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This page was generated on 2024-03-28 11:32:24 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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

Package 1234/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylSig 1.14.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/methylSig
git_branch: RELEASE_3_18
git_last_commit: 341d23b
git_last_commit_date: 2023-10-24 11:21:41 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for methylSig on kjohnson1


To the developers/maintainers of the methylSig package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: methylSig
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylSig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylSig_1.14.0.tar.gz
StartedAt: 2024-03-27 18:51:12 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 18:57:29 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 377.3 seconds
RetCode: 0
Status:   OK  
CheckDir: methylSig.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylSig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylSig_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/methylSig.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylSig/DESCRIPTION’ ... OK
* this is package ‘methylSig’ version ‘1.14.0’
* 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 4.869  0.497   5.181
* 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 ... 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylSig
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
 33.731   1.508  35.368 

Example timings

methylSig.Rcheck/methylSig-Ex.timings

nameusersystemelapsed
bsseq_destranded0.0030.0010.004
bsseq_multichrom0.0010.0010.001
bsseq_stranded0.0010.0010.002
diff_binomial3.0700.1413.224
diff_dss_fit1.8020.1191.923
diff_dss_test1.9480.0682.024
diff_methylsig1.7080.0621.789
filter_loci_by_coverage4.8690.4975.181
filter_loci_by_group_coverage0.6170.1880.807
filter_loci_by_location0.0330.0060.043
promoters_gr0.0010.0010.002
tile_by_regions0.2750.0630.341
tile_by_windows0.1330.0230.160