Tiago Silva
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MethReg |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1a84a50 |
| git_last_commit_date: 2021-05-27 17:34:34 -0400 (Thu, 27 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1101/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethReg 1.2.1 (landing page) Tiago Silva
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.2.1 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MethReg_1.2.1.tar.gz |
| StartedAt: 2021-10-14 10:32:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:38:16 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 373.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethReg.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MethReg_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MethReg.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.1’
* 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 28.810 1.488 30.328
create_triplet_regulon_based 22.423 1.172 23.599
get_tf_in_region 19.978 0.200 20.178
* 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: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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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══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (7)
• empty test (2)
[ FAIL 0 | WARN 0 | SKIP 9 | PASS 155 ]
>
> proc.time()
user system elapsed
107.403 4.467 112.960
MethReg.Rcheck/MethReg-Ex.timings
| name | user | system | elapsed | |
| cor_dnam_target_gene | 0.038 | 0.000 | 0.039 | |
| cor_tf_target_gene | 0.016 | 0.000 | 0.016 | |
| create_triplet_distance_based | 28.810 | 1.488 | 30.328 | |
| create_triplet_regulon_based | 22.423 | 1.172 | 23.599 | |
| filter_dnam_by_quant_diff | 0.082 | 0.000 | 0.082 | |
| filter_exp_by_quant_mean_FC | 0.681 | 0.032 | 0.714 | |
| get_human_tfs | 0.711 | 0.026 | 0.732 | |
| get_met_probes_info | 0.019 | 0.000 | 0.019 | |
| get_promoter_avg | 0.000 | 0.001 | 0.001 | |
| get_region_target_gene | 2.924 | 0.019 | 2.944 | |
| get_residuals | 0.042 | 0.000 | 0.042 | |
| get_tf_ES | 0.982 | 0.044 | 1.026 | |
| get_tf_in_region | 19.978 | 0.200 | 20.178 | |
| interaction_model | 0.058 | 0.004 | 0.062 | |
| make_dnam_se | 0.094 | 0.000 | 0.093 | |
| make_exp_se | 0.113 | 0.000 | 0.113 | |
| make_granges_from_names | 0.019 | 0.000 | 0.019 | |
| make_names_from_granges | 0.02 | 0.00 | 0.02 | |
| plot_interaction_model | 1.149 | 0.015 | 1.164 | |
| stratified_model | 0.05 | 0.00 | 0.05 | |