Tiago Silva
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: devel |
| git_last_commit: ba3e766 |
| git_last_commit_date: 2024-10-29 10:50:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: MethReg |
| Version: 1.17.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MethReg_1.17.0.tar.gz |
| StartedAt: 2024-12-24 08:27:21 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 08:39:06 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 704.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethReg.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MethReg_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.17.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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 58.540 0.694 59.445
create_triplet_regulon_based 56.393 0.575 57.086
get_tf_in_region 53.513 0.630 54.278
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/MethReg.Rcheck/00check.log’
for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
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Status freq
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2 Regions above threshold 1
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2 Regions above threshold 1
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2 Regions above threshold 1
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[ 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
116.130 3.389 128.917
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.039 | 0.004 | 0.043 | |
| cor_tf_target_gene | 0.02 | 0.00 | 0.02 | |
| create_triplet_distance_based | 58.540 | 0.694 | 59.445 | |
| create_triplet_regulon_based | 56.393 | 0.575 | 57.086 | |
| export_results_to_table | 1.951 | 0.024 | 1.981 | |
| filter_dnam_by_quant_diff | 0.126 | 0.004 | 0.131 | |
| filter_exp_by_quant_mean_FC | 1.112 | 0.000 | 1.115 | |
| get_human_tfs | 0.806 | 0.050 | 4.416 | |
| get_met_probes_info | 0.019 | 0.000 | 0.019 | |
| get_promoter_avg | 0 | 0 | 0 | |
| get_region_target_gene | 4.085 | 0.111 | 4.209 | |
| get_residuals | 0.061 | 0.003 | 0.064 | |
| get_tf_ES | 3.198 | 0.327 | 3.544 | |
| get_tf_in_region | 53.513 | 0.630 | 54.278 | |
| interaction_model | 0.254 | 0.024 | 0.279 | |
| make_dnam_se | 0.088 | 0.000 | 0.089 | |
| make_exp_se | 0.113 | 0.000 | 0.113 | |
| make_granges_from_names | 0.020 | 0.000 | 0.019 | |
| make_names_from_granges | 0.02 | 0.00 | 0.02 | |
| plot_interaction_model | 2.103 | 0.076 | 2.184 | |
| stratified_model | 0.093 | 0.000 | 0.093 | |