Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:19 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 MethReg on machv2


To the developers/maintainers of the MethReg package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethReg.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 1114/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.4.0  (landing page)
Tiago Silva
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: RELEASE_3_14
git_last_commit: 4dae66b
git_last_commit_date: 2021-10-26 13:02:56 -0400 (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: MethReg
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethReg_1.4.0.tar.gz
StartedAt: 2022-04-12 15:16:34 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:25:34 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 539.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MethReg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethReg_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MethReg.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.4.0’
* 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 ‘MethReg’ 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
create_triplet_distance_based 40.776  2.289  43.247
create_triplet_regulon_based  33.911  1.147  35.085
get_tf_in_region              29.473  0.910  30.407
* 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

MethReg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MethReg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MethReg’ ...
** 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 (MethReg)

Tests output

MethReg.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(MethReg)
> 
> test_check("MethReg")

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                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1
                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1
                   Status freq
1 Regions below threshold    1
2 Regions above threshold    1

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                 Status freq
1 Genes above threshold    1
2                  <NA>    1

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[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (6)
• On CRAN (2)
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]
> 
> proc.time()
   user  system elapsed 
123.443   4.917 129.054 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.1620.0060.168
cor_tf_target_gene0.0940.0030.097
create_triplet_distance_based40.776 2.28943.247
create_triplet_regulon_based33.911 1.14735.085
filter_dnam_by_quant_diff0.2170.0040.222
filter_exp_by_quant_mean_FC1.3630.0581.422
get_human_tfs1.3960.0441.425
get_met_probes_info0.0350.0010.035
get_promoter_avg0.0000.0010.000
get_region_target_gene4.7610.1164.880
get_residuals0.0810.0070.088
get_tf_ES1.5560.0891.648
get_tf_in_region29.473 0.91030.407
interaction_model0.2930.0040.297
make_dnam_se0.1800.0020.181
make_exp_se0.210.010.22
make_granges_from_names0.0300.0010.030
make_names_from_granges0.0380.0010.038
plot_interaction_model2.2230.0262.250
stratified_model0.2660.0040.271