Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:10 -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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MethReg_1.8.0.tar.gz |
StartedAt: 2023-04-10 21:51:38 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:01:51 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 613.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MethReg.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MethReg.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MethReg_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 31.714 1.012 32.741 create_triplet_regulon_based 23.422 0.544 23.966 get_tf_in_region 23.255 0.176 23.431 * 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 ... ‘MethReg.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.16-bioc/meat/MethReg.Rcheck/00check.log’ for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 ** 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-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. 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0 | WARN 4 | SKIP 10 | PASS 152 ] > > proc.time() user system elapsed 96.968 3.908 102.115
MethReg.Rcheck/MethReg-Ex.timings
name | user | system | elapsed | |
cor_dnam_target_gene | 0.062 | 0.012 | 0.074 | |
cor_tf_target_gene | 0.014 | 0.000 | 0.014 | |
create_triplet_distance_based | 31.714 | 1.012 | 32.741 | |
create_triplet_regulon_based | 23.422 | 0.544 | 23.966 | |
filter_dnam_by_quant_diff | 0.082 | 0.008 | 0.091 | |
filter_exp_by_quant_mean_FC | 0.733 | 0.016 | 0.749 | |
get_human_tfs | 0.410 | 0.024 | 0.426 | |
get_met_probes_info | 0.014 | 0.000 | 0.014 | |
get_promoter_avg | 0.001 | 0.000 | 0.000 | |
get_region_target_gene | 3.051 | 0.060 | 3.112 | |
get_residuals | 0.046 | 0.000 | 0.046 | |
get_tf_ES | 1.087 | 0.040 | 1.127 | |
get_tf_in_region | 23.255 | 0.176 | 23.431 | |
interaction_model | 0.209 | 0.016 | 0.224 | |
make_dnam_se | 0.066 | 0.000 | 0.065 | |
make_exp_se | 0.083 | 0.000 | 0.083 | |
make_granges_from_names | 0.015 | 0.000 | 0.015 | |
make_names_from_granges | 0.012 | 0.004 | 0.016 | |
plot_interaction_model | 1.610 | 0.056 | 1.667 | |
stratified_model | 0.045 | 0.000 | 0.044 | |