Tiago Silva
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: RELEASE_3_16 |
| git_last_commit: 6235257 |
| git_last_commit_date: 2022-11-01 11:22:54 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:14 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 1166/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.8.0 (landing page) Tiago Silva
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MethReg |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2023-04-10 21:07:41 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:13:45 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 363.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MethReg.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.8.0’
* 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 ... WARNING
'::' or ':::' imports not declared from:
‘data.table’ ‘openxlsx’
Missing or unexported object: ‘downloader::download.file’
* 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 ... WARNING
Undocumented arguments in documentation object 'methReg_analysis'
‘tf.dnam.classifier.pval.threshold’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 28.451 2.269 30.871
create_triplet_regulon_based 20.833 1.155 22.043
get_tf_in_region 20.038 1.131 21.221
* 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: 2 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck/00check.log’
for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
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2 Regions above threshold 1
Status freq
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Status freq
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[ FAIL 0 | WARN 4 | SKIP 10 | PASS 152 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (6)
• On CRAN (2)
• empty test (2)
[ FAIL 0 | WARN 4 | SKIP 10 | PASS 152 ]
>
> proc.time()
user system elapsed
81.696 6.145 89.122
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.042 | 0.008 | 0.051 | |
| cor_tf_target_gene | 0.017 | 0.004 | 0.020 | |
| create_triplet_distance_based | 28.451 | 2.269 | 30.871 | |
| create_triplet_regulon_based | 20.833 | 1.155 | 22.043 | |
| filter_dnam_by_quant_diff | 0.075 | 0.003 | 0.079 | |
| filter_exp_by_quant_mean_FC | 0.626 | 0.031 | 0.660 | |
| get_human_tfs | 0.403 | 0.142 | 0.465 | |
| get_met_probes_info | 0.014 | 0.000 | 0.014 | |
| get_promoter_avg | 0 | 0 | 0 | |
| get_region_target_gene | 2.582 | 0.113 | 2.700 | |
| get_residuals | 0.034 | 0.003 | 0.037 | |
| get_tf_ES | 1.047 | 0.103 | 1.156 | |
| get_tf_in_region | 20.038 | 1.131 | 21.221 | |
| interaction_model | 0.212 | 0.003 | 0.216 | |
| make_dnam_se | 0.051 | 0.001 | 0.052 | |
| make_exp_se | 0.062 | 0.001 | 0.063 | |
| make_granges_from_names | 0.011 | 0.000 | 0.011 | |
| make_names_from_granges | 0.011 | 0.000 | 0.011 | |
| plot_interaction_model | 1.411 | 0.053 | 1.468 | |
| stratified_model | 0.035 | 0.001 | 0.037 | |