Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1215/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethReg 1.17.0 (landing page) Tiago Silva
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 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: 1.17.0 |
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_1.17.0.tar.gz |
StartedAt: 2024-12-23 23:38:23 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:54:52 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 989.2 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_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MethReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethReg’ version ‘1.17.0’ * 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 27.047 1.960 29.049 create_triplet_regulon_based 22.698 0.844 23.560 get_tf_in_region 20.714 0.358 21.072 * 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’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** testing if installed package can be loaded from final location No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** testing if installed package keeps a record of temporary installation path * DONE (MethReg)
MethReg.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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) No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools' > > 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 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|=================================================== |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 79.085 3.966 83.861
MethReg.Rcheck/MethReg-Ex.timings
name | user | system | elapsed | |
cor_dnam_target_gene | 0.031 | 0.001 | 0.032 | |
cor_tf_target_gene | 0.016 | 0.001 | 0.017 | |
create_triplet_distance_based | 27.047 | 1.960 | 29.049 | |
create_triplet_regulon_based | 22.698 | 0.844 | 23.560 | |
export_results_to_table | 1.304 | 0.025 | 1.342 | |
filter_dnam_by_quant_diff | 0.080 | 0.000 | 0.081 | |
filter_exp_by_quant_mean_FC | 0.719 | 0.041 | 0.761 | |
get_human_tfs | 0.635 | 0.051 | 1.560 | |
get_met_probes_info | 0.014 | 0.001 | 0.015 | |
get_promoter_avg | 0.000 | 0.000 | 0.001 | |
get_region_target_gene | 3.832 | 0.174 | 4.007 | |
get_residuals | 0.036 | 0.001 | 0.038 | |
get_tf_ES | 1.164 | 0.039 | 1.203 | |
get_tf_in_region | 20.714 | 0.358 | 21.072 | |
interaction_model | 0.189 | 0.017 | 0.205 | |
make_dnam_se | 0.058 | 0.004 | 0.061 | |
make_exp_se | 0.080 | 0.001 | 0.081 | |
make_granges_from_names | 0.015 | 0.000 | 0.014 | |
make_names_from_granges | 0.016 | 0.000 | 0.017 | |
plot_interaction_model | 1.514 | 0.039 | 1.554 | |
stratified_model | 0.042 | 0.001 | 0.044 | |