Tiago Silva
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: RELEASE_3_14 |
| git_last_commit: 4dae66b |
| git_last_commit_date: 2021-10-26 13:02:56 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:19 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the MethReg package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1114/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.4.0 (landing page) Tiago Silva
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MethReg |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2022-04-12 15:16:34 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 15:25:34 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 539.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethReg.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MethReg.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethReg’ version ‘1.4.0’
* 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 R 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 ... OK
* 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 40.776 2.289 43.247
create_triplet_regulon_based 33.911 1.147 35.085
get_tf_in_region 29.473 0.910 30.407
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
MethReg.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
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Status freq
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Status freq
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2 <NA> 1
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[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (6)
• On CRAN (2)
• empty test (2)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 152 ]
>
> proc.time()
user system elapsed
123.443 4.917 129.054
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.162 | 0.006 | 0.168 | |
| cor_tf_target_gene | 0.094 | 0.003 | 0.097 | |
| create_triplet_distance_based | 40.776 | 2.289 | 43.247 | |
| create_triplet_regulon_based | 33.911 | 1.147 | 35.085 | |
| filter_dnam_by_quant_diff | 0.217 | 0.004 | 0.222 | |
| filter_exp_by_quant_mean_FC | 1.363 | 0.058 | 1.422 | |
| get_human_tfs | 1.396 | 0.044 | 1.425 | |
| get_met_probes_info | 0.035 | 0.001 | 0.035 | |
| get_promoter_avg | 0.000 | 0.001 | 0.000 | |
| get_region_target_gene | 4.761 | 0.116 | 4.880 | |
| get_residuals | 0.081 | 0.007 | 0.088 | |
| get_tf_ES | 1.556 | 0.089 | 1.648 | |
| get_tf_in_region | 29.473 | 0.910 | 30.407 | |
| interaction_model | 0.293 | 0.004 | 0.297 | |
| make_dnam_se | 0.180 | 0.002 | 0.181 | |
| make_exp_se | 0.21 | 0.01 | 0.22 | |
| make_granges_from_names | 0.030 | 0.001 | 0.030 | |
| make_names_from_granges | 0.038 | 0.001 | 0.038 | |
| plot_interaction_model | 2.223 | 0.026 | 2.250 | |
| stratified_model | 0.266 | 0.004 | 0.271 | |