Back to Multiple platform build/check report for BioC 3.16: simplified long 

This page was generated on 20230324 11:05:33 0400 (Fri, 24 Mar 2023).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo2  Linux (Ubuntu 20.04.5 LTS)  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4286 
palomino4  Windows Server 2022 Datacenter  x64  4.2.3 (20230315 ucrt)  "Shortstop Beagle"  4276 
lconway  macOS 12.5.1 Monterey  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4303 
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/bbs3.16bioc/R/bin/R CMD check install=check:MethReg.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings MethReg_1.8.0.tar.gz 
StartedAt: 20230322 22:03:28 0400 (Wed, 22 Mar 2023) 
EndedAt: 20230322 22:14:07 0400 (Wed, 22 Mar 2023) 
EllapsedTime: 639.0 seconds 
RetCode: 0 
Status: WARNINGS 
CheckDir: MethReg.Rcheck 
Warnings: 2 
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD check install=check:MethReg.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings MethReg_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs3.16bioc/meat/MethReg.Rcheck’ * using R version 4.2.3 (20230315) * using platform: x86_64pclinuxgnu (64bit) * using session charset: UTF8 * checking for file ‘MethReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethReg’ version ‘1.8.0’ * package encoding: UTF8 * 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 metainformation ... OK * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for nonASCII 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 crossreferences ... 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 nonASCII 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 31.888 1.032 32.936 get_tf_in_region 23.582 0.164 23.746 create_triplet_regulon_based 23.111 0.420 23.532 * 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 ‘UTF8’... OK NONE * checking rebuilding of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs3.16bioc/meat/MethReg.Rcheck/00check.log’ for details.
MethReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD INSTALL MethReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs3.16bioc/R/sitelibrary’ * installing *source* package ‘MethReg’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** bytecompile 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 (20230315)  "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64pclinuxgnu (64bit) 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 online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(MethReg) > > test_check("MethReg")   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0%  0.16% ~1 s remaining  0.32% ~1 s remaining  0.48% ~1 s remaining  0.64% ~1 s remaining  0.8% ~1 s remaining  0.96% ~1 s remaining  1.12% ~1 s remaining  1.28% ~1 s remaining  1.44% ~1 s remaining  1.6% ~1 s remaining  1.76% ~1 s remaining  1.92% ~1 s remaining = 2.08% ~1 s remaining = 2.24% 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================================================ 93.44% ~0 s remaining ================================================ 93.6% ~0 s remaining ================================================ 93.76% ~0 s remaining ================================================ 93.92% ~0 s remaining ================================================ 94.08% ~0 s remaining ================================================= 94.24% ~0 s remaining ================================================= 94.4% ~0 s remaining ================================================= 94.56% ~0 s remaining ================================================= 94.72% ~0 s remaining ================================================= 94.88% ~0 s remaining ================================================= 95.04% ~0 s remaining ================================================= 95.2% ~0 s remaining ================================================= 95.36% ~0 s remaining ================================================= 95.52% ~0 s remaining ================================================= 95.68% ~0 s remaining ================================================= 95.84% ~0 s remaining =================================================  96% ~0 s remaining ================================================== 96.16% ~0 s remaining ================================================== 96.32% ~0 s remaining ================================================== 96.48% ~0 s remaining ================================================== 96.64% ~0 s remaining ================================================== 96.8% ~0 s remaining ================================================== 96.96% ~0 s remaining ================================================== 97.12% ~0 s remaining ================================================== 97.28% ~0 s remaining ================================================== 97.44% ~0 s remaining ================================================== 97.6% ~0 s remaining ================================================== 97.76% ~0 s remaining ================================================== 97.92% ~0 s remaining =================================================== 98.08% ~0 s remaining =================================================== 98.24% ~0 s remaining =================================================== 98.4% ~0 s remaining =================================================== 98.56% ~0 s remaining =================================================== 98.72% ~0 s remaining =================================================== 98.88% ~0 s remaining =================================================== 99.04% ~0 s remaining =================================================== 99.2% ~0 s remaining =================================================== 99.36% ~0 s remaining =================================================== 99.52% ~0 s remaining =================================================== 99.68% ~0 s remaining =================================================== 99.84% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 1 s Status freq 1 Regions below threshold 1 2 Regions above threshold 1 Status freq 1 Regions below threshold 1 2 Regions above threshold 1 Status freq 1 Regions below threshold 1 2 Regions above threshold 1   0% ==========================  50% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s Status freq 1 Genes above threshold 1 2 <NA> 1   0% ================= 33.33333% ~0 s remaining ================================== 66.66667% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ==========================  50% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ================= 33.33333% ~0 s remaining ================================== 66.66667% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ======= 14.28571% ~0 s remaining ============== 28.57143% ~0 s remaining ====================== 42.85714% ~0 s remaining ============================= 57.14286% ~0 s remaining ===================================== 71.42857% ~0 s remaining ============================================ 85.71429% ~0 s remaining ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s   0% ====================================================100% ~0 s remaining ====================================================100% Completed after 0 s [ FAIL 0  WARN 5  SKIP 10  PASS 152 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (6) • On CRAN (2) • empty test (2) [ FAIL 0  WARN 5  SKIP 10  PASS 152 ] > > proc.time() user system elapsed 98.051 2.813 102.132
MethReg.Rcheck/MethRegEx.timings
name  user  system  elapsed  
cor_dnam_target_gene  0.075  0.012  0.087  
cor_tf_target_gene  0.017  0.000  0.017  
create_triplet_distance_based  31.888  1.032  32.936  
create_triplet_regulon_based  23.111  0.420  23.532  
filter_dnam_by_quant_diff  0.082  0.003  0.086  
filter_exp_by_quant_mean_FC  0.696  0.025  0.720  
get_human_tfs  0.399  0.044  0.436  
get_met_probes_info  0.014  0.000  0.015  
get_promoter_avg  0  0  0  
get_region_target_gene  2.816  0.044  2.860  
get_residuals  0.038  0.004  0.043  
get_tf_ES  1.137  0.072  1.209  
get_tf_in_region  23.582  0.164  23.746  
interaction_model  0.228  0.012  0.240  
make_dnam_se  0.119  0.032  0.151  
make_exp_se  0.083  0.000  0.083  
make_granges_from_names  0.017  0.000  0.016  
make_names_from_granges  0.016  0.000  0.016  
plot_interaction_model  1.577  0.032  1.608  
stratified_model  0.048  0.000  0.048  