Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MEAT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEAT.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 1062/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEAT 1.4.0 (landing page) Sarah Voisin
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: MEAT |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MEAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MEAT_1.4.0.tar.gz |
StartedAt: 2021-10-14 10:28:35 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:34:11 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 336.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MEAT.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MEAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MEAT_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MEAT.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 ‘MEAT/DESCRIPTION’ ... OK * this is package ‘MEAT’ 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 ‘MEAT’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 5.7Mb * 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 ... WARNING Data codoc mismatches from documentation object 'CpGs_in_MEAT': Variables in data frame 'CpGs_in_MEAT' Code: Chromatin_state_male_SM Chromosome Coefficient CpG Gene Position Docs: Chromatin_state_male_SM Chromosome Coefficient CpGs Gene Position Data codoc mismatches from documentation object 'CpGs_in_MEAT2.0': Variables in data frame 'CpGs_in_MEAT2.0' Code: Chromatin_state_female_SM Chromatin_state_male_SM Chromosome Coefficient CpG Gene Position Docs: Chromatin_state_male_SM Chromosome Coefficient CpGs Gene Position * 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 ... WARNING LazyData DB of 5.7 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BMIQcalibration 19.917 0.616 20.534 epiage_estimation 18.266 0.696 18.963 * 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/MEAT.Rcheck/00check.log’ for details.
MEAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MEAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘MEAT’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (MEAT)
MEAT.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(MEAT) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' > > test_check("MEAT") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 15.827 0.636 16.451
MEAT.Rcheck/MEAT-Ex.timings
name | user | system | elapsed | |
BMIQcalibration | 19.917 | 0.616 | 20.534 | |
clean_beta | 1.193 | 0.068 | 1.261 | |
epiage_estimation | 18.266 | 0.696 | 18.963 | |