William Nickols
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 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 2025-12-11 12:03 -0500 (Thu, 11 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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. |
| 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: 2025-12-09 00:59:09 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 01:20:54 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 1304.4 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 43.325 0.439 43.766
maaslin_plot_results 43.264 0.264 43.487
maaslin3 19.931 0.424 20.358
maaslin_contrast_test 18.336 0.361 18.697
maaslin_write_results_lefse_format 14.912 0.099 15.011
maaslin_write_results 13.252 0.100 13.352
maaslin_fit 12.514 0.177 12.691
* 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")
2025-12-09 01:05:25.910535 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:05:25.997552 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:05:26.092633 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:05:26.114279 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:05:26.149276 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:05:26.226852 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:05:26.240379 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:05:26.252888 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:05:26.349386 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:05:26.354998 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:05:26.404883 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:05:26.452347 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:05:26.464241 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:05:26.504015 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:05:26.573204 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:05:41.841812 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:05:41.922219 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:05:41.9987 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:05:42.020018 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:05:42.054142 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:05:42.129799 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:05:42.135299 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:05:42.146967 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:05:42.243622 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:05:42.249147 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:05:42.299911 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:05:42.340311 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:05:42.352383 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:05:42.39404 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:05:42.477566 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:06:06.938564 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:06:07.019595 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:06:07.095282 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:06:07.117257 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:06:07.151351 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:06:07.229111 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:06:07.235113 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:06:07.247913 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:06:07.348126 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:06:07.35428 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:06:07.411473 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:06:07.456949 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:06:07.47026 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:06:07.530332 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:06:07.598735 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:06:20.574814 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:06:20.651245 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:06:20.725651 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:06:20.748486 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:06:20.784239 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:06:20.861394 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:06:20.866827 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:06:20.87888 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:06:20.97465 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:06:20.980181 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:06:21.030531 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:06:21.093048 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:06:21.105944 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:06:21.148078 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:06:21.217375 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:06:21.420596 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_linear.rds
2025-12-09 01:06:21.481966 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_linear.rds
2025-12-09 01:06:21.54542 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_logistic.rds
2025-12-09 01:06:21.846168 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_logistic.rds
2025-12-09 01:06:44.621076 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:06:44.714921 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:06:44.805944 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:06:44.830621 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:06:44.871809 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:06:44.973027 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:06:44.978412 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:06:44.990448 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:06:45.086805 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:06:45.092296 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:06:45.144211 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:06:45.18697 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:06:45.199475 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:06:45.242829 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:06:45.313866 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:06:57.307086 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:06:57.385079 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:06:57.462045 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:06:57.484338 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:06:57.5199 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:06:57.598238 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:06:57.60381 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:06:57.616342 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:06:57.716357 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:06:57.722368 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:06:57.783705 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:06:57.827287 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:06:57.839524 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:06:57.881589 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:06:57.955134 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:06:58.196049 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_linear.rds
2025-12-09 01:06:58.257205 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_linear.rds
2025-12-09 01:06:58.32088 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_logistic.rds
2025-12-09 01:06:58.619987 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_logistic.rds
2025-12-09 01:07:21.70987 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:07:21.787594 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:07:21.864968 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:07:21.887479 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:07:21.923064 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:07:22.00607 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:07:22.012446 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:07:22.026415 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:07:22.125261 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:07:22.131037 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:07:22.182041 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:07:22.22378 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:07:22.236628 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:07:22.277823 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:07:22.351009 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:07:33.634193 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:07:33.710994 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:07:33.787803 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:07:33.810455 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:07:33.870917 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:07:33.950178 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:07:33.956131 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:07:33.968898 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:07:34.076065 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:07:34.082611 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:07:34.13475 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:07:34.177402 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:07:34.18964 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:07:34.230764 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:07:34.301534 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:07:34.510241 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_linear.rds
2025-12-09 01:07:34.572433 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_linear.rds
2025-12-09 01:07:34.635915 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/residuals_logistic.rds
2025-12-09 01:07:34.93872 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393a148f4b10/fits/fitted_logistic.rds
2025-12-09 01:07:57.866823 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:07:57.947592 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:07:58.024968 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:07:58.066609 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:07:58.101334 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:07:58.178498 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:07:58.183817 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:07:58.195422 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:07:58.290553 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:07:58.296071 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:07:58.345598 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:07:58.385775 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:07:58.397814 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:07:58.438479 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:07:58.506987 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:08:09.234473 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:08:09.314313 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:08:09.395483 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:08:09.416991 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:08:09.4516 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:08:09.55582 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:08:09.561217 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:08:09.574033 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:08:09.673543 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:08:09.679113 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:08:09.729591 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:08:09.770828 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:08:09.782712 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:08:09.824461 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:08:09.895751 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:08:34.931413 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:08:43.784425 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:09:09.253019 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:09:20.093944 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:09:20.722723 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_linear.rds
2025-12-09 01:09:20.784427 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_linear.rds
2025-12-09 01:09:20.823053 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_logistic.rds
2025-12-09 01:09:20.893059 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_logistic.rds
2025-12-09 01:09:43.909526 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:09:50.415001 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:09:50.735859 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_linear.rds
2025-12-09 01:09:50.798061 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_linear.rds
2025-12-09 01:09:50.837062 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_logistic.rds
2025-12-09 01:09:50.90663 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_logistic.rds
2025-12-09 01:10:09.763268 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:10:16.128048 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 01:10:16.43507 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_linear.rds
2025-12-09 01:10:16.498247 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_linear.rds
2025-12-09 01:10:16.538038 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_logistic.rds
2025-12-09 01:10:16.609399 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_logistic.rds
2025-12-09 01:10:35.76926 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:10:35.869039 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:10:35.945619 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:10:35.968062 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:10:36.002822 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:10:36.079608 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:10:36.085248 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:10:36.097479 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:10:36.197597 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:10:36.203229 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:10:36.254218 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:10:36.294604 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:10:36.306377 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:10:36.346362 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:10:36.415575 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:10:47.245945 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 01:10:47.321484 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 01:10:47.400098 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 01:10:47.424569 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 01:10:47.461408 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 01:10:47.53833 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 01:10:47.544385 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 01:10:47.557081 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 01:10:47.653301 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 01:10:47.658866 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 01:10:47.711333 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 01:10:47.755158 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 01:10:47.768542 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 01:10:47.810453 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 01:10:47.880806 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 01:10:48.162697 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_linear.rds
2025-12-09 01:10:48.22416 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_linear.rds
2025-12-09 01:10:48.287655 WARNING::Deleting existing residuals file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/residuals_logistic.rds
2025-12-09 01:10:48.587852 WARNING::Deleting existing fitted file: /tmp/RtmpSLzOKK/file22393aa06f0e2/fits/fitted_logistic.rds
2025-12-09 01:11:09.536557 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-09 01:11:09.554187 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-09 01:11:09.565892 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-09 01:11:09.619496 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-09 01:11:09.636607 ERROR::Effect name not found in metadata: d
2025-12-09 01:11:09.6483 ERROR::No user formula provided
2025-12-09 01:11:09.679922 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-09 01:11:09.691776 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-09 01:11:12.660246 INFO::Writing function arguments to log file
2025-12-09 01:11:12.675893 INFO::Verifying options selected are valid
2025-12-09 01:11:15.105559 INFO::Writing function arguments to log file
2025-12-09 01:11:15.118381 INFO::Verifying options selected are valid
2025-12-09 01:11:15.119565 INFO::Determining format of input files
2025-12-09 01:11:15.120602 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 01:11:15.123063 INFO::Running selected normalization method: TSS
2025-12-09 01:11:15.124622 INFO::Creating output feature tables folder
2025-12-09 01:11:15.125629 INFO::Writing normalized data to file /tmp/RtmpSLzOKK/file22393a5abd111d/features/data_norm.tsv
2025-12-09 01:11:15.127193 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-09 01:11:15.12813 INFO::Total samples in data: 16
2025-12-09 01:11:15.129075 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-09 01:11:15.13 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-09 01:11:15.132046 INFO::Total filtered features: 0
2025-12-09 01:11:15.133021 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-09 01:11:15.134233 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-09 01:11:15.135208 INFO::Filtered feature names from variance filtering:
2025-12-09 01:11:15.136118 INFO::Writing filtered data to file /tmp/RtmpSLzOKK/file22393a5abd111d/features/filtered_data.tsv
2025-12-09 01:11:15.137737 INFO::Running selected transform method: LOG
2025-12-09 01:11:15.138995 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpSLzOKK/file22393a5abd111d/features/data_transformed.tsv
2025-12-09 01:11:15.140764 INFO::Applying z-score to standardize continuous metadata
2025-12-09 01:11:15.146608 INFO::Running the linear model component
2025-12-09 01:11:15.161618 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:15.166899 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:15.171661 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:15.17954 INFO::Counting total values for each feature
2025-12-09 01:11:15.181632 INFO::Running the logistic model component
2025-12-09 01:11:15.196247 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:15.20365 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:15.210547 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:15.220996 INFO::Counting total values for each feature
2025-12-09 01:11:15.223692 INFO::Re-running abundances for warn_prevalence
2025-12-09 01:11:15.224923 INFO::Running selected normalization method: TSS
2025-12-09 01:11:15.226752 INFO::Running selected transform method: LOG
2025-12-09 01:11:15.242161 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:15.247663 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:15.252397 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:15.349928 INFO::Creating fits folder
2025-12-09 01:11:15.351517 INFO::Writing residuals to file /tmp/RtmpSLzOKK/file22393a5abd111d/fits/residuals_linear.rds
2025-12-09 01:11:15.352934 INFO::Writing fitted values to file /tmp/RtmpSLzOKK/file22393a5abd111d/fits/fitted_linear.rds
2025-12-09 01:11:15.354418 INFO::Writing residuals to file /tmp/RtmpSLzOKK/file22393a5abd111d/fits/residuals_logistic.rds
2025-12-09 01:11:15.355781 INFO::Writing fitted values to file /tmp/RtmpSLzOKK/file22393a5abd111d/fits/fitted_logistic.rds
2025-12-09 01:11:15.359133 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpSLzOKK/file22393a5abd111d/all_results.tsv
2025-12-09 01:11:15.361112 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/RtmpSLzOKK/file22393a5abd111d/significant_results.tsv
2025-12-09 01:11:15.3627 INFO::Creating output figures folder
2025-12-09 01:11:15.364236 INFO::Writing summary plot of significant
results to file: /tmp/RtmpSLzOKK/file22393a5abd111d/figures/summary_plot.pdf
2025-12-09 01:11:17.028131 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpSLzOKK/file22393a5abd111d/figures
2025-12-09 01:11:17.03025 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 01:11:17.035607 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 01:11:17.587882 INFO::Writing summary plot of
significant results to file: /tmp/RtmpSLzOKK/file22393a5abd111d/figures/summary_plot.pdf
2025-12-09 01:11:19.283966 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpSLzOKK/file22393a5abd111d/figures
2025-12-09 01:11:19.285659 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 01:11:19.291241 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 01:11:19.818052 INFO::Running the linear model component
2025-12-09 01:11:19.826869 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:19.83109 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:19.835035 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:19.841851 INFO::Counting total values for each feature
2025-12-09 01:11:19.84344 INFO::Running the logistic model component
2025-12-09 01:11:19.851654 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:19.857543 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:19.863085 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:19.871553 INFO::Counting total values for each feature
2025-12-09 01:11:19.873492 INFO::Re-running abundances for warn_prevalence
2025-12-09 01:11:19.874239 INFO::Running selected normalization method: TSS
2025-12-09 01:11:19.875567 INFO::Running selected transform method: LOG
2025-12-09 01:11:19.884142 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:19.888289 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:19.89226 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:19.978126 INFO::Creating output folder
2025-12-09 01:11:19.979164 INFO::Creating output figures folder
2025-12-09 01:11:19.980467 INFO::Writing summary plot of significant
results to file: /tmp/RtmpSLzOKK/file22393a6cac85d7/figures/summary_plot.pdf
2025-12-09 01:11:21.62687 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpSLzOKK/file22393a6cac85d7/figures
2025-12-09 01:11:21.628561 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 01:11:21.633482 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 01:11:22.693052 INFO::Applying z-score to standardize continuous metadata
2025-12-09 01:11:22.70125 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-09 01:11:22.702172 INFO::Bypass z-score application to metadata
2025-12-09 01:11:22.70479 INFO::Bypass z-score application to metadata
2025-12-09 01:11:22.723933 INFO::Determining format of input files
2025-12-09 01:11:22.724927 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 01:11:22.725791 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-09 01:11:22.733244 INFO::Determining format of input files
2025-12-09 01:11:22.734251 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-09 01:11:22.73556 INFO::Input format is feature_specific_covariate samples as columns
2025-12-09 01:11:22.743655 INFO::Determining format of input files
2025-12-09 01:11:22.744651 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 01:11:22.745704 INFO::Input format is feature_specific_covariate samples as columns
2025-12-09 01:11:22.747412 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-09 01:11:22.748204 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-09 01:11:22.759979 INFO::Running selected transform method: LOG
2025-12-09 01:11:22.76117 INFO::Creating output feature tables folder
2025-12-09 01:11:22.762056 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpSLzOKK/file22393a383eeaa1/features/data_transformed.tsv
2025-12-09 01:11:22.766089 INFO::Running selected transform method: LOG
2025-12-09 01:11:22.767155 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpSLzOKK/file22393a383eeaa1/features/data_transformed.tsv
2025-12-09 01:11:22.771186 INFO::Running selected transform method: PLOG
2025-12-09 01:11:22.772817 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpSLzOKK/file22393a383eeaa1/features/data_transformed.tsv
2025-12-09 01:11:22.775805 INFO::Running selected transform method: NONE
2025-12-09 01:11:22.77658 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpSLzOKK/file22393a383eeaa1/features/data_transformed.tsv
2025-12-09 01:11:22.784647 INFO::Running the linear model component
2025-12-09 01:11:22.793663 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:22.798358 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:22.802888 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:22.810781 INFO::Counting total values for each feature
2025-12-09 01:11:22.812741 INFO::Running the logistic model component
2025-12-09 01:11:22.82202 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:22.828633 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:22.850377 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:22.860893 INFO::Counting total values for each feature
2025-12-09 01:11:22.863415 INFO::Re-running abundances for warn_prevalence
2025-12-09 01:11:22.864403 INFO::Running selected normalization method: TSS
2025-12-09 01:11:22.86604 INFO::Running selected transform method: LOG
2025-12-09 01:11:22.877221 INFO::Fitting model to feature number 1, a
2025-12-09 01:11:22.882544 INFO::Fitting model to feature number 2, b
2025-12-09 01:11:22.887238 INFO::Fitting model to feature number 3, c
2025-12-09 01:11:22.97577 INFO::Creating output folder
2025-12-09 01:11:22.976743 INFO::Creating fits folder
2025-12-09 01:11:22.977577 INFO::Writing residuals to file /tmp/RtmpSLzOKK/file22393a2ac5ffe4/fits/residuals_linear.rds
2025-12-09 01:11:22.978607 INFO::Writing fitted values to file /tmp/RtmpSLzOKK/file22393a2ac5ffe4/fits/fitted_linear.rds
2025-12-09 01:11:22.979678 INFO::Writing residuals to file /tmp/RtmpSLzOKK/file22393a2ac5ffe4/fits/residuals_logistic.rds
2025-12-09 01:11:22.9807 INFO::Writing fitted values to file /tmp/RtmpSLzOKK/file22393a2ac5ffe4/fits/fitted_logistic.rds
2025-12-09 01:11:22.983229 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpSLzOKK/file22393a2ac5ffe4/all_results.tsv
2025-12-09 01:11:22.984773 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/RtmpSLzOKK/file22393a2ac5ffe4/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
363.070 5.073 368.145
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.931 | 0.424 | 20.358 | |
| maaslin_check_arguments | 0.144 | 0.000 | 0.144 | |
| maaslin_check_formula | 0.134 | 0.002 | 0.136 | |
| maaslin_compute_formula | 0.169 | 0.000 | 0.168 | |
| maaslin_contrast_test | 18.336 | 0.361 | 18.697 | |
| maaslin_filter | 0.434 | 0.005 | 0.439 | |
| maaslin_fit | 12.514 | 0.177 | 12.691 | |
| maaslin_log_arguments | 0.127 | 0.001 | 0.127 | |
| maaslin_normalize | 0.280 | 0.005 | 0.284 | |
| maaslin_plot_results | 43.264 | 0.264 | 43.487 | |
| maaslin_plot_results_from_output | 43.325 | 0.439 | 43.766 | |
| maaslin_process_metadata | 0.461 | 0.024 | 0.485 | |
| maaslin_read_data | 0.133 | 0.001 | 0.133 | |
| maaslin_reorder_data | 0.134 | 0.002 | 0.136 | |
| maaslin_transform | 0.552 | 0.028 | 0.580 | |
| maaslin_write_results | 13.252 | 0.100 | 13.352 | |
| maaslin_write_results_lefse_format | 14.912 | 0.099 | 15.011 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |