Tiago Silva
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: RELEASE_3_21 |
| git_last_commit: cc9ab7e |
| git_last_commit_date: 2025-04-15 12:09:21 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1247/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.18.0 (landing page) Tiago Silva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: MethReg |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MethReg_1.18.0.tar.gz |
| StartedAt: 2025-10-16 00:52:02 -0400 (Thu, 16 Oct 2025) |
| EndedAt: 2025-10-16 01:08:01 -0400 (Thu, 16 Oct 2025) |
| EllapsedTime: 959.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethReg.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MethReg_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 loading without being on the library search path ... 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 24.025 0.783 24.847
create_triplet_regulon_based 21.938 0.531 22.504
get_tf_in_region 21.406 0.218 21.626
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck/00check.log’
for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MethReg’ ... ** this is package ‘MethReg’ version ‘1.18.0’ ** 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)
MethReg.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
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
| | 0%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
Status freq
1 Genes above threshold 1
2 <NA> 1
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
| |0.8928571% ~0 s remaining
| |1.785714% ~0 s remaining
|= |2.678571% ~0 s remaining
|= |3.571429% ~0 s remaining
|== |4.464286% ~0 s remaining
|== |5.357143% ~0 s remaining
|=== |6.25% ~0 s remaining
|=== |7.142857% ~0 s remaining
|==== |8.035714% ~0 s remaining
|==== |8.928571% ~0 s remaining
|===== |9.821429% ~0 s remaining
|===== |10.71429% ~0 s remaining
|====== |11.60714% ~0 s remaining
|====== |12.5% ~0 s remaining
|====== |13.39286% ~0 s remaining
|======= |14.28571% ~0 s remaining
|======= |15.17857% ~0 s remaining
|======== |16.07143% ~0 s remaining
|======== |16.96429% ~0 s remaining
|========= |17.85714% ~0 s remaining
|========= |18.75% ~0 s remaining
|========== |19.64286% ~0 s remaining
|========== |20.53571% ~0 s remaining
|=========== |21.42857% ~0 s remaining
|=========== |22.32143% ~0 s remaining
|============ |23.21429% ~0 s remaining
|============ |24.10714% ~0 s remaining
|============= | 25% ~0 s remaining
|============= |25.89286% ~0 s remaining
|============= |26.78571% ~0 s remaining
|============== |27.67857% ~0 s remaining
|============== |28.57143% ~0 s remaining
|=============== |29.46429% ~0 s remaining
|=============== |30.35714% ~0 s remaining
|================ |31.25% ~0 s remaining
|================ |32.14286% ~0 s remaining
|================= |33.03571% ~0 s remaining
|================= |33.92857% ~0 s remaining
|================== |34.82143% ~0 s remaining
|================== |35.71429% ~0 s remaining
|=================== |36.60714% ~0 s remaining
|=================== |37.5% ~0 s remaining
|=================== |38.39286% ~0 s remaining
|==================== |39.28571% ~0 s remaining
|==================== |40.17857% ~0 s remaining
|===================== |41.07143% ~0 s remaining
|===================== |41.96429% ~0 s remaining
|====================== |42.85714% ~0 s remaining
|====================== |43.75% ~0 s remaining
|======================= |44.64286% ~0 s remaining
|======================= |45.53571% ~0 s remaining
|======================== |46.42857% ~0 s remaining
|======================== |47.32143% ~0 s remaining
|========================= |48.21429% ~0 s remaining
|========================= |49.10714% ~0 s remaining
|========================== | 50% ~0 s remaining
|========================== |50.89286% ~0 s remaining
|========================== |51.78571% ~0 s remaining
|=========================== |52.67857% ~0 s remaining
|=========================== |53.57143% ~0 s remaining
|============================ |54.46429% ~0 s remaining
|============================ |55.35714% ~0 s remaining
|============================= |56.25% ~0 s remaining
|============================= |57.14286% ~0 s remaining
|============================== |58.03571% ~0 s remaining
|============================== |58.92857% ~0 s remaining
|=============================== |59.82143% ~0 s remaining
|=============================== |60.71429% ~0 s remaining
|================================ |61.60714% ~0 s remaining
|================================ |62.5% ~0 s remaining
|================================ |63.39286% ~0 s remaining
|================================= |64.28571% ~0 s remaining
|================================= |65.17857% ~0 s remaining
|================================== |66.07143% ~0 s remaining
|================================== |66.96429% ~0 s remaining
|=================================== |67.85714% ~0 s remaining
|=================================== |68.75% ~0 s remaining
|==================================== |69.64286% ~0 s remaining
|==================================== |70.53571% ~0 s remaining
|===================================== |71.42857% ~0 s remaining
|===================================== |72.32143% ~0 s remaining
|====================================== |73.21429% ~0 s remaining
|====================================== |74.10714% ~0 s remaining
|======================================= | 75% ~0 s remaining
|======================================= |75.89286% ~0 s remaining
|======================================= |76.78571% ~0 s remaining
|======================================== |77.67857% ~0 s remaining
|======================================== |78.57143% ~0 s remaining
|========================================= |79.46429% ~0 s remaining
|========================================= |80.35714% ~0 s remaining
|========================================== |81.25% ~0 s remaining
|========================================== |82.14286% ~0 s remaining
|=========================================== |83.03571% ~0 s remaining
|=========================================== |83.92857% ~0 s remaining
|============================================ |84.82143% ~0 s remaining
|============================================ |85.71429% ~0 s remaining
|============================================= |86.60714% ~0 s remaining
|============================================= |87.5% ~0 s remaining
|============================================= |88.39286% ~0 s remaining
|============================================== |89.28571% ~0 s remaining
|============================================== |90.17857% ~0 s remaining
|=============================================== |91.07143% ~0 s remaining
|=============================================== |91.96429% ~0 s remaining
|================================================ |92.85714% ~0 s remaining
|================================================ |93.75% ~0 s remaining
|================================================= |94.64286% ~0 s remaining
|================================================= |95.53571% ~0 s remaining
|================================================== |96.42857% ~0 s remaining
|================================================== |97.32143% ~0 s remaining
|=================================================== |98.21429% ~0 s remaining
|=================================================== |99.10714% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
[ 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
67.562 2.452 70.786
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.032 | 0.008 | 0.040 | |
| cor_tf_target_gene | 0.013 | 0.004 | 0.018 | |
| create_triplet_distance_based | 24.025 | 0.783 | 24.847 | |
| create_triplet_regulon_based | 21.938 | 0.531 | 22.504 | |
| export_results_to_table | 1.227 | 0.012 | 1.239 | |
| filter_dnam_by_quant_diff | 0.078 | 0.001 | 0.080 | |
| filter_exp_by_quant_mean_FC | 0.728 | 0.033 | 0.761 | |
| get_human_tfs | 0.515 | 0.041 | 0.542 | |
| get_met_probes_info | 0.012 | 0.002 | 0.015 | |
| get_promoter_avg | 0 | 0 | 0 | |
| get_region_target_gene | 2.885 | 0.022 | 2.906 | |
| get_residuals | 0.031 | 0.005 | 0.036 | |
| get_tf_ES | 1.292 | 0.054 | 1.347 | |
| get_tf_in_region | 21.406 | 0.218 | 21.626 | |
| interaction_model | 0.184 | 0.010 | 0.194 | |
| make_dnam_se | 0.055 | 0.001 | 0.055 | |
| make_exp_se | 0.107 | 0.006 | 0.114 | |
| make_granges_from_names | 0.014 | 0.000 | 0.014 | |
| make_names_from_granges | 0.014 | 0.000 | 0.014 | |
| plot_interaction_model | 4.128 | 0.132 | 4.261 | |
| stratified_model | 0.030 | 0.004 | 0.034 | |