Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-01-21 13:06:39 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for methylSig on tokay2


To the developers/maintainers of the methylSig package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylSig.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 1128/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylSig 1.6.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/methylSig
git_branch: RELEASE_3_14
git_last_commit: 61d61b1
git_last_commit_date: 2021-10-26 12:59:11 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: methylSig
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylSig.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylSig_1.6.0.tar.gz
StartedAt: 2022-01-20 22:50:53 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 22:58:45 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 472.7 seconds
RetCode: 0
Status:   OK  
CheckDir: methylSig.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylSig.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylSig_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/methylSig.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.6.0'
* 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 LazyData ... 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
filter_loci_by_coverage 2.93   0.08   28.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
filter_loci_by_coverage  2.9   0.09   30.55
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/methylSig_1.6.0.tar.gz && rm -rf methylSig.buildbin-libdir && mkdir methylSig.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylSig.buildbin-libdir methylSig_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL methylSig_1.6.0.zip && rm methylSig_1.6.0.tar.gz methylSig_1.6.0.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
100 60293  100 60293    0     0   386k      0 --:--:-- --:--:-- --:--:--  389k

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_1.6.0.zip
* DONE (methylSig)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'methylSig' successfully unpacked and MD5 sums checked

Tests output

methylSig.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(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: [ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
  30.62    2.92   33.59 

methylSig.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(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: [ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
  33.65    2.01   35.68 

Example timings

methylSig.Rcheck/examples_i386/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded000
bsseq_multichrom000
bsseq_stranded000
diff_binomial3.750.113.85
diff_dss_fit1.640.171.82
diff_dss_test1.750.332.08
diff_methylsig1.850.202.04
filter_loci_by_coverage 2.93 0.0828.44
filter_loci_by_group_coverage2.240.192.42
filter_loci_by_location0.050.000.05
promoters_gr000
tile_by_regions0.260.030.30
tile_by_windows0.220.000.21

methylSig.Rcheck/examples_x64/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded000
bsseq_multichrom000
bsseq_stranded000
diff_binomial3.360.143.50
diff_dss_fit1.410.301.71
diff_dss_test1.670.281.95
diff_methylsig1.660.191.84
filter_loci_by_coverage 2.90 0.0930.55
filter_loci_by_group_coverage0.640.200.85
filter_loci_by_location0.050.000.04
promoters_gr0.020.000.02
tile_by_regions0.260.000.28
tile_by_windows0.220.020.24