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This page was generated on 2024-10-16 11:48 -0400 (Wed, 16 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4473
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4730
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4478
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4509
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4457
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4457
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 1216/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethReg 1.15.0  (landing page)
Tiago Silva
Snapshot Date: 2024-10-15 13:40 -0400 (Tue, 15 Oct 2024)
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: devel
git_last_commit: aeb2a7e
git_last_commit_date: 2024-04-30 11:27:17 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MethReg on kjohnson3

To the developers/maintainers of the MethReg package:
- 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 Troubleshooting Build Report for more information.
- 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: MethReg
Version: 1.15.0
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_1.15.0.tar.gz
StartedAt: 2024-10-16 00:40:57 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 00:47:13 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 376.6 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MethReg.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 ... 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 ... 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 7.072  0.434   7.527
create_triplet_regulon_based  5.901  0.258   6.159
get_tf_in_region              5.403  0.295   5.700
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 3 | SKIP 11 | PASS 148 ]

══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On Bioconductor (7): 'test-create_triplet_distance_based.R:2:3',
  'test-get_promoter_avg.R:3:5', 'test-get_promoter_avg.R:15:5',
  'test-get_promoter_avg.R:30:5', 'test-get_promoter_avg.R:47:5',
  'test-plot_interaction_model.R:3:5', 'test-plot_stratified_model.R:3:5'
• On CRAN (2): 'test-get_human_tfs.R:2:5', 'test-get_tf_in_region.R:3:5'
• empty test (2): 'test-get_residuals.R:1:1', 'test-get_tf_in_region.R:16:1'

[ FAIL 0 | WARN 3 | SKIP 11 | PASS 148 ]
> 
> proc.time()
   user  system elapsed 
 22.380   0.994  24.415 

Example timings

MethReg.Rcheck/MethReg-Ex.timings

nameusersystemelapsed
cor_dnam_target_gene0.0110.0010.013
cor_tf_target_gene0.0030.0000.004
create_triplet_distance_based7.0720.4347.527
create_triplet_regulon_based5.9010.2586.159
export_results_to_table0.4040.0160.421
filter_dnam_by_quant_diff0.0320.0010.033
filter_exp_by_quant_mean_FC0.1870.0060.195
get_human_tfs0.1330.0170.144
get_met_probes_info0.0040.0010.005
get_promoter_avg000
get_region_target_gene1.3960.0551.451
get_residuals0.0120.0020.014
get_tf_ES0.4410.0300.473
get_tf_in_region5.4030.2955.700
interaction_model0.0560.0030.057
make_dnam_se0.0150.0000.015
make_exp_se0.0360.0040.039
make_granges_from_names0.0030.0000.003
make_names_from_granges0.0030.0000.003
plot_interaction_model0.3930.0090.401
stratified_model0.0100.0010.011