William Nickols
| Snapshot Date: 2025-12-15 13:45 -0500 (Mon, 15 Dec 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 2025-12-18 12:07 -0500 (Thu, 18 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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. - 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: 2025-12-16 12:41:32 -0000 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 13:02:34 -0000 (Tue, 16 Dec 2025) |
| EllapsedTime: 1261.6 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 66.405 0.350 81.748
maaslin_plot_results 65.148 0.432 77.094
maaslin_contrast_test 29.352 0.350 34.269
maaslin3 29.142 0.454 34.822
maaslin_write_results_lefse_format 24.666 0.095 30.492
maaslin_write_results 22.122 0.202 27.375
maaslin_fit 21.151 0.063 24.221
* 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")
2025-12-16 12:52:07.455573 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:52:07.596637 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:52:07.749836 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:52:07.785795 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:52:07.840942 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:52:07.97634 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:52:07.984614 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:52:08.003197 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:52:08.154615 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:52:08.163045 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:52:08.241298 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:52:08.330364 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:52:08.348778 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:52:08.412144 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:52:08.522259 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:52:37.912796 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:52:38.15709 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:52:38.289134 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:52:38.327081 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:52:38.387794 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:52:38.531671 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:52:38.54242 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:52:38.563798 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:52:38.743386 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:52:38.753497 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:52:38.842237 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:52:38.913896 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:52:38.935058 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:52:39.061143 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:52:39.319207 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:53:18.159298 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:53:18.28736 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:53:18.411453 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:53:18.448346 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:53:18.507859 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:53:18.639979 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:53:18.648733 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:53:18.668679 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:53:18.846525 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:53:18.855152 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:53:18.938531 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:53:19.011788 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:53:19.032376 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:53:19.103143 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:53:19.223525 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:53:43.95009 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:53:44.07671 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:53:44.200289 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:53:44.236343 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:53:44.296143 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:53:44.426417 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:53:44.435433 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:53:44.455216 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:53:44.639485 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:53:44.66091 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:53:44.789368 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:53:44.862006 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:53:44.883667 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:53:44.952685 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:53:45.071597 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:53:45.39958 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_linear.rds
2025-12-16 12:53:45.544069 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_linear.rds
2025-12-16 12:53:45.694903 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_logistic.rds
2025-12-16 12:53:46.432506 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_logistic.rds
2025-12-16 12:54:22.992209 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:54:23.118434 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:54:23.244215 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:54:23.280919 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:54:23.339863 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:54:23.486162 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:54:23.503504 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:54:23.550043 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:54:23.823681 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:54:23.845365 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:54:24.006265 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:54:24.147627 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:54:24.187627 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:54:24.329302 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:54:24.571312 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:54:52.814594 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:54:52.950247 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:54:53.167322 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:54:53.206736 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:54:53.270524 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:54:53.403334 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:54:53.412195 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:54:53.431845 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:54:53.594646 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:54:53.603452 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:54:53.71813 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:54:53.862919 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:54:53.904596 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:54:54.040919 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:54:54.223283 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:54:54.554046 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_linear.rds
2025-12-16 12:54:54.622415 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_linear.rds
2025-12-16 12:54:54.692894 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_logistic.rds
2025-12-16 12:54:55.075079 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_logistic.rds
2025-12-16 12:55:42.512202 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:55:42.645525 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:55:42.778535 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:55:42.818236 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:55:42.880346 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:55:43.01662 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:55:43.025577 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:55:43.047203 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:55:43.227352 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:55:43.236496 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:55:43.325465 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:55:43.392492 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:55:43.412452 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:55:43.507156 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:55:43.627535 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:56:06.148832 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:56:06.285068 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:56:06.547584 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:56:06.587176 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:56:06.648963 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:56:06.781586 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:56:06.790312 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:56:06.810334 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:56:06.975901 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:56:06.984956 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:56:07.070359 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:56:07.142468 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:56:07.163332 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:56:07.231691 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:56:07.349102 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:56:07.809018 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_linear.rds
2025-12-16 12:56:07.880787 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_linear.rds
2025-12-16 12:56:07.954693 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/residuals_logistic.rds
2025-12-16 12:56:08.320856 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374279e66c/fits/fitted_logistic.rds
2025-12-16 12:56:41.84559 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:56:42.071838 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:56:42.227129 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:56:42.26917 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:56:42.335161 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:56:42.473741 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:56:42.483103 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:56:42.504455 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:56:42.679557 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:56:42.688849 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:56:42.782502 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:56:42.855077 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:56:42.876193 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:56:43.030759 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:56:43.319636 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:57:07.6202 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 12:57:07.76225 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 12:57:07.923064 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 12:57:08.007833 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 12:57:08.124186 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 12:57:08.335531 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 12:57:08.357447 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 12:57:08.399431 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 12:57:08.775456 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 12:57:08.797487 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 12:57:09.013171 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 12:57:09.188935 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 12:57:09.23875 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 12:57:09.375337 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 12:57:09.521518 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 12:57:52.401674 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:58:10.217891 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:58:52.859164 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:59:11.602634 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:59:12.81467 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_linear.rds
2025-12-16 12:59:12.884653 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_linear.rds
2025-12-16 12:59:12.929287 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_logistic.rds
2025-12-16 12:59:13.01028 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_logistic.rds
2025-12-16 12:59:47.090943 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:59:56.348994 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 12:59:56.845577 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_linear.rds
2025-12-16 12:59:56.915044 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_linear.rds
2025-12-16 12:59:56.959647 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_logistic.rds
2025-12-16 12:59:57.044179 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_logistic.rds
2025-12-16 13:00:25.49597 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 13:00:35.154643 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 13:00:35.71891 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_linear.rds
2025-12-16 13:00:35.812348 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_linear.rds
2025-12-16 13:00:35.856932 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_logistic.rds
2025-12-16 13:00:35.937231 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_logistic.rds
2025-12-16 13:01:04.198318 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 13:01:04.334142 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 13:01:04.470496 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 13:01:04.509213 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 13:01:04.569356 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 13:01:04.704646 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 13:01:04.71396 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 13:01:04.734882 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 13:01:04.934695 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 13:01:04.944395 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 13:01:05.038009 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 13:01:05.115079 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 13:01:05.136287 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 13:01:05.21099 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 13:01:05.33956 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 13:01:28.283802 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 13:01:28.411185 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 13:01:28.535401 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 13:01:28.571915 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 13:01:28.628956 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 13:01:28.756664 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 13:01:28.765501 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 13:01:28.785252 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 13:01:28.952154 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 13:01:28.96108 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 13:01:29.050803 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 13:01:29.122121 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 13:01:29.143259 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 13:01:29.217723 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 13:01:29.427119 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 13:01:30.202768 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_linear.rds
2025-12-16 13:01:30.344031 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_linear.rds
2025-12-16 13:01:30.462423 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/residuals_logistic.rds
2025-12-16 13:01:30.807548 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpadK9Jz/filed27374949fb05/fits/fitted_logistic.rds
2025-12-16 13:02:02.213137 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-16 13:02:02.239727 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-16 13:02:02.258165 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-16 13:02:02.340261 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-16 13:02:02.366458 ERROR::Effect name not found in metadata: d
2025-12-16 13:02:02.390747 ERROR::No user formula provided
2025-12-16 13:02:02.438717 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-16 13:02:02.473826 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-16 13:02:10.121346 INFO::Writing function arguments to log file
2025-12-16 13:02:10.169117 INFO::Verifying options selected are valid
2025-12-16 13:02:13.810071 INFO::Writing function arguments to log file
2025-12-16 13:02:13.831229 INFO::Verifying options selected are valid
2025-12-16 13:02:13.833023 INFO::Determining format of input files
2025-12-16 13:02:13.834615 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 13:02:13.838263 INFO::Running selected normalization method: TSS
2025-12-16 13:02:13.840535 INFO::Creating output feature tables folder
2025-12-16 13:02:13.842106 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/features/data_norm.tsv
2025-12-16 13:02:13.84425 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-16 13:02:13.845677 INFO::Total samples in data: 16
2025-12-16 13:02:13.84701 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-16 13:02:13.848327 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-16 13:02:13.851302 INFO::Total filtered features: 0
2025-12-16 13:02:13.852785 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-16 13:02:13.854513 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-16 13:02:13.855935 INFO::Filtered feature names from variance filtering:
2025-12-16 13:02:13.857372 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/features/filtered_data.tsv
2025-12-16 13:02:13.859589 INFO::Running selected transform method: LOG
2025-12-16 13:02:13.861482 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/features/data_transformed.tsv
2025-12-16 13:02:13.863814 INFO::Applying z-score to standardize continuous metadata
2025-12-16 13:02:13.871349 INFO::Running the linear model component
2025-12-16 13:02:13.893114 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:13.899985 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:13.907147 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:13.92262 INFO::Counting total values for each feature
2025-12-16 13:02:13.926404 INFO::Running the logistic model component
2025-12-16 13:02:13.94996 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:13.959564 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:13.969058 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:13.982762 INFO::Counting total values for each feature
2025-12-16 13:02:13.986123 INFO::Re-running abundances for warn_prevalence
2025-12-16 13:02:13.987517 INFO::Running selected normalization method: TSS
2025-12-16 13:02:13.989763 INFO::Running selected transform method: LOG
2025-12-16 13:02:14.011922 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:14.01862 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:14.025292 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:14.160263 INFO::Creating fits folder
2025-12-16 13:02:14.162028 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/fits/residuals_linear.rds
2025-12-16 13:02:14.163615 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/fits/fitted_linear.rds
2025-12-16 13:02:14.165369 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/fits/residuals_logistic.rds
2025-12-16 13:02:14.167032 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/fits/fitted_logistic.rds
2025-12-16 13:02:14.171112 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/all_results.tsv
2025-12-16 13:02:14.1737 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/RtmpadK9Jz/filed273719b2a538/significant_results.tsv
2025-12-16 13:02:14.175646 INFO::Creating output figures folder
2025-12-16 13:02:14.177895 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/figures/summary_plot.pdf
2025-12-16 13:02:17.524295 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/figures
2025-12-16 13:02:17.527121 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 13:02:17.534531 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 13:02:18.301857 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/figures/summary_plot.pdf
2025-12-16 13:02:20.687155 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpadK9Jz/filed273719b2a538/figures
2025-12-16 13:02:20.689443 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 13:02:20.696568 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 13:02:21.41419 INFO::Running the linear model component
2025-12-16 13:02:21.428189 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:21.434679 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:21.441201 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:21.451935 INFO::Counting total values for each feature
2025-12-16 13:02:21.454614 INFO::Running the logistic model component
2025-12-16 13:02:21.467873 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:21.47726 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:21.486193 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:21.499107 INFO::Counting total values for each feature
2025-12-16 13:02:21.502337 INFO::Re-running abundances for warn_prevalence
2025-12-16 13:02:21.503563 INFO::Running selected normalization method: TSS
2025-12-16 13:02:21.505696 INFO::Running selected transform method: LOG
2025-12-16 13:02:21.51941 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:21.525641 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:21.531763 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:21.664676 INFO::Creating output folder
2025-12-16 13:02:21.666218 INFO::Creating output figures folder
2025-12-16 13:02:21.668276 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpadK9Jz/filed2737311ace24/figures/summary_plot.pdf
2025-12-16 13:02:24.34766 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpadK9Jz/filed2737311ace24/figures
2025-12-16 13:02:24.350306 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 13:02:24.357988 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 13:02:25.94037 INFO::Applying z-score to standardize continuous metadata
2025-12-16 13:02:25.95121 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-16 13:02:25.952414 INFO::Bypass z-score application to metadata
2025-12-16 13:02:25.956085 INFO::Bypass z-score application to metadata
2025-12-16 13:02:25.98128 INFO::Determining format of input files
2025-12-16 13:02:25.982658 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 13:02:25.983881 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-16 13:02:25.995014 INFO::Determining format of input files
2025-12-16 13:02:25.99667 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-16 13:02:25.998732 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 13:02:26.011125 INFO::Determining format of input files
2025-12-16 13:02:26.012712 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 13:02:26.014433 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 13:02:26.017135 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-16 13:02:26.018432 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-16 13:02:26.034856 INFO::Running selected transform method: LOG
2025-12-16 13:02:26.036506 INFO::Creating output feature tables folder
2025-12-16 13:02:26.037892 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273716fb4fa2/features/data_transformed.tsv
2025-12-16 13:02:26.043867 INFO::Running selected transform method: LOG
2025-12-16 13:02:26.045681 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273716fb4fa2/features/data_transformed.tsv
2025-12-16 13:02:26.051762 INFO::Running selected transform method: PLOG
2025-12-16 13:02:26.054397 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273716fb4fa2/features/data_transformed.tsv
2025-12-16 13:02:26.059149 INFO::Running selected transform method: NONE
2025-12-16 13:02:26.060451 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpadK9Jz/filed273716fb4fa2/features/data_transformed.tsv
2025-12-16 13:02:26.071216 INFO::Running the linear model component
2025-12-16 13:02:26.085283 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:26.092007 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:26.098712 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:26.109402 INFO::Counting total values for each feature
2025-12-16 13:02:26.111929 INFO::Running the logistic model component
2025-12-16 13:02:26.125554 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:26.135092 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:26.14398 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:26.157196 INFO::Counting total values for each feature
2025-12-16 13:02:26.16029 INFO::Re-running abundances for warn_prevalence
2025-12-16 13:02:26.161488 INFO::Running selected normalization method: TSS
2025-12-16 13:02:26.163485 INFO::Running selected transform method: LOG
2025-12-16 13:02:26.177422 INFO::Fitting model to feature number 1, a
2025-12-16 13:02:26.183873 INFO::Fitting model to feature number 2, b
2025-12-16 13:02:26.190459 INFO::Fitting model to feature number 3, c
2025-12-16 13:02:26.328907 INFO::Creating output folder
2025-12-16 13:02:26.330425 INFO::Creating fits folder
2025-12-16 13:02:26.331714 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpadK9Jz/filed27375e2f567f/fits/residuals_linear.rds
2025-12-16 13:02:26.333362 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpadK9Jz/filed27375e2f567f/fits/fitted_linear.rds
2025-12-16 13:02:26.334918 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpadK9Jz/filed27375e2f567f/fits/residuals_logistic.rds
2025-12-16 13:02:26.336465 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpadK9Jz/filed27375e2f567f/fits/fitted_logistic.rds
2025-12-16 13:02:26.3594 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpadK9Jz/filed27375e2f567f/all_results.tsv
2025-12-16 13:02:26.363395 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/RtmpadK9Jz/filed27375e2f567f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
524.627 5.380 635.843
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 29.142 | 0.454 | 34.822 | |
| maaslin_check_arguments | 0.208 | 0.000 | 0.252 | |
| maaslin_check_formula | 0.203 | 0.004 | 0.210 | |
| maaslin_compute_formula | 0.202 | 0.011 | 0.215 | |
| maaslin_contrast_test | 29.352 | 0.350 | 34.269 | |
| maaslin_filter | 0.670 | 0.000 | 0.756 | |
| maaslin_fit | 21.151 | 0.063 | 24.221 | |
| maaslin_log_arguments | 0.194 | 0.005 | 0.198 | |
| maaslin_normalize | 0.362 | 0.012 | 0.376 | |
| maaslin_plot_results | 65.148 | 0.432 | 77.094 | |
| maaslin_plot_results_from_output | 66.405 | 0.350 | 81.748 | |
| maaslin_process_metadata | 0.648 | 0.020 | 0.676 | |
| maaslin_read_data | 0.197 | 0.000 | 0.198 | |
| maaslin_reorder_data | 0.199 | 0.008 | 0.207 | |
| maaslin_transform | 0.762 | 0.011 | 0.820 | |
| maaslin_write_results | 22.122 | 0.202 | 27.375 | |
| maaslin_write_results_lefse_format | 24.666 | 0.095 | 30.492 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.010 | |
| preprocess_taxa_mtx | 0.007 | 0.000 | 0.016 | |