Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 1685/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
recountmethylation 1.15.0 (landing page) Sean K Maden
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the recountmethylation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recountmethylation.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: recountmethylation |
Version: 1.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recountmethylation_1.15.0.tar.gz |
StartedAt: 2024-08-26 22:47:57 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:50:06 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 129.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: recountmethylation.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recountmethylation_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/recountmethylation.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recountmethylation/DESCRIPTION’ ... OK * this is package ‘recountmethylation’ version ‘1.15.0’ * 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 ‘recountmethylation’ 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE get_fh : <anonymous>: no visible global function definition for ‘make_fhmatrix_autolabel’ make_si : <anonymous>: no visible global function definition for ‘make_hnsw_si’ query_si: no visible binding for global variable ‘v’ query_si : <anonymous>: no visible global function definition for ‘make_dfk_sampleid’ Undefined global functions or variables: make_dfk_sampleid make_fhmatrix_autolabel make_hnsw_si v * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bactrl 14.890 0.757 15.806 gds_idat2rg 7.006 0.526 25.329 gds_idatquery 0.525 0.280 17.624 get_rmdl 0.090 0.021 9.276 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-servermatrix.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/recountmethylation.Rcheck/00check.log’ for details.
recountmethylation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recountmethylation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘recountmethylation’ ... ** using staged installation ** R ** 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 (recountmethylation)
recountmethylation.Rcheck/tests/test-servermatrix.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > testthat::context("Test the server matrix properties") > > testthat::test_that("Properties of server matrix returned from get_rmdl + and servermatrix", { + sm <- recountmethylation::get_servermatrix() + testthat::expect_true(is(sm, "matrix")) + testthat::expect_equal(ncol(sm), 4) + testthat::expect_true(is(sm[,1], "character")) + }) Test passed 😸 > > proc.time() user system elapsed 1.338 0.158 6.563
recountmethylation.Rcheck/recountmethylation-Ex.timings
name | user | system | elapsed | |
bactrl | 14.890 | 0.757 | 15.806 | |
bathresh | 0.002 | 0.000 | 0.003 | |
data_mdpost | 0.012 | 0.002 | 0.016 | |
gds_idat2rg | 7.006 | 0.526 | 25.329 | |
gds_idatquery | 0.525 | 0.280 | 17.624 | |
get_crossreactive_cpgs | 0.295 | 0.012 | 0.309 | |
get_fh | 0 | 0 | 0 | |
get_qcsignal | 2.727 | 0.166 | 2.918 | |
get_rmdl | 0.090 | 0.021 | 9.276 | |
get_servermatrix | 0.004 | 0.001 | 0.006 | |
getdb | 0 | 0 | 0 | |
getrg | 0.101 | 0.010 | 0.111 | |
hread | 0.006 | 0.001 | 0.006 | |
make_si | 0.001 | 0.000 | 0.000 | |
matchds_1to2 | 0.001 | 0.000 | 0.001 | |
query_si | 0.000 | 0.001 | 0.000 | |
rgse | 0.266 | 0.031 | 0.298 | |
servermatrix | 0.007 | 0.002 | 0.303 | |
smfilt | 0.001 | 0.000 | 0.001 | |