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This page was generated on 2022-08-15 11:07:54 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4378
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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 lconway


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 1144/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.7.0  (landing page)
Tiago Silva
Snapshot Date: 2022-08-14 14:00:05 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: master
git_last_commit: 062b8a4
git_last_commit_date: 2022-04-28 13:32:26 -0400 (Thu, 28 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MethReg
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2022-08-14 20:59:38 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 21:05:47 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 368.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MethReg.Rcheck
Warnings: 2

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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* 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 ‘1.7.0’
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘data.table’ ‘openxlsx’
Missing or unexported object: ‘downloader::download.file’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readRemap2022: no visible binding for global variable ‘biotype’
Undefined global functions or variables:
  biotype
* 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 ... WARNING
Undocumented arguments in documentation object 'methReg_analysis'
  ‘tf.dnam.classifier.pval.threshold’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 28.884  2.275  31.299
create_triplet_regulon_based  22.294  1.162  23.524
get_tf_in_region              19.694  1.039  20.798
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck/00check.log’
for details.



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/4.2/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 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
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 
 84.393   5.560  91.261 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.0900.0130.103
cor_tf_target_gene0.0400.0050.045
create_triplet_distance_based28.884 2.27531.299
create_triplet_regulon_based22.294 1.16223.524
filter_dnam_by_quant_diff0.0810.0020.084
filter_exp_by_quant_mean_FC0.7010.0330.736
get_human_tfs0.5040.1220.573
get_met_probes_info0.0170.0000.016
get_promoter_avg0.0000.0010.000
get_region_target_gene2.9360.0853.028
get_residuals0.0400.0030.043
get_tf_ES1.0890.0981.198
get_tf_in_region19.694 1.03920.798
interaction_model0.3250.0030.330
make_dnam_se0.0660.0010.067
make_exp_se0.0780.0010.080
make_granges_from_names0.0140.0000.014
make_names_from_granges0.0150.0010.015
plot_interaction_model1.2410.0391.281
stratified_model0.1360.0030.139