Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-12 11:40 -0400 (Thu, 12 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 1209/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethReg 1.15.0 (landing page) Tiago Silva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.15.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MethReg_1.15.0.tar.gz |
StartedAt: 2024-09-12 00:22:40 -0400 (Thu, 12 Sep 2024) |
EndedAt: 2024-09-12 00:39:37 -0400 (Thu, 12 Sep 2024) |
EllapsedTime: 1017.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethReg.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MethReg_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MethReg.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * 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 ... 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 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 26.067 0.699 26.791 create_triplet_regulon_based 23.393 0.464 23.858 get_tf_in_region 22.525 0.696 23.221 * 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-3.20-bioc/meat/MethReg.Rcheck/00check.log’ for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)
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: 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 |============== 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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 4 | 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 4 | SKIP 11 | PASS 148 ] > > proc.time() user system elapsed 69.926 3.222 74.151
MethReg.Rcheck/MethReg-Ex.timings
name | user | system | elapsed | |
cor_dnam_target_gene | 0.041 | 0.000 | 0.041 | |
cor_tf_target_gene | 0.013 | 0.004 | 0.018 | |
create_triplet_distance_based | 26.067 | 0.699 | 26.791 | |
create_triplet_regulon_based | 23.393 | 0.464 | 23.858 | |
export_results_to_table | 1.230 | 0.056 | 1.286 | |
filter_dnam_by_quant_diff | 0.077 | 0.000 | 0.077 | |
filter_exp_by_quant_mean_FC | 0.698 | 0.028 | 0.727 | |
get_human_tfs | 0.461 | 0.024 | 0.484 | |
get_met_probes_info | 0.016 | 0.000 | 0.015 | |
get_promoter_avg | 0 | 0 | 0 | |
get_region_target_gene | 2.787 | 0.032 | 2.819 | |
get_residuals | 0.039 | 0.000 | 0.040 | |
get_tf_ES | 1.233 | 0.056 | 1.289 | |
get_tf_in_region | 22.525 | 0.696 | 23.221 | |
interaction_model | 0.235 | 0.016 | 0.251 | |
make_dnam_se | 0.068 | 0.012 | 0.080 | |
make_exp_se | 0.129 | 0.032 | 0.161 | |
make_granges_from_names | 0.014 | 0.000 | 0.014 | |
make_names_from_granges | 0.015 | 0.000 | 0.015 | |
plot_interaction_model | 1.684 | 0.032 | 1.716 | |
stratified_model | 0.037 | 0.000 | 0.037 | |