Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-15 12:06 -0400 (Wed, 15 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4866 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4653 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4598 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1161/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.1.2 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.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: maaslin3 |
Version: 1.1.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.2.tar.gz |
StartedAt: 2025-10-14 20:51:16 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 20:56:05 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 289.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maaslin3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maaslin3/DESCRIPTION’ ... OK * this is package ‘maaslin3’ version ‘1.1.2’ * 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 ‘maaslin3’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed maaslin_plot_results_from_output 16.386 0.586 17.074 maaslin_plot_results 16.156 0.691 16.885 maaslin3 8.278 0.470 8.774 maaslin_contrast_test 6.867 0.677 7.594 maaslin_write_results 5.551 0.542 6.115 maaslin_fit 5.272 0.613 5.916 maaslin_write_results_lefse_format 5.357 0.483 5.858 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.2’ ** 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 (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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. > library(testthat) > library(maaslin3) > > test_check("maaslin3") 2025-10-14 20:53:43.491083 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:53:43.517349 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:53:43.550721 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:53:43.55802 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:53:43.569137 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:53:43.593854 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:53:43.595791 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:53:43.599881 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:53:43.635948 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:53:43.637865 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:53:43.654507 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:53:43.6677 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:53:43.67162 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:53:43.688258 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:53:43.710166 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:53:50.462358 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:53:50.489429 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:53:50.525876 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:53:50.534061 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:53:50.547312 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:53:50.57385 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:53:50.575749 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:53:50.579662 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:53:50.611444 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:53:50.613376 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:53:50.629902 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:53:50.643299 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:53:50.647296 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:53:50.660499 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:53:50.683197 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:53:52.161 R[21403:463241082] XType: Using static font registry. 2025-10-14 20:54:00.012175 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:00.038701 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:00.065374 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:00.073517 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:00.086403 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:00.11482 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:00.117068 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:00.12138 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:00.15595 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:00.158134 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:00.176726 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:00.191352 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:00.195737 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:00.210203 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:00.235327 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:05.521744 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:05.547744 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:05.573033 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:05.580858 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:05.59285 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:05.61948 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:05.621415 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:05.625505 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:05.657723 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:05.659837 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:05.67949 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:05.693941 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:05.698331 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:05.71273 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:05.740224 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:05.829973 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds 2025-10-14 20:54:05.862384 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds 2025-10-14 20:54:05.896056 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds 2025-10-14 20:54:06.069754 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds 2025-10-14 20:54:14.305521 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:14.332448 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:14.359326 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:14.36714 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:14.379159 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:14.406151 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:14.408255 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:14.41256 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:14.446186 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:14.448253 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:14.468531 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:14.482838 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:14.977433 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:14.990862 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:15.014278 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:20.012179 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:20.058809 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:20.084572 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:20.09227 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:20.104259 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:20.130478 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:20.13255 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:20.136543 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:20.169533 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:20.171472 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:20.18834 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:20.202424 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:20.20662 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:20.220642 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:20.244955 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:20.320332 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds 2025-10-14 20:54:20.352963 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds 2025-10-14 20:54:20.386591 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds 2025-10-14 20:54:20.560813 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds 2025-10-14 20:54:28.754512 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:28.781219 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:28.813186 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:28.821669 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:28.834434 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:28.864117 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:28.866718 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:28.870944 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:28.905364 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:28.907552 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:28.926064 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:28.944285 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:28.948793 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:28.962612 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:28.988195 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:34.115835 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:34.141957 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:34.167513 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:34.175202 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:34.187377 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:34.213677 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:34.215677 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:34.219851 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:34.253957 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:34.256043 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:34.273288 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:34.287704 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:34.292156 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:34.30751 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:34.334425 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:34.420598 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds 2025-10-14 20:54:34.453163 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds 2025-10-14 20:54:34.486856 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds 2025-10-14 20:54:34.663278 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds 2025-10-14 20:54:42.829866 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:42.857218 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:42.884157 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:42.892354 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:42.904434 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:42.931154 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:42.933215 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:42.93739 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:42.971154 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:42.973256 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:42.99064 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:43.027401 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:43.032495 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:43.048029 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:43.074709 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:48.139886 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:54:48.167051 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:54:48.193125 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:54:48.201592 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:54:48.214275 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:54:48.240129 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:54:48.242015 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:54:48.245944 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:54:48.27818 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:54:48.280198 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:54:48.297161 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:54:48.310817 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:54:48.315071 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:54:48.328675 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:54:48.351626 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:54:57.467868 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:01.344276 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:10.667054 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:14.442668 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:14.640829 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds 2025-10-14 20:55:14.674066 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds 2025-10-14 20:55:14.696113 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds 2025-10-14 20:55:14.736923 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds 2025-10-14 20:55:23.549601 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:26.163473 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:26.26654 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds 2025-10-14 20:55:26.300483 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds 2025-10-14 20:55:26.323189 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds 2025-10-14 20:55:26.363419 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds 2025-10-14 20:55:33.684329 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:36.294811 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 20:55:36.394542 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds 2025-10-14 20:55:36.429166 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds 2025-10-14 20:55:36.451411 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds 2025-10-14 20:55:36.49225 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds 2025-10-14 20:55:43.557192 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:55:43.5841 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:55:43.610513 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:55:43.618549 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:55:43.63088 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:55:43.673791 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:55:43.675859 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:55:43.679925 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:55:43.71346 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:55:43.715481 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:55:43.733052 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:55:43.74796 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:55:43.752399 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:55:43.766675 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:55:43.790946 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:55:48.748509 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 20:55:48.775778 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 20:55:48.801754 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 20:55:48.809835 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 20:55:48.822318 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 20:55:48.84939 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 20:55:48.851484 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 20:55:48.855869 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 20:55:48.894346 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 20:55:48.896722 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 20:55:48.917249 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 20:55:48.934796 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 20:55:48.939998 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 20:55:48.982654 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 20:55:49.006605 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 20:55:49.094671 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds 2025-10-14 20:55:49.132585 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds 2025-10-14 20:55:49.167 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds 2025-10-14 20:55:49.333534 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds 2025-10-14 20:55:57.128938 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-10-14 20:55:57.134379 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-10-14 20:55:57.138084 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-10-14 20:55:57.154703 ERROR::No fixed, group, or ordered effects included in formula. 2025-10-14 20:55:57.160192 ERROR::Effect name not found in metadata: d 2025-10-14 20:55:57.164084 ERROR::No user formula provided 2025-10-14 20:55:57.173989 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-10-14 20:55:57.177955 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-10-14 20:55:58.193559 INFO::Writing function arguments to log file 2025-10-14 20:55:58.198741 INFO::Verifying options selected are valid 2025-10-14 20:55:59.166869 INFO::Writing function arguments to log file 2025-10-14 20:55:59.172394 INFO::Verifying options selected are valid 2025-10-14 20:55:59.172801 INFO::Determining format of input files 2025-10-14 20:55:59.17313 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 20:55:59.173969 INFO::Running selected normalization method: TSS 2025-10-14 20:55:59.174516 INFO::Creating output feature tables folder 2025-10-14 20:55:59.174933 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/data_norm.tsv 2025-10-14 20:55:59.175543 INFO::Filter data based on min abundance, min prevalence, and max prevalence 2025-10-14 20:55:59.175864 INFO::Total samples in data: 16 2025-10-14 20:55:59.176154 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-10-14 20:55:59.176449 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000 2025-10-14 20:55:59.177103 INFO::Total filtered features: 0 2025-10-14 20:55:59.177453 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering: 2025-10-14 20:55:59.177846 INFO::Total features filtered by non-zero variance filtering: 0 2025-10-14 20:55:59.178173 INFO::Filtered feature names from variance filtering: 2025-10-14 20:55:59.178483 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/filtered_data.tsv 2025-10-14 20:55:59.179044 INFO::Running selected transform method: LOG 2025-10-14 20:55:59.179462 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/data_transformed.tsv 2025-10-14 20:55:59.180081 INFO::Applying z-score to standardize continuous metadata 2025-10-14 20:55:59.182076 INFO::Running the linear model component 2025-10-14 20:55:59.187609 INFO::Fitting model to feature number 1, a 2025-10-14 20:55:59.189226 INFO::Fitting model to feature number 2, b 2025-10-14 20:55:59.190737 INFO::Fitting model to feature number 3, c 2025-10-14 20:55:59.193323 INFO::Counting total values for each feature 2025-10-14 20:55:59.194034 INFO::Running the logistic model component 2025-10-14 20:55:59.204787 INFO::Fitting model to feature number 1, a 2025-10-14 20:55:59.208043 INFO::Fitting model to feature number 2, b 2025-10-14 20:55:59.210925 INFO::Fitting model to feature number 3, c 2025-10-14 20:55:59.214879 INFO::Counting total values for each feature 2025-10-14 20:55:59.215879 INFO::Re-running abundances for warn_prevalence 2025-10-14 20:55:59.216397 INFO::Running selected normalization method: TSS 2025-10-14 20:55:59.217091 INFO::Running selected transform method: LOG 2025-10-14 20:55:59.2233 INFO::Fitting model to feature number 1, a 2025-10-14 20:55:59.225096 INFO::Fitting model to feature number 2, b 2025-10-14 20:55:59.226766 INFO::Fitting model to feature number 3, c 2025-10-14 20:55:59.254727 INFO::Creating fits folder 2025-10-14 20:55:59.255297 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/residuals_linear.rds 2025-10-14 20:55:59.255794 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/fitted_linear.rds 2025-10-14 20:55:59.256252 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/residuals_logistic.rds 2025-10-14 20:55:59.256719 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/fitted_logistic.rds 2025-10-14 20:55:59.257648 INFO::Writing all the results to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/all_results.tsv 2025-10-14 20:55:59.25833 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/significant_results.tsv 2025-10-14 20:55:59.258846 INFO::Creating output figures folder 2025-10-14 20:55:59.259324 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures/summary_plot.pdf 2025-10-14 20:55:59.845569 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures 2025-10-14 20:55:59.846323 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 20:55:59.848248 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 20:56:00.042536 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures/summary_plot.pdf 2025-10-14 20:56:00.642897 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures 2025-10-14 20:56:00.643477 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 20:56:00.645328 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 20:56:00.84297 INFO::Running the linear model component 2025-10-14 20:56:00.845679 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:00.847068 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:00.848238 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:00.850492 INFO::Counting total values for each feature 2025-10-14 20:56:00.851033 INFO::Running the logistic model component 2025-10-14 20:56:00.85353 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:00.855438 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:00.85714 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:00.859778 INFO::Counting total values for each feature 2025-10-14 20:56:00.860411 INFO::Re-running abundances for warn_prevalence 2025-10-14 20:56:00.860639 INFO::Running selected normalization method: TSS 2025-10-14 20:56:00.861033 INFO::Running selected transform method: LOG 2025-10-14 20:56:00.863627 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:00.864881 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:00.866021 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:00.892149 INFO::Creating output folder 2025-10-14 20:56:00.8926 INFO::Creating output figures folder 2025-10-14 20:56:00.893054 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3bc9c008/figures/summary_plot.pdf 2025-10-14 20:56:01.484243 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3bc9c008/figures 2025-10-14 20:56:01.484929 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 20:56:01.486973 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 20:56:01.884784 INFO::Applying z-score to standardize continuous metadata 2025-10-14 20:56:01.887493 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-10-14 20:56:01.887772 INFO::Bypass z-score application to metadata 2025-10-14 20:56:01.888513 INFO::Bypass z-score application to metadata 2025-10-14 20:56:01.894719 INFO::Determining format of input files 2025-10-14 20:56:01.895028 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 20:56:01.895275 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-10-14 20:56:01.897426 INFO::Determining format of input files 2025-10-14 20:56:01.897752 INFO::Input format is data samples as columns and metadata samples as rows 2025-10-14 20:56:01.898134 INFO::Input format is feature_specific_covariate samples as columns 2025-10-14 20:56:01.90054 INFO::Determining format of input files 2025-10-14 20:56:01.900832 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 20:56:01.901139 INFO::Input format is feature_specific_covariate samples as columns 2025-10-14 20:56:01.901607 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-10-14 20:56:01.901821 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-10-14 20:56:01.905341 INFO::Running selected transform method: LOG 2025-10-14 20:56:01.905689 INFO::Creating output feature tables folder 2025-10-14 20:56:01.906052 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv 2025-10-14 20:56:01.907316 INFO::Running selected transform method: LOG 2025-10-14 20:56:01.907628 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv 2025-10-14 20:56:01.908753 INFO::Running selected transform method: PLOG 2025-10-14 20:56:01.909229 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv 2025-10-14 20:56:01.910089 INFO::Running selected transform method: NONE 2025-10-14 20:56:01.910317 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv 2025-10-14 20:56:01.912769 INFO::Running the linear model component 2025-10-14 20:56:01.915394 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:01.916772 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:01.917975 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:01.920226 INFO::Counting total values for each feature 2025-10-14 20:56:01.920744 INFO::Running the logistic model component 2025-10-14 20:56:01.92325 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:01.925155 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:01.926941 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:01.929637 INFO::Counting total values for each feature 2025-10-14 20:56:01.930279 INFO::Re-running abundances for warn_prevalence 2025-10-14 20:56:01.930513 INFO::Running selected normalization method: TSS 2025-10-14 20:56:01.930922 INFO::Running selected transform method: LOG 2025-10-14 20:56:01.933525 INFO::Fitting model to feature number 1, a 2025-10-14 20:56:01.934791 INFO::Fitting model to feature number 2, b 2025-10-14 20:56:01.935972 INFO::Fitting model to feature number 3, c 2025-10-14 20:56:01.962361 INFO::Creating output folder 2025-10-14 20:56:01.962816 INFO::Creating fits folder 2025-10-14 20:56:01.963128 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/residuals_linear.rds 2025-10-14 20:56:01.963592 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/fitted_linear.rds 2025-10-14 20:56:01.963963 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/residuals_logistic.rds 2025-10-14 20:56:01.964339 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/fitted_logistic.rds 2025-10-14 20:56:01.96522 INFO::Writing all the results to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/all_results.tsv 2025-10-14 20:56:01.965814 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 137.054 5.106 143.086
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 8.278 | 0.470 | 8.774 | |
maaslin_check_arguments | 0.057 | 0.002 | 0.058 | |
maaslin_check_formula | 0.060 | 0.003 | 0.063 | |
maaslin_compute_formula | 0.056 | 0.004 | 0.061 | |
maaslin_contrast_test | 6.867 | 0.677 | 7.594 | |
maaslin_filter | 0.222 | 0.023 | 0.245 | |
maaslin_fit | 5.272 | 0.613 | 5.916 | |
maaslin_log_arguments | 0.056 | 0.006 | 0.061 | |
maaslin_normalize | 0.126 | 0.011 | 0.138 | |
maaslin_plot_results | 16.156 | 0.691 | 16.885 | |
maaslin_plot_results_from_output | 16.386 | 0.586 | 17.074 | |
maaslin_process_metadata | 0.213 | 0.020 | 0.234 | |
maaslin_read_data | 0.050 | 0.003 | 0.052 | |
maaslin_reorder_data | 0.051 | 0.003 | 0.054 | |
maaslin_transform | 0.264 | 0.025 | 0.290 | |
maaslin_write_results | 5.551 | 0.542 | 6.115 | |
maaslin_write_results_lefse_format | 5.357 | 0.483 | 5.858 | |
preprocess_dna_mtx | 0.001 | 0.001 | 0.002 | |
preprocess_taxa_mtx | 0.002 | 0.000 | 0.001 | |