William Nickols
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 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" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-11-14 11:05:06 -0000 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 11:22:25 -0000 (Fri, 14 Nov 2025) |
| EllapsedTime: 1038.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 loading without being on the library search path ... 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 65.090 0.467 65.741
maaslin_plot_results 62.520 0.351 62.993
maaslin3 29.317 0.487 29.883
maaslin_contrast_test 29.228 0.383 29.696
maaslin_write_results_lefse_format 25.571 0.152 25.798
maaslin_write_results 22.200 0.143 22.412
maaslin_fit 21.347 0.164 21.585
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")
2025-11-14 11:13:43.487534 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:13:43.626208 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:13:43.79098 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:13:43.827994 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:13:43.887398 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:13:44.019498 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:13:44.02787 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:13:44.04721 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:13:44.222107 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:13:44.230475 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:13:44.311874 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:13:44.379501 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:13:44.400493 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:13:44.478848 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:13:44.592588 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:14:08.120238 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:14:08.248377 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:14:08.396217 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:14:08.435225 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:14:08.495368 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:14:08.631092 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:14:08.64014 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:14:08.660945 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:14:08.836164 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:14:08.846024 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:14:08.935619 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:14:09.012415 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:14:09.032617 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:14:09.10451 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:14:09.229577 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:14:41.810596 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:14:41.948024 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:14:42.085358 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:14:42.125942 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:14:42.189448 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:14:42.332227 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:14:42.341699 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:14:42.362868 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:14:42.550083 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:14:42.560095 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:14:42.655965 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:14:42.733294 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:14:42.755412 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:14:42.833116 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:14:42.968888 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:15:03.842876 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:15:04.011134 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:15:04.148478 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:15:04.186607 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:15:04.245642 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:15:04.37527 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:15:04.384056 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:15:04.403868 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:15:04.569189 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:15:04.578377 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:15:04.665843 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:15:04.735524 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:15:04.755042 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:15:04.822026 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:15:04.937421 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:15:05.240079 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_linear.rds
2025-11-14 11:15:05.322034 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_linear.rds
2025-11-14 11:15:05.404878 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_logistic.rds
2025-11-14 11:15:05.860731 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_logistic.rds
2025-11-14 11:15:35.734248 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:15:35.861218 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:15:35.986117 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:15:36.020355 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:15:36.075294 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:15:36.195867 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:15:36.204006 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:15:36.222768 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:15:36.375098 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:15:36.384052 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:15:36.466431 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:15:36.533496 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:15:36.641947 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:15:36.710758 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:15:36.828709 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:15:58.436614 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:15:58.571648 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:15:58.708286 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:15:58.745683 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:15:58.804874 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:15:58.937148 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:15:58.946599 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:15:58.968304 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:15:59.141525 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:15:59.150661 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:15:59.242475 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:15:59.314925 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:15:59.336985 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:15:59.411814 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:15:59.54268 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:15:59.853361 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_linear.rds
2025-11-14 11:15:59.921739 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_linear.rds
2025-11-14 11:15:59.99172 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_logistic.rds
2025-11-14 11:16:00.338817 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_logistic.rds
2025-11-14 11:16:31.205095 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:16:31.338694 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:16:31.466418 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:16:31.503679 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:16:31.562901 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:16:31.696268 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:16:31.705143 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:16:31.725441 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:16:31.893794 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:16:31.903018 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:16:32.032167 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:16:32.105071 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:16:32.126388 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:16:32.196277 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:16:32.321817 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:16:51.419428 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:16:51.565433 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:16:51.694 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:16:51.730901 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:16:51.789979 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:16:51.926157 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:16:51.935414 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:16:51.95682 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:16:52.133678 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:16:52.143802 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:16:52.238431 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:16:52.311582 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:16:52.33292 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:16:52.406014 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:16:52.531469 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:16:52.841121 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_linear.rds
2025-11-14 11:16:52.910292 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_linear.rds
2025-11-14 11:16:52.980678 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/residuals_logistic.rds
2025-11-14 11:16:53.328122 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf45d29aef/fits/fitted_logistic.rds
2025-11-14 11:17:22.74203 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:17:22.927484 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:17:23.069065 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:17:23.108365 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:17:23.16965 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:17:23.311768 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:17:23.321586 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:17:23.343462 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:17:23.525183 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:17:23.535577 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:17:23.628609 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:17:23.696992 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:17:23.716584 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:17:23.784306 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:17:23.902892 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:17:44.094707 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:17:44.231294 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:17:44.358344 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:17:44.394598 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:17:44.452451 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:17:44.584851 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:17:44.594084 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:17:44.613497 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:17:44.781722 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:17:44.791391 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:17:44.884457 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:17:44.957658 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:17:44.978935 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:17:45.05154 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:17:45.183696 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:18:18.344668 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:18:32.117882 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:19:07.865507 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:19:21.785934 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:19:22.850179 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_linear.rds
2025-11-14 11:19:22.912901 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_linear.rds
2025-11-14 11:19:22.953788 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_logistic.rds
2025-11-14 11:19:23.025816 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_logistic.rds
2025-11-14 11:19:55.650004 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:20:05.566578 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:20:06.050797 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_linear.rds
2025-11-14 11:20:06.119607 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_linear.rds
2025-11-14 11:20:06.163085 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_logistic.rds
2025-11-14 11:20:06.240911 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_logistic.rds
2025-11-14 11:20:32.136592 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:20:42.083718 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 11:20:42.62276 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_linear.rds
2025-11-14 11:20:42.692359 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_linear.rds
2025-11-14 11:20:42.736094 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_logistic.rds
2025-11-14 11:20:42.815152 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_logistic.rds
2025-11-14 11:21:08.821145 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:21:08.963217 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:21:09.109755 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:21:09.153934 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:21:09.226968 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:21:09.412148 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:21:09.421571 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:21:09.4421 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:21:09.611313 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:21:09.621159 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:21:09.709577 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:21:09.782525 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:21:09.805122 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:21:09.88014 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:21:10.004796 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:21:30.853616 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 11:21:30.983929 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 11:21:31.112685 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 11:21:31.150377 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 11:21:31.209946 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 11:21:31.341254 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 11:21:31.350443 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 11:21:31.370428 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 11:21:31.536338 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 11:21:31.545805 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 11:21:31.630301 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 11:21:31.698381 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 11:21:31.718158 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 11:21:31.785873 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 11:21:31.903511 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 11:21:32.283465 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_linear.rds
2025-11-14 11:21:32.354852 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_linear.rds
2025-11-14 11:21:32.419649 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/residuals_logistic.rds
2025-11-14 11:21:32.734165 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf50b3114b/fits/fitted_logistic.rds
2025-11-14 11:22:00.992192 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-14 11:22:01.018284 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-14 11:22:01.036198 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-14 11:22:01.116377 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-14 11:22:01.141661 ERROR::Effect name not found in metadata: d
2025-11-14 11:22:01.159176 ERROR::No user formula provided
2025-11-14 11:22:01.204034 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-14 11:22:01.221786 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-14 11:22:06.36071 INFO::Writing function arguments to log file
2025-11-14 11:22:06.38378 INFO::Verifying options selected are valid
2025-11-14 11:22:09.758922 INFO::Writing function arguments to log file
2025-11-14 11:22:09.777311 INFO::Verifying options selected are valid
2025-11-14 11:22:09.778892 INFO::Determining format of input files
2025-11-14 11:22:09.780336 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 11:22:09.783809 INFO::Running selected normalization method: TSS
2025-11-14 11:22:09.786034 INFO::Creating output feature tables folder
2025-11-14 11:22:09.787489 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/features/data_norm.tsv
2025-11-14 11:22:09.789654 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-14 11:22:09.791018 INFO::Total samples in data: 16
2025-11-14 11:22:09.792328 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-14 11:22:09.793696 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-14 11:22:09.796665 INFO::Total filtered features: 0
2025-11-14 11:22:09.798361 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-14 11:22:09.800128 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-14 11:22:09.801688 INFO::Filtered feature names from variance filtering:
2025-11-14 11:22:09.803058 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/features/filtered_data.tsv
2025-11-14 11:22:09.80534 INFO::Running selected transform method: LOG
2025-11-14 11:22:09.807184 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/features/data_transformed.tsv
2025-11-14 11:22:09.809676 INFO::Applying z-score to standardize continuous metadata
2025-11-14 11:22:09.817411 INFO::Running the linear model component
2025-11-14 11:22:09.839195 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:09.846094 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:09.853051 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:09.864491 INFO::Counting total values for each feature
2025-11-14 11:22:09.867509 INFO::Running the logistic model component
2025-11-14 11:22:09.889224 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:09.899434 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:09.909799 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:09.92429 INFO::Counting total values for each feature
2025-11-14 11:22:09.927863 INFO::Re-running abundances for warn_prevalence
2025-11-14 11:22:09.929529 INFO::Running selected normalization method: TSS
2025-11-14 11:22:09.931909 INFO::Running selected transform method: LOG
2025-11-14 11:22:09.955328 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:09.962445 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:09.969688 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:10.109227 INFO::Creating fits folder
2025-11-14 11:22:10.111135 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/fits/residuals_linear.rds
2025-11-14 11:22:10.112893 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/fits/fitted_linear.rds
2025-11-14 11:22:10.114767 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/fits/residuals_logistic.rds
2025-11-14 11:22:10.116579 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/fits/fitted_logistic.rds
2025-11-14 11:22:10.120806 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/all_results.tsv
2025-11-14 11:22:10.123573 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): /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/significant_results.tsv
2025-11-14 11:22:10.125804 INFO::Creating output figures folder
2025-11-14 11:22:10.128061 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/figures/summary_plot.pdf
2025-11-14 11:22:12.491688 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/figures
2025-11-14 11:22:12.494514 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 11:22:12.502189 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 11:22:13.249658 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/figures/summary_plot.pdf
2025-11-14 11:22:15.580169 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf7965a2fd/figures
2025-11-14 11:22:15.582412 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 11:22:15.589832 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 11:22:16.293332 INFO::Running the linear model component
2025-11-14 11:22:16.30735 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:16.314324 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:16.320849 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:16.33136 INFO::Counting total values for each feature
2025-11-14 11:22:16.33401 INFO::Running the logistic model component
2025-11-14 11:22:16.347356 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:16.356847 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:16.366109 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:16.379467 INFO::Counting total values for each feature
2025-11-14 11:22:16.382633 INFO::Re-running abundances for warn_prevalence
2025-11-14 11:22:16.383775 INFO::Running selected normalization method: TSS
2025-11-14 11:22:16.385862 INFO::Running selected transform method: LOG
2025-11-14 11:22:16.399659 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:16.406232 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:16.41261 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:16.547934 INFO::Creating output folder
2025-11-14 11:22:16.549416 INFO::Creating output figures folder
2025-11-14 11:22:16.551167 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf275fa31f/figures/summary_plot.pdf
2025-11-14 11:22:18.876159 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpQDQwuN/file379cbf275fa31f/figures
2025-11-14 11:22:18.87887 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 11:22:18.886573 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 11:22:20.283202 INFO::Applying z-score to standardize continuous metadata
2025-11-14 11:22:20.294611 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-14 11:22:20.295935 INFO::Bypass z-score application to metadata
2025-11-14 11:22:20.299783 INFO::Bypass z-score application to metadata
2025-11-14 11:22:20.326651 INFO::Determining format of input files
2025-11-14 11:22:20.328149 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 11:22:20.32957 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-14 11:22:20.340451 INFO::Determining format of input files
2025-11-14 11:22:20.342143 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-14 11:22:20.344099 INFO::Input format is feature_specific_covariate samples as columns
2025-11-14 11:22:20.355685 INFO::Determining format of input files
2025-11-14 11:22:20.357268 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 11:22:20.358822 INFO::Input format is feature_specific_covariate samples as columns
2025-11-14 11:22:20.361397 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-14 11:22:20.362605 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-14 11:22:20.378604 INFO::Running selected transform method: LOG
2025-11-14 11:22:20.380241 INFO::Creating output feature tables folder
2025-11-14 11:22:20.381642 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf79334813/features/data_transformed.tsv
2025-11-14 11:22:20.387509 INFO::Running selected transform method: LOG
2025-11-14 11:22:20.389394 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf79334813/features/data_transformed.tsv
2025-11-14 11:22:20.395171 INFO::Running selected transform method: PLOG
2025-11-14 11:22:20.397846 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf79334813/features/data_transformed.tsv
2025-11-14 11:22:20.402233 INFO::Running selected transform method: NONE
2025-11-14 11:22:20.40355 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf79334813/features/data_transformed.tsv
2025-11-14 11:22:20.415025 INFO::Running the linear model component
2025-11-14 11:22:20.428925 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:20.458069 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:20.466169 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:20.479231 INFO::Counting total values for each feature
2025-11-14 11:22:20.48215 INFO::Running the logistic model component
2025-11-14 11:22:20.497068 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:20.507653 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:20.51842 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:20.533705 INFO::Counting total values for each feature
2025-11-14 11:22:20.537003 INFO::Re-running abundances for warn_prevalence
2025-11-14 11:22:20.538378 INFO::Running selected normalization method: TSS
2025-11-14 11:22:20.540601 INFO::Running selected transform method: LOG
2025-11-14 11:22:20.554656 INFO::Fitting model to feature number 1, a
2025-11-14 11:22:20.561223 INFO::Fitting model to feature number 2, b
2025-11-14 11:22:20.567497 INFO::Fitting model to feature number 3, c
2025-11-14 11:22:20.697648 INFO::Creating output folder
2025-11-14 11:22:20.699033 INFO::Creating fits folder
2025-11-14 11:22:20.700191 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/fits/residuals_linear.rds
2025-11-14 11:22:20.701624 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/fits/fitted_linear.rds
2025-11-14 11:22:20.703061 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/fits/residuals_logistic.rds
2025-11-14 11:22:20.70447 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/fits/fitted_logistic.rds
2025-11-14 11:22:20.708057 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/all_results.tsv
2025-11-14 11:22:20.710381 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): /home/biocbuild/tmp/RtmpQDQwuN/file379cbf1fe92229/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
523.728 6.528 531.582
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 29.317 | 0.487 | 29.883 | |
| maaslin_check_arguments | 0.216 | 0.000 | 0.218 | |
| maaslin_check_formula | 0.214 | 0.000 | 0.215 | |
| maaslin_compute_formula | 0.245 | 0.000 | 0.246 | |
| maaslin_contrast_test | 29.228 | 0.383 | 29.696 | |
| maaslin_filter | 0.629 | 0.010 | 0.640 | |
| maaslin_fit | 21.347 | 0.164 | 21.585 | |
| maaslin_log_arguments | 0.194 | 0.000 | 0.194 | |
| maaslin_normalize | 0.359 | 0.012 | 0.372 | |
| maaslin_plot_results | 62.520 | 0.351 | 62.993 | |
| maaslin_plot_results_from_output | 65.090 | 0.467 | 65.741 | |
| maaslin_process_metadata | 0.635 | 0.035 | 0.671 | |
| maaslin_read_data | 0.194 | 0.009 | 0.203 | |
| maaslin_reorder_data | 0.216 | 0.000 | 0.216 | |
| maaslin_transform | 0.798 | 0.032 | 0.832 | |
| maaslin_write_results | 22.200 | 0.143 | 22.412 | |
| maaslin_write_results_lefse_format | 25.571 | 0.152 | 25.798 | |
| preprocess_dna_mtx | 0.002 | 0.003 | 0.006 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |