Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-20 12:06 -0400 (Mon, 20 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" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 1164/2353 | 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: 2025-10-19 20:25:40 -0400 (Sun, 19 Oct 2025) |
EndedAt: 2025-10-19 20:30:31 -0400 (Sun, 19 Oct 2025) |
EllapsedTime: 290.7 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 16.293 0.777 17.754 maaslin_plot_results 16.206 0.813 18.445 maaslin3 8.300 0.508 9.184 maaslin_contrast_test 7.103 0.547 7.771 maaslin_write_results 6.136 0.571 6.744 maaslin_write_results_lefse_format 6.016 0.537 6.590 maaslin_fit 4.955 0.606 5.823 * 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") 2025-10-19 20:28:10.145458 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:10.172213 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:10.205744 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:10.213066 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:10.224266 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:10.248675 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:10.250541 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:10.254341 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:10.28867 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:10.290582 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:10.306263 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:10.319129 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:10.323134 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:10.339407 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:10.361419 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:17.120231 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:17.146083 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:17.171441 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:17.178939 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:17.190632 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:17.216711 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:17.218717 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:17.222798 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:17.264465 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:17.266466 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:17.283516 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:17.297215 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:17.301379 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:17.315334 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:17.339233 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:18.790 R[48238:498595345] XType: Using static font registry. 2025-10-19 20:28:26.634497 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:26.659202 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:26.684389 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:26.692004 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:26.704047 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:26.732562 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:26.734769 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:26.738907 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:26.771921 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:26.773969 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:26.791281 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:26.806112 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:26.810626 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:26.825185 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:26.850033 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:31.984627 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:32.010289 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:32.045534 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:32.052928 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:32.064345 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:32.089192 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:32.091135 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:32.095487 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:32.128928 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:32.131106 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:32.149311 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:32.16359 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:32.167739 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:32.181924 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:32.206322 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:32.277949 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds 2025-10-19 20:28:32.310544 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds 2025-10-19 20:28:32.34441 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds 2025-10-19 20:28:32.510548 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds 2025-10-19 20:28:40.333606 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:40.359635 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:40.385204 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:40.392852 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:40.40494 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:40.431679 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:40.433719 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:40.437796 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:40.46785 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:40.469716 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:40.485564 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:40.498343 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:40.569524 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:40.58317 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:40.604918 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:45.690153 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:45.717612 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:45.74529 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:45.753398 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:45.766043 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:45.818367 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:45.820422 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:45.824441 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:45.857762 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:45.859718 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:45.87627 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:45.889779 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:45.893888 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:45.907289 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:45.929889 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:28:46.002354 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds 2025-10-19 20:28:46.035804 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds 2025-10-19 20:28:46.069462 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds 2025-10-19 20:28:46.236673 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds 2025-10-19 20:28:54.390439 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:28:54.417466 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:28:54.444051 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:28:54.452052 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:28:54.464213 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:28:54.507886 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:28:54.511215 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:28:54.516119 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:28:54.550978 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:28:54.553388 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:28:54.571743 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:28:54.586075 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:28:54.590495 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:28:54.604802 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:28:54.629686 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:29:00.063203 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:29:00.088917 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:29:00.114271 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:29:00.121795 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:29:00.133452 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:29:00.159239 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:29:00.161191 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:29:00.165229 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:29:00.197722 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:29:00.199682 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:29:00.216521 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:29:00.229905 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:29:00.234125 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:29:00.247812 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:29:00.270972 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:29:00.365403 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds 2025-10-19 20:29:00.397602 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds 2025-10-19 20:29:00.431389 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds 2025-10-19 20:29:00.601355 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds 2025-10-19 20:29:08.606385 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:29:08.637378 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:29:08.665502 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:29:08.673735 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:29:08.686323 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:29:08.713349 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:29:08.715408 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:29:08.71962 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:29:08.754272 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:29:08.756332 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:29:08.773899 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:29:08.788812 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:29:08.793061 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:29:08.807086 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:29:08.831081 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:29:13.472059 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:29:13.498957 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:29:13.524542 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:29:13.532455 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:29:13.543917 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:29:13.568901 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:29:13.570829 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:29:13.574747 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:29:13.606435 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:29:13.608407 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:29:13.624997 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:29:13.638465 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:29:13.642687 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:29:13.656341 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:29:13.679625 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:29:23.269318 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:26.628746 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:36.051319 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:40.051183 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:40.248168 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds 2025-10-19 20:29:40.280598 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds 2025-10-19 20:29:40.303281 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds 2025-10-19 20:29:40.344751 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds 2025-10-19 20:29:49.067252 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:51.282919 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:29:51.407707 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds 2025-10-19 20:29:51.441488 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds 2025-10-19 20:29:51.464261 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds 2025-10-19 20:29:51.505187 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds 2025-10-19 20:29:58.892382 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:30:01.622293 WARNING::Fitting problem for feature 124 returning NA 2025-10-19 20:30:01.729515 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds 2025-10-19 20:30:01.762835 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds 2025-10-19 20:30:01.786022 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds 2025-10-19 20:30:01.826617 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds 2025-10-19 20:30:08.995731 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:30:09.023128 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:30:09.049885 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:30:09.057871 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:30:09.070547 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:30:09.097466 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:30:09.099569 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:30:09.103624 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:30:09.13601 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:30:09.138017 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:30:09.155173 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:30:09.1691 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:30:09.173558 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:30:09.187609 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:30:09.235572 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:30:14.268416 WARNING::Fitting problem for feature 50 returning NA 2025-10-19 20:30:14.293872 WARNING::Fitting problem for feature 62 returning NA 2025-10-19 20:30:14.319636 WARNING::Fitting problem for feature 74 returning NA 2025-10-19 20:30:14.327334 WARNING::Fitting problem for feature 78 returning NA 2025-10-19 20:30:14.339066 WARNING::Fitting problem for feature 84 returning NA 2025-10-19 20:30:14.365076 WARNING::Fitting problem for feature 96 returning NA 2025-10-19 20:30:14.367128 WARNING::Fitting problem for feature 97 returning NA 2025-10-19 20:30:14.371284 WARNING::Fitting problem for feature 99 returning NA 2025-10-19 20:30:14.404004 WARNING::Fitting problem for feature 114 returning NA 2025-10-19 20:30:14.406032 WARNING::Fitting problem for feature 115 returning NA 2025-10-19 20:30:14.422883 WARNING::Fitting problem for feature 123 returning NA 2025-10-19 20:30:14.436757 WARNING::Fitting problem for feature 130 returning NA 2025-10-19 20:30:14.440983 WARNING::Fitting problem for feature 132 returning NA 2025-10-19 20:30:14.454899 WARNING::Fitting problem for feature 139 returning NA 2025-10-19 20:30:14.478387 WARNING::Fitting problem for feature 150 returning NA 2025-10-19 20:30:14.564572 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds 2025-10-19 20:30:14.597172 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds 2025-10-19 20:30:14.631013 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds 2025-10-19 20:30:14.796699 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds 2025-10-19 20:30:22.486367 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-10-19 20:30:22.492163 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-10-19 20:30:22.49605 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-10-19 20:30:22.513357 ERROR::No fixed, group, or ordered effects included in formula. 2025-10-19 20:30:22.519205 ERROR::Effect name not found in metadata: d 2025-10-19 20:30:22.523204 ERROR::No user formula provided 2025-10-19 20:30:22.534412 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-10-19 20:30:22.538736 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-10-19 20:30:23.555448 INFO::Writing function arguments to log file 2025-10-19 20:30:23.561087 INFO::Verifying options selected are valid 2025-10-19 20:30:24.399571 INFO::Writing function arguments to log file 2025-10-19 20:30:24.404093 INFO::Verifying options selected are valid 2025-10-19 20:30:24.404464 INFO::Determining format of input files 2025-10-19 20:30:24.404786 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-19 20:30:24.405568 INFO::Running selected normalization method: TSS 2025-10-19 20:30:24.406066 INFO::Creating output feature tables folder 2025-10-19 20:30:24.406462 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/data_norm.tsv 2025-10-19 20:30:24.407084 INFO::Filter data based on min abundance, min prevalence, and max prevalence 2025-10-19 20:30:24.407409 INFO::Total samples in data: 16 2025-10-19 20:30:24.407689 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-10-19 20:30:24.407962 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000 2025-10-19 20:30:24.408577 INFO::Total filtered features: 0 2025-10-19 20:30:24.408909 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering: 2025-10-19 20:30:24.409282 INFO::Total features filtered by non-zero variance filtering: 0 2025-10-19 20:30:24.409582 INFO::Filtered feature names from variance filtering: 2025-10-19 20:30:24.409857 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/filtered_data.tsv 2025-10-19 20:30:24.410404 INFO::Running selected transform method: LOG 2025-10-19 20:30:24.410791 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/data_transformed.tsv 2025-10-19 20:30:24.411376 INFO::Applying z-score to standardize continuous metadata 2025-10-19 20:30:24.413177 INFO::Running the linear model component 2025-10-19 20:30:24.418215 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:24.4197 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:24.42101 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:24.423288 INFO::Counting total values for each feature 2025-10-19 20:30:24.423941 INFO::Running the logistic model component 2025-10-19 20:30:24.429122 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:24.431253 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:24.433163 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:24.435979 INFO::Counting total values for each feature 2025-10-19 20:30:24.436748 INFO::Re-running abundances for warn_prevalence 2025-10-19 20:30:24.437129 INFO::Running selected normalization method: TSS 2025-10-19 20:30:24.437639 INFO::Running selected transform method: LOG 2025-10-19 20:30:24.442772 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:24.444178 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:24.445474 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:24.470894 INFO::Creating fits folder 2025-10-19 20:30:24.471444 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/residuals_linear.rds 2025-10-19 20:30:24.471943 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/fitted_linear.rds 2025-10-19 20:30:24.472408 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/residuals_logistic.rds 2025-10-19 20:30:24.472861 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/fitted_logistic.rds 2025-10-19 20:30:24.473756 INFO::Writing all the results to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/all_results.tsv 2025-10-19 20:30:24.474401 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//RtmpOSIB15/filebc6e7da5aa24/significant_results.tsv 2025-10-19 20:30:24.474905 INFO::Creating output figures folder 2025-10-19 20:30:24.47539 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures/summary_plot.pdf 2025-10-19 20:30:25.05034 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures 2025-10-19 20:30:25.051118 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-19 20:30:25.053121 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-19 20:30:25.252552 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures/summary_plot.pdf 2025-10-19 20:30:25.832559 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures 2025-10-19 20:30:25.83314 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-19 20:30:25.834931 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-19 20:30:26.026475 INFO::Running the linear model component 2025-10-19 20:30:26.029145 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:26.036124 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:26.037467 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:26.039844 INFO::Counting total values for each feature 2025-10-19 20:30:26.040382 INFO::Running the logistic model component 2025-10-19 20:30:26.042904 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:26.044759 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:26.046504 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:26.049398 INFO::Counting total values for each feature 2025-10-19 20:30:26.050082 INFO::Re-running abundances for warn_prevalence 2025-10-19 20:30:26.050338 INFO::Running selected normalization method: TSS 2025-10-19 20:30:26.050794 INFO::Running selected transform method: LOG 2025-10-19 20:30:26.053513 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:26.054971 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:26.056204 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:26.085517 INFO::Creating output folder 2025-10-19 20:30:26.086043 INFO::Creating output figures folder 2025-10-19 20:30:26.086545 INFO::Writing summary plot of significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e4e69f4a4/figures/summary_plot.pdf 2025-10-19 20:30:26.680546 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e4e69f4a4/figures 2025-10-19 20:30:26.681329 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-19 20:30:26.683946 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-19 20:30:27.079483 INFO::Applying z-score to standardize continuous metadata 2025-10-19 20:30:27.082035 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-10-19 20:30:27.0823 INFO::Bypass z-score application to metadata 2025-10-19 20:30:27.083019 INFO::Bypass z-score application to metadata 2025-10-19 20:30:27.08916 INFO::Determining format of input files 2025-10-19 20:30:27.089436 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-19 20:30:27.089675 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-10-19 20:30:27.09172 INFO::Determining format of input files 2025-10-19 20:30:27.092029 INFO::Input format is data samples as columns and metadata samples as rows 2025-10-19 20:30:27.092404 INFO::Input format is feature_specific_covariate samples as columns 2025-10-19 20:30:27.094699 INFO::Determining format of input files 2025-10-19 20:30:27.094976 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-19 20:30:27.095276 INFO::Input format is feature_specific_covariate samples as columns 2025-10-19 20:30:27.095733 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-10-19 20:30:27.095949 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-10-19 20:30:27.099266 INFO::Running selected transform method: LOG 2025-10-19 20:30:27.09959 INFO::Creating output feature tables folder 2025-10-19 20:30:27.099952 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv 2025-10-19 20:30:27.101211 INFO::Running selected transform method: LOG 2025-10-19 20:30:27.101526 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv 2025-10-19 20:30:27.102655 INFO::Running selected transform method: PLOG 2025-10-19 20:30:27.103131 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv 2025-10-19 20:30:27.104014 INFO::Running selected transform method: NONE 2025-10-19 20:30:27.104246 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv 2025-10-19 20:30:27.106764 INFO::Running the linear model component 2025-10-19 20:30:27.109373 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:27.110743 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:27.111921 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:27.114138 INFO::Counting total values for each feature 2025-10-19 20:30:27.114665 INFO::Running the logistic model component 2025-10-19 20:30:27.11717 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:27.119047 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:27.120838 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:27.123547 INFO::Counting total values for each feature 2025-10-19 20:30:27.124195 INFO::Re-running abundances for warn_prevalence 2025-10-19 20:30:27.124423 INFO::Running selected normalization method: TSS 2025-10-19 20:30:27.124836 INFO::Running selected transform method: LOG 2025-10-19 20:30:27.127441 INFO::Fitting model to feature number 1, a 2025-10-19 20:30:27.12875 INFO::Fitting model to feature number 2, b 2025-10-19 20:30:27.13637 INFO::Fitting model to feature number 3, c 2025-10-19 20:30:27.164742 INFO::Creating output folder 2025-10-19 20:30:27.165181 INFO::Creating fits folder 2025-10-19 20:30:27.165494 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/residuals_linear.rds 2025-10-19 20:30:27.167853 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/fitted_linear.rds 2025-10-19 20:30:27.169269 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/residuals_logistic.rds 2025-10-19 20:30:27.170262 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/fitted_logistic.rds 2025-10-19 20:30:27.171809 INFO::Writing all the results to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/all_results.tsv 2025-10-19 20:30:27.172442 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//RtmpOSIB15/filebc6e18c4bf0a/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 135.590 5.469 141.589
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 8.300 | 0.508 | 9.184 | |
maaslin_check_arguments | 0.062 | 0.002 | 0.068 | |
maaslin_check_formula | 0.056 | 0.004 | 0.069 | |
maaslin_compute_formula | 0.057 | 0.004 | 0.073 | |
maaslin_contrast_test | 7.103 | 0.547 | 7.771 | |
maaslin_filter | 0.209 | 0.018 | 0.228 | |
maaslin_fit | 4.955 | 0.606 | 5.823 | |
maaslin_log_arguments | 0.055 | 0.003 | 0.072 | |
maaslin_normalize | 0.127 | 0.017 | 0.201 | |
maaslin_plot_results | 16.206 | 0.813 | 18.445 | |
maaslin_plot_results_from_output | 16.293 | 0.777 | 17.754 | |
maaslin_process_metadata | 0.244 | 0.019 | 0.264 | |
maaslin_read_data | 0.059 | 0.003 | 0.063 | |
maaslin_reorder_data | 0.056 | 0.003 | 0.060 | |
maaslin_transform | 0.273 | 0.028 | 0.302 | |
maaslin_write_results | 6.136 | 0.571 | 6.744 | |
maaslin_write_results_lefse_format | 6.016 | 0.537 | 6.590 | |
preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |