.54
filter_loci_by_location0.040.010.07
promoters_gr000
tile_by_regions0.240.030.67
tile_by_windows0.260.020.28

methylSig.Rcheck/examples_x64/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded0.000.010.02
bsseq_multichrom000
bsseq_stranded000
diff_binomial4.120.224.34
diff_dss_fit1.950.272.22
diff_dss_test2.300.262.57
diff_methylsig2.170.362.53
filter_loci_by_coverage 2.61 0.0517.72
filter_loci_by_group_coverage0.720.281.00
filter_loci_by_location0.050.000.05
promoters_gr000
tile_by_regions0.280.000.34
tile_by_windows0.200.030.24