William Nickols
| Snapshot Date: 2026-03-08 13:45 -0400 (Sun, 08 Mar 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-09 11:57 -0400 (Mon, 09 Mar 2026).
| 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" | 4892 |
| 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 | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-03-09 00:52:50 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 01:14:40 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 1309.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 43.900 0.379 44.283
maaslin_plot_results 43.294 0.235 43.492
maaslin3 20.260 0.532 20.795
maaslin_contrast_test 19.192 0.350 19.543
maaslin_write_results_lefse_format 14.420 0.042 14.462
maaslin_fit 13.416 0.096 13.513
maaslin_write_results 12.916 0.102 13.018
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2026-03-09 00:59:06.0012 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 00:59:06.086746 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 00:59:06.178798 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 00:59:06.199885 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 00:59:06.23388 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 00:59:06.308877 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 00:59:06.32119 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 00:59:06.333005 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 00:59:06.427451 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 00:59:06.433061 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 00:59:06.483889 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 00:59:06.531583 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 00:59:06.543439 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 00:59:06.584851 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 00:59:06.656606 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 00:59:22.591339 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 00:59:22.667692 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 00:59:22.74155 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 00:59:22.763136 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 00:59:22.797395 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 00:59:22.886861 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 00:59:22.892003 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 00:59:22.903522 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 00:59:22.997661 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 00:59:23.002896 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 00:59:23.050913 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 00:59:23.089968 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 00:59:23.101515 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 00:59:23.140861 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 00:59:23.208101 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 00:59:47.622009 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 00:59:47.697943 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 00:59:47.772535 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 00:59:47.794617 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 00:59:47.829593 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 00:59:47.906263 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 00:59:47.911827 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 00:59:47.924376 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 00:59:48.023734 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 00:59:48.029168 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 00:59:48.080677 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 00:59:48.122439 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 00:59:48.13492 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 00:59:48.176894 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 00:59:48.252068 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:00:01.145229 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:00:01.246719 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:00:01.321824 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:00:01.343869 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:00:01.378325 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:00:01.457154 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:00:01.462569 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:00:01.474602 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:00:01.572814 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:00:01.578288 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:00:01.628985 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:00:01.669207 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:00:01.681077 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:00:01.72129 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:00:01.793463 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:00:01.996441 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_linear.rds
2026-03-09 01:00:02.058192 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_linear.rds
2026-03-09 01:00:02.122059 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_logistic.rds
2026-03-09 01:00:02.424107 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_logistic.rds
2026-03-09 01:00:24.692398 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:00:24.77307 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:00:24.880566 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:00:24.903488 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:00:24.939543 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:00:25.018797 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:00:25.024406 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:00:25.036752 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:00:25.134836 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:00:25.140548 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:00:25.193623 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:00:25.23554 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:00:25.273369 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:00:25.316111 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:00:25.388158 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:00:37.451645 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:00:37.53659 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:00:37.618648 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:00:37.643957 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:00:37.682732 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:00:37.762272 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:00:37.767707 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:00:37.779737 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:00:37.877227 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:00:37.882708 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:00:37.933368 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:00:37.973966 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:00:37.985994 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:00:38.027896 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:00:38.097969 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:00:38.298173 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_linear.rds
2026-03-09 01:00:38.359242 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_linear.rds
2026-03-09 01:00:38.421999 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_logistic.rds
2026-03-09 01:00:38.722231 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_logistic.rds
2026-03-09 01:01:00.308084 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:01:00.390773 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:01:00.473315 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:01:00.498576 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:01:00.536883 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:01:00.639884 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:01:00.645769 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:01:00.658309 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:01:00.761827 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:01:00.767604 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:01:00.820804 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:01:00.863248 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:01:00.875706 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:01:00.919974 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:01:00.99156 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:01:13.088445 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:01:13.170708 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:01:13.246089 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:01:13.267776 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:01:13.301701 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:01:13.377657 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:01:13.383109 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:01:13.395087 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:01:13.492406 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:01:13.498082 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:01:13.549463 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:01:13.59172 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:01:13.603922 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:01:13.645968 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:01:13.718395 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:01:13.930654 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_linear.rds
2026-03-09 01:01:13.991588 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_linear.rds
2026-03-09 01:01:14.054519 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/residuals_logistic.rds
2026-03-09 01:01:14.355115 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db483b8e158c/fits/fitted_logistic.rds
2026-03-09 01:01:35.966545 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:01:36.047001 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:01:36.125042 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:01:36.146988 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:01:36.181906 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:01:36.258462 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:01:36.264297 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:01:36.276647 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:01:36.374924 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:01:36.380732 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:01:36.432654 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:01:36.477753 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:01:36.491598 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:01:36.535866 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:01:36.608757 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:01:48.625494 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:01:48.706037 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:01:48.784889 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:01:48.807662 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:01:48.844006 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:01:48.924809 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:01:48.930437 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:01:48.943001 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:01:49.043772 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:01:49.049607 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:01:49.102957 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:01:49.144536 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:01:49.156831 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:01:49.200056 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:01:49.274628 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:02:15.529375 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:02:24.372476 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:02:49.543894 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:02:59.498765 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:03:00.140981 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_linear.rds
2026-03-09 01:03:00.203117 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_linear.rds
2026-03-09 01:03:00.242482 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_logistic.rds
2026-03-09 01:03:00.312287 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_logistic.rds
2026-03-09 01:03:23.509378 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:03:28.880554 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:03:29.18113 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_linear.rds
2026-03-09 01:03:29.242671 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_linear.rds
2026-03-09 01:03:29.281477 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_logistic.rds
2026-03-09 01:03:29.350779 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_logistic.rds
2026-03-09 01:03:48.385971 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:03:54.916121 WARNING::Fitting problem for feature 124 returning NA
2026-03-09 01:03:55.215818 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_linear.rds
2026-03-09 01:03:55.277595 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_linear.rds
2026-03-09 01:03:55.316168 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_logistic.rds
2026-03-09 01:03:55.385059 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_logistic.rds
2026-03-09 01:04:14.595292 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:04:14.674583 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:04:14.752926 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:04:14.776075 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:04:14.811232 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:04:14.889559 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:04:14.895099 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:04:14.932902 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:04:15.03202 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:04:15.037601 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:04:15.088573 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:04:15.13043 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:04:15.142803 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:04:15.183478 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:04:15.253712 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:04:26.168995 WARNING::Fitting problem for feature 50 returning NA
2026-03-09 01:04:26.249232 WARNING::Fitting problem for feature 62 returning NA
2026-03-09 01:04:26.327403 WARNING::Fitting problem for feature 74 returning NA
2026-03-09 01:04:26.349654 WARNING::Fitting problem for feature 78 returning NA
2026-03-09 01:04:26.38526 WARNING::Fitting problem for feature 84 returning NA
2026-03-09 01:04:26.461714 WARNING::Fitting problem for feature 96 returning NA
2026-03-09 01:04:26.467264 WARNING::Fitting problem for feature 97 returning NA
2026-03-09 01:04:26.479328 WARNING::Fitting problem for feature 99 returning NA
2026-03-09 01:04:26.575768 WARNING::Fitting problem for feature 114 returning NA
2026-03-09 01:04:26.581197 WARNING::Fitting problem for feature 115 returning NA
2026-03-09 01:04:26.631666 WARNING::Fitting problem for feature 123 returning NA
2026-03-09 01:04:26.673491 WARNING::Fitting problem for feature 130 returning NA
2026-03-09 01:04:26.686392 WARNING::Fitting problem for feature 132 returning NA
2026-03-09 01:04:26.728916 WARNING::Fitting problem for feature 139 returning NA
2026-03-09 01:04:26.80069 WARNING::Fitting problem for feature 150 returning NA
2026-03-09 01:04:27.087502 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_linear.rds
2026-03-09 01:04:27.148617 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_linear.rds
2026-03-09 01:04:27.211482 WARNING::Deleting existing residuals file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/residuals_logistic.rds
2026-03-09 01:04:27.512994 WARNING::Deleting existing fitted file: /tmp/RtmpT4YUyb/file1db487c7c0b47/fits/fitted_logistic.rds
2026-03-09 01:04:48.208017 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-09 01:04:48.225402 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-09 01:04:48.237075 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-09 01:04:48.289664 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-09 01:04:48.30637 ERROR::Effect name not found in metadata: d
2026-03-09 01:04:48.318248 ERROR::No user formula provided
2026-03-09 01:04:48.349406 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-09 01:04:48.361265 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-09 01:04:51.211475 INFO::Writing function arguments to log file
2026-03-09 01:04:51.226545 INFO::Verifying options selected are valid
2026-03-09 01:04:53.565525 INFO::Writing function arguments to log file
2026-03-09 01:04:53.577868 INFO::Verifying options selected are valid
2026-03-09 01:04:53.578992 INFO::Determining format of input files
2026-03-09 01:04:53.579996 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-09 01:04:53.58234 INFO::Running selected normalization method: TSS
2026-03-09 01:04:53.58387 INFO::Creating output feature tables folder
2026-03-09 01:04:53.584902 INFO::Writing normalized data to file /tmp/RtmpT4YUyb/file1db48105c0900/features/data_norm.tsv
2026-03-09 01:04:53.586382 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-09 01:04:53.587283 INFO::Total samples in data: 16
2026-03-09 01:04:53.588165 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-09 01:04:53.589046 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-09 01:04:53.591021 INFO::Total filtered features: 0
2026-03-09 01:04:53.591997 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-09 01:04:53.593169 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-09 01:04:53.594125 INFO::Filtered feature names from variance filtering:
2026-03-09 01:04:53.595022 INFO::Writing filtered data to file /tmp/RtmpT4YUyb/file1db48105c0900/features/filtered_data.tsv
2026-03-09 01:04:53.596526 INFO::Running selected transform method: LOG
2026-03-09 01:04:53.597723 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT4YUyb/file1db48105c0900/features/data_transformed.tsv
2026-03-09 01:04:53.59938 INFO::Applying z-score to standardize continuous metadata
2026-03-09 01:04:53.603983 INFO::Running the linear model component
2026-03-09 01:04:53.618307 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:53.62313 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:53.627564 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:53.635028 INFO::Counting total values for each feature
2026-03-09 01:04:53.636999 INFO::Running the logistic model component
2026-03-09 01:04:53.651122 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:53.657859 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:53.664264 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:53.673594 INFO::Counting total values for each feature
2026-03-09 01:04:53.675909 INFO::Re-running abundances for warn_prevalence
2026-03-09 01:04:53.676917 INFO::Running selected normalization method: TSS
2026-03-09 01:04:53.678517 INFO::Running selected transform method: LOG
2026-03-09 01:04:53.693313 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:53.698111 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:53.702694 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:53.782353 INFO::Creating fits folder
2026-03-09 01:04:53.78355 INFO::Writing residuals to file /tmp/RtmpT4YUyb/file1db48105c0900/fits/residuals_linear.rds
2026-03-09 01:04:53.784703 INFO::Writing fitted values to file /tmp/RtmpT4YUyb/file1db48105c0900/fits/fitted_linear.rds
2026-03-09 01:04:53.785919 INFO::Writing residuals to file /tmp/RtmpT4YUyb/file1db48105c0900/fits/residuals_logistic.rds
2026-03-09 01:04:53.787135 INFO::Writing fitted values to file /tmp/RtmpT4YUyb/file1db48105c0900/fits/fitted_logistic.rds
2026-03-09 01:04:53.789563 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpT4YUyb/file1db48105c0900/all_results.tsv
2026-03-09 01:04:53.791187 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): /tmp/RtmpT4YUyb/file1db48105c0900/significant_results.tsv
2026-03-09 01:04:53.792537 INFO::Creating output figures folder
2026-03-09 01:04:53.793895 INFO::Writing summary plot of significant
results to file: /tmp/RtmpT4YUyb/file1db48105c0900/figures/summary_plot.pdf
2026-03-09 01:04:55.472422 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT4YUyb/file1db48105c0900/figures
2026-03-09 01:04:55.47434 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-09 01:04:55.479423 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-09 01:04:56.003432 INFO::Writing summary plot of
significant results to file: /tmp/RtmpT4YUyb/file1db48105c0900/figures/summary_plot.pdf
2026-03-09 01:04:57.690915 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT4YUyb/file1db48105c0900/figures
2026-03-09 01:04:57.692713 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-09 01:04:57.697805 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-09 01:04:58.220859 INFO::Running the linear model component
2026-03-09 01:04:58.22969 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:58.234172 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:58.238349 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:58.245471 INFO::Counting total values for each feature
2026-03-09 01:04:58.247201 INFO::Running the logistic model component
2026-03-09 01:04:58.255556 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:58.261881 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:58.267769 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:58.276542 INFO::Counting total values for each feature
2026-03-09 01:04:58.278604 INFO::Re-running abundances for warn_prevalence
2026-03-09 01:04:58.279381 INFO::Running selected normalization method: TSS
2026-03-09 01:04:58.280744 INFO::Running selected transform method: LOG
2026-03-09 01:04:58.289362 INFO::Fitting model to feature number 1, a
2026-03-09 01:04:58.293955 INFO::Fitting model to feature number 2, b
2026-03-09 01:04:58.298037 INFO::Fitting model to feature number 3, c
2026-03-09 01:04:58.376255 INFO::Creating output folder
2026-03-09 01:04:58.377264 INFO::Creating output figures folder
2026-03-09 01:04:58.378545 INFO::Writing summary plot of significant
results to file: /tmp/RtmpT4YUyb/file1db483e73e5b4/figures/summary_plot.pdf
2026-03-09 01:05:00.036987 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT4YUyb/file1db483e73e5b4/figures
2026-03-09 01:05:00.038908 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-09 01:05:00.05873 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-09 01:05:01.042335 INFO::Applying z-score to standardize continuous metadata
2026-03-09 01:05:01.049831 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-09 01:05:01.050763 INFO::Bypass z-score application to metadata
2026-03-09 01:05:01.053461 INFO::Bypass z-score application to metadata
2026-03-09 01:05:01.084563 INFO::Determining format of input files
2026-03-09 01:05:01.086386 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-09 01:05:01.08752 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-09 01:05:01.098204 INFO::Determining format of input files
2026-03-09 01:05:01.099409 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-09 01:05:01.100819 INFO::Input format is feature_specific_covariate samples as columns
2026-03-09 01:05:01.109778 INFO::Determining format of input files
2026-03-09 01:05:01.110932 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-09 01:05:01.112103 INFO::Input format is feature_specific_covariate samples as columns
2026-03-09 01:05:01.113825 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-09 01:05:01.114618 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-09 01:05:01.126868 INFO::Running selected transform method: LOG
2026-03-09 01:05:01.128096 INFO::Creating output feature tables folder
2026-03-09 01:05:01.128993 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT4YUyb/file1db48751ca3cc/features/data_transformed.tsv
2026-03-09 01:05:01.133204 INFO::Running selected transform method: LOG
2026-03-09 01:05:01.134283 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT4YUyb/file1db48751ca3cc/features/data_transformed.tsv
2026-03-09 01:05:01.141571 INFO::Running selected transform method: PLOG
2026-03-09 01:05:01.14324 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT4YUyb/file1db48751ca3cc/features/data_transformed.tsv
2026-03-09 01:05:01.146266 INFO::Running selected transform method: NONE
2026-03-09 01:05:01.14704 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT4YUyb/file1db48751ca3cc/features/data_transformed.tsv
2026-03-09 01:05:01.154823 INFO::Running the linear model component
2026-03-09 01:05:01.163598 INFO::Fitting model to feature number 1, a
2026-03-09 01:05:01.168129 INFO::Fitting model to feature number 2, b
2026-03-09 01:05:01.172358 INFO::Fitting model to feature number 3, c
2026-03-09 01:05:01.179633 INFO::Counting total values for each feature
2026-03-09 01:05:01.181418 INFO::Running the logistic model component
2026-03-09 01:05:01.190066 INFO::Fitting model to feature number 1, a
2026-03-09 01:05:01.196696 INFO::Fitting model to feature number 2, b
2026-03-09 01:05:01.20321 INFO::Fitting model to feature number 3, c
2026-03-09 01:05:01.212554 INFO::Counting total values for each feature
2026-03-09 01:05:01.214771 INFO::Re-running abundances for warn_prevalence
2026-03-09 01:05:01.215642 INFO::Running selected normalization method: TSS
2026-03-09 01:05:01.217049 INFO::Running selected transform method: LOG
2026-03-09 01:05:01.225671 INFO::Fitting model to feature number 1, a
2026-03-09 01:05:01.22997 INFO::Fitting model to feature number 2, b
2026-03-09 01:05:01.234088 INFO::Fitting model to feature number 3, c
2026-03-09 01:05:01.315932 INFO::Creating output folder
2026-03-09 01:05:01.316885 INFO::Creating fits folder
2026-03-09 01:05:01.317685 INFO::Writing residuals to file /tmp/RtmpT4YUyb/file1db48152c8ccd/fits/residuals_linear.rds
2026-03-09 01:05:01.318636 INFO::Writing fitted values to file /tmp/RtmpT4YUyb/file1db48152c8ccd/fits/fitted_linear.rds
2026-03-09 01:05:01.319676 INFO::Writing residuals to file /tmp/RtmpT4YUyb/file1db48152c8ccd/fits/residuals_logistic.rds
2026-03-09 01:05:01.320682 INFO::Writing fitted values to file /tmp/RtmpT4YUyb/file1db48152c8ccd/fits/fitted_logistic.rds
2026-03-09 01:05:01.322906 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpT4YUyb/file1db48152c8ccd/all_results.tsv
2026-03-09 01:05:01.324381 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): /tmp/RtmpT4YUyb/file1db48152c8ccd/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
361.972 4.480 366.461
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.260 | 0.532 | 20.795 | |
| maaslin_check_arguments | 0.138 | 0.002 | 0.140 | |
| maaslin_check_formula | 0.159 | 0.001 | 0.159 | |
| maaslin_compute_formula | 0.150 | 0.003 | 0.154 | |
| maaslin_contrast_test | 19.192 | 0.350 | 19.543 | |
| maaslin_filter | 0.474 | 0.029 | 0.504 | |
| maaslin_fit | 13.416 | 0.096 | 13.513 | |
| maaslin_log_arguments | 0.134 | 0.002 | 0.135 | |
| maaslin_normalize | 0.270 | 0.002 | 0.272 | |
| maaslin_plot_results | 43.294 | 0.235 | 43.492 | |
| maaslin_plot_results_from_output | 43.900 | 0.379 | 44.283 | |
| maaslin_process_metadata | 0.453 | 0.013 | 0.465 | |
| maaslin_read_data | 0.125 | 0.002 | 0.127 | |
| maaslin_reorder_data | 0.128 | 0.005 | 0.133 | |
| maaslin_transform | 0.562 | 0.014 | 0.576 | |
| maaslin_write_results | 12.916 | 0.102 | 13.018 | |
| maaslin_write_results_lefse_format | 14.420 | 0.042 | 14.462 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.001 | 0.004 | |