Back to Multiple platform build/check report for BioC 3.17
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-12-09 11:06:05 -0500 (Fri, 09 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4449
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4194
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4237
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 nebbiolo1


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? 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 1163/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylSig 1.11.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2022-12-08 14:00:20 -0500 (Thu, 08 Dec 2022)
git_url: https://git.bioconductor.org/packages/methylSig
git_branch: master
git_last_commit: 5d89bed
git_last_commit_date: 2022-11-01 11:21:55 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'bsseq' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'bsseq' which is not available

Summary

Package: methylSig
Version: 1.11.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylSig.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methylSig_1.11.0.tar.gz
StartedAt: 2022-12-08 21:33:20 -0500 (Thu, 08 Dec 2022)
EndedAt: 2022-12-08 21:39:09 -0500 (Thu, 08 Dec 2022)
EllapsedTime: 348.2 seconds
RetCode: 0
Status:   OK  
CheckDir: methylSig.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylSig.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methylSig_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methylSig.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘methylSig/DESCRIPTION’ ... OK
* this is package ‘methylSig’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
filter_loci_by_coverage 4.796  0.511   5.048
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘updating-methylSig-code.Rmd’ using ‘UTF-8’... OK
  ‘using-methylSig.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

methylSig.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL methylSig
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* 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
** 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
* DONE (methylSig)

Tests output

methylSig.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 31.305   1.671  32.966 

Example timings

methylSig.Rcheck/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded0.0000.0020.002
bsseq_multichrom0.0000.0010.001
bsseq_stranded0.0010.0000.002
diff_binomial1.7200.1881.909
diff_dss_fit2.5680.1522.720
diff_dss_test1.8020.1441.946
diff_methylsig0.6950.1080.804
filter_loci_by_coverage4.7960.5115.048
filter_loci_by_group_coverage0.4950.0630.557
filter_loci_by_location0.0430.0000.044
promoters_gr0.0010.0000.002
tile_by_regions0.2470.0120.258
tile_by_windows0.1680.0160.183