William Nickols
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:03 -0500 (Thu, 20 Nov 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 2025-11-18 05:32:59 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 05:54:59 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 1320.5 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 44.159 0.405 44.569
maaslin_plot_results 43.814 0.331 44.106
maaslin3 19.461 0.505 19.967
maaslin_contrast_test 18.205 0.323 18.528
maaslin_write_results_lefse_format 14.959 0.132 15.092
maaslin_write_results 13.708 0.077 13.787
maaslin_fit 12.747 0.089 12.837
* 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")
2025-11-18 05:39:18.963175 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:39:19.047675 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:39:19.155301 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:39:19.1782 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:39:19.213017 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:39:19.293714 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:39:19.29981 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:39:19.313049 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:39:19.431066 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:39:19.436774 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:39:19.486506 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:39:19.52693 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:39:19.53893 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:39:19.597556 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:39:19.669206 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:39:36.08619 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:39:36.166091 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:39:36.243911 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:39:36.267172 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:39:36.301499 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:39:36.376953 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:39:36.382724 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:39:36.394682 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:39:36.490994 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:39:36.496721 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:39:36.551022 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:39:36.612047 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:39:36.624717 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:39:36.669474 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:39:36.744359 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:40:01.699203 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:40:01.779092 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:40:01.857384 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:40:01.88055 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:40:01.916573 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:40:01.997726 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:40:02.003747 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:40:02.017653 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:40:02.126525 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:40:02.132786 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:40:02.190474 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:40:02.236537 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:40:02.249934 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:40:02.291761 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:40:02.364344 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:40:15.138871 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:40:15.217608 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:40:15.293099 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:40:15.315673 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:40:15.350982 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:40:15.427328 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:40:15.432738 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:40:15.444657 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:40:15.546793 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:40:15.552799 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:40:15.605908 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:40:15.648966 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:40:15.662357 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:40:15.730863 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:40:15.80532 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:40:16.022439 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_linear.rds
2025-11-18 05:40:16.084402 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_linear.rds
2025-11-18 05:40:16.147952 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_logistic.rds
2025-11-18 05:40:16.448476 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_logistic.rds
2025-11-18 05:40:38.25028 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:40:38.326763 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:40:38.404528 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:40:38.426264 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:40:38.461174 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:40:38.537566 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:40:38.542965 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:40:38.554942 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:40:38.650757 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:40:38.656339 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:40:38.706787 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:40:38.747615 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:40:38.846174 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:40:38.888625 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:40:38.959016 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:40:51.863713 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:40:51.94473 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:40:52.025448 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:40:52.048326 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:40:52.11541 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:40:52.200349 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:40:52.206508 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:40:52.219578 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:40:52.323374 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:40:52.329556 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:40:52.383251 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:40:52.423849 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:40:52.435983 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:40:52.478328 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:40:52.547088 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:40:52.750215 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_linear.rds
2025-11-18 05:40:52.811449 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_linear.rds
2025-11-18 05:40:52.874653 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_logistic.rds
2025-11-18 05:40:53.176708 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_logistic.rds
2025-11-18 05:41:15.115935 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:41:15.199528 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:41:15.277134 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:41:15.299277 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:41:15.334906 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:41:15.410993 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:41:15.41684 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:41:15.429375 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:41:15.525792 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:41:15.531356 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:41:15.58153 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:41:15.622321 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:41:15.634507 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:41:15.676474 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:41:15.745628 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:41:28.28617 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:41:28.371903 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:41:28.460905 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:41:28.483572 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:41:28.518415 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:41:28.60217 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:41:28.607811 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:41:28.619838 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:41:28.716438 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:41:28.72241 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:41:28.773333 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:41:28.814649 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:41:28.826556 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:41:28.867076 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:41:28.936724 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:41:29.155096 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_linear.rds
2025-11-18 05:41:29.216241 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_linear.rds
2025-11-18 05:41:29.27929 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/residuals_logistic.rds
2025-11-18 05:41:29.578999 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d470de6841/fits/fitted_logistic.rds
2025-11-18 05:41:52.563397 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:41:52.641431 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:41:52.720546 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:41:52.743328 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:41:52.779803 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:41:52.861956 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:41:52.867502 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:41:52.879456 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:41:52.974149 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:41:52.979792 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:41:53.030844 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:41:53.073905 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:41:53.086186 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:41:53.128087 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:41:53.199144 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:42:04.172455 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:42:04.250906 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:42:04.32769 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:42:04.349786 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:42:04.384642 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:42:04.460145 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:42:04.46552 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:42:04.477268 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:42:04.570921 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:42:04.576439 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:42:04.659135 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:42:04.701405 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:42:04.713684 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:42:04.755936 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:42:04.827695 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:42:30.099812 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:42:40.227311 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:43:05.924673 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:43:15.967646 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:43:16.60771 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_linear.rds
2025-11-18 05:43:16.66945 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_linear.rds
2025-11-18 05:43:16.708265 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_logistic.rds
2025-11-18 05:43:16.778989 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_logistic.rds
2025-11-18 05:43:40.777923 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:43:45.850994 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:43:46.166528 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_linear.rds
2025-11-18 05:43:46.229441 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_linear.rds
2025-11-18 05:43:46.268897 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_logistic.rds
2025-11-18 05:43:46.340449 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_logistic.rds
2025-11-18 05:44:04.991904 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:44:11.451834 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 05:44:11.751134 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_linear.rds
2025-11-18 05:44:11.812831 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_linear.rds
2025-11-18 05:44:11.851411 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_logistic.rds
2025-11-18 05:44:11.923063 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_logistic.rds
2025-11-18 05:44:30.300341 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:44:30.382587 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:44:30.461506 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:44:30.485322 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:44:30.521947 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:44:30.627258 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:44:30.632697 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:44:30.644874 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:44:30.742989 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:44:30.748503 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:44:30.799648 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:44:30.840975 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:44:30.853039 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:44:30.89451 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:44:30.96641 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:44:43.261397 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 05:44:43.343011 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 05:44:43.419983 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 05:44:43.443618 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 05:44:43.480493 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 05:44:43.55937 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 05:44:43.565209 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 05:44:43.577693 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 05:44:43.679195 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 05:44:43.684992 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 05:44:43.736523 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 05:44:43.778639 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 05:44:43.790887 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 05:44:43.832227 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 05:44:43.903813 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 05:44:44.167834 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_linear.rds
2025-11-18 05:44:44.230005 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_linear.rds
2025-11-18 05:44:44.293935 WARNING::Deleting existing residuals file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/residuals_logistic.rds
2025-11-18 05:44:44.596022 WARNING::Deleting existing fitted file: /tmp/RtmpUkO7bN/file1980d459f54da3/fits/fitted_logistic.rds
2025-11-18 05:45:05.629127 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-18 05:45:05.647145 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-18 05:45:05.659668 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-18 05:45:05.713585 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-18 05:45:05.730809 ERROR::Effect name not found in metadata: d
2025-11-18 05:45:05.743014 ERROR::No user formula provided
2025-11-18 05:45:05.776378 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-18 05:45:05.788636 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-18 05:45:08.795611 INFO::Writing function arguments to log file
2025-11-18 05:45:08.809722 INFO::Verifying options selected are valid
2025-11-18 05:45:11.129688 INFO::Writing function arguments to log file
2025-11-18 05:45:11.142311 INFO::Verifying options selected are valid
2025-11-18 05:45:11.143472 INFO::Determining format of input files
2025-11-18 05:45:11.144527 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 05:45:11.146993 INFO::Running selected normalization method: TSS
2025-11-18 05:45:11.148594 INFO::Creating output feature tables folder
2025-11-18 05:45:11.1496 INFO::Writing normalized data to file /tmp/RtmpUkO7bN/file1980d45a44739a/features/data_norm.tsv
2025-11-18 05:45:11.151151 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-18 05:45:11.152083 INFO::Total samples in data: 16
2025-11-18 05:45:11.152981 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-18 05:45:11.153885 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-18 05:45:11.155903 INFO::Total filtered features: 0
2025-11-18 05:45:11.156892 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-18 05:45:11.158088 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-18 05:45:11.159082 INFO::Filtered feature names from variance filtering:
2025-11-18 05:45:11.16001 INFO::Writing filtered data to file /tmp/RtmpUkO7bN/file1980d45a44739a/features/filtered_data.tsv
2025-11-18 05:45:11.16157 INFO::Running selected transform method: LOG
2025-11-18 05:45:11.162824 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUkO7bN/file1980d45a44739a/features/data_transformed.tsv
2025-11-18 05:45:11.164622 INFO::Applying z-score to standardize continuous metadata
2025-11-18 05:45:11.170414 INFO::Running the linear model component
2025-11-18 05:45:11.18506 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:11.189879 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:11.194458 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:11.202074 INFO::Counting total values for each feature
2025-11-18 05:45:11.204004 INFO::Running the logistic model component
2025-11-18 05:45:11.218355 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:11.225357 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:11.232201 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:11.241779 INFO::Counting total values for each feature
2025-11-18 05:45:11.244132 INFO::Re-running abundances for warn_prevalence
2025-11-18 05:45:11.245146 INFO::Running selected normalization method: TSS
2025-11-18 05:45:11.246714 INFO::Running selected transform method: LOG
2025-11-18 05:45:11.260996 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:11.26564 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:11.27 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:11.359574 INFO::Creating fits folder
2025-11-18 05:45:11.360786 INFO::Writing residuals to file /tmp/RtmpUkO7bN/file1980d45a44739a/fits/residuals_linear.rds
2025-11-18 05:45:11.362002 INFO::Writing fitted values to file /tmp/RtmpUkO7bN/file1980d45a44739a/fits/fitted_linear.rds
2025-11-18 05:45:11.363254 INFO::Writing residuals to file /tmp/RtmpUkO7bN/file1980d45a44739a/fits/residuals_logistic.rds
2025-11-18 05:45:11.364445 INFO::Writing fitted values to file /tmp/RtmpUkO7bN/file1980d45a44739a/fits/fitted_logistic.rds
2025-11-18 05:45:11.367096 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpUkO7bN/file1980d45a44739a/all_results.tsv
2025-11-18 05:45:11.368754 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/RtmpUkO7bN/file1980d45a44739a/significant_results.tsv
2025-11-18 05:45:11.370095 INFO::Creating output figures folder
2025-11-18 05:45:11.371505 INFO::Writing summary plot of significant
results to file: /tmp/RtmpUkO7bN/file1980d45a44739a/figures/summary_plot.pdf
2025-11-18 05:45:13.052278 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUkO7bN/file1980d45a44739a/figures
2025-11-18 05:45:13.054412 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 05:45:13.059946 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 05:45:13.592386 INFO::Writing summary plot of
significant results to file: /tmp/RtmpUkO7bN/file1980d45a44739a/figures/summary_plot.pdf
2025-11-18 05:45:15.224176 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUkO7bN/file1980d45a44739a/figures
2025-11-18 05:45:15.225777 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 05:45:15.231035 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 05:45:15.788959 INFO::Running the linear model component
2025-11-18 05:45:15.798069 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:15.80257 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:15.806968 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:15.814525 INFO::Counting total values for each feature
2025-11-18 05:45:15.816314 INFO::Running the logistic model component
2025-11-18 05:45:15.825178 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:15.831722 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:15.838003 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:15.847315 INFO::Counting total values for each feature
2025-11-18 05:45:15.84957 INFO::Re-running abundances for warn_prevalence
2025-11-18 05:45:15.850437 INFO::Running selected normalization method: TSS
2025-11-18 05:45:15.851855 INFO::Running selected transform method: LOG
2025-11-18 05:45:15.86096 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:15.865341 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:15.869554 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:15.960091 INFO::Creating output folder
2025-11-18 05:45:15.961129 INFO::Creating output figures folder
2025-11-18 05:45:15.962526 INFO::Writing summary plot of significant
results to file: /tmp/RtmpUkO7bN/file1980d45b3be851/figures/summary_plot.pdf
2025-11-18 05:45:18.801239 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUkO7bN/file1980d45b3be851/figures
2025-11-18 05:45:18.80328 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 05:45:18.808429 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 05:45:19.75616 INFO::Applying z-score to standardize continuous metadata
2025-11-18 05:45:19.764358 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-18 05:45:19.765306 INFO::Bypass z-score application to metadata
2025-11-18 05:45:19.767869 INFO::Bypass z-score application to metadata
2025-11-18 05:45:19.786967 INFO::Determining format of input files
2025-11-18 05:45:19.787959 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 05:45:19.788828 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-18 05:45:19.796242 INFO::Determining format of input files
2025-11-18 05:45:19.797299 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-18 05:45:19.798587 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 05:45:19.806694 INFO::Determining format of input files
2025-11-18 05:45:19.807766 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 05:45:19.808867 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 05:45:19.810607 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-18 05:45:19.811389 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-18 05:45:19.823739 INFO::Running selected transform method: LOG
2025-11-18 05:45:19.824962 INFO::Creating output feature tables folder
2025-11-18 05:45:19.825862 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUkO7bN/file1980d43bf44fb8/features/data_transformed.tsv
2025-11-18 05:45:19.829952 INFO::Running selected transform method: LOG
2025-11-18 05:45:19.831007 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUkO7bN/file1980d43bf44fb8/features/data_transformed.tsv
2025-11-18 05:45:19.835177 INFO::Running selected transform method: PLOG
2025-11-18 05:45:19.837006 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUkO7bN/file1980d43bf44fb8/features/data_transformed.tsv
2025-11-18 05:45:19.840228 INFO::Running selected transform method: NONE
2025-11-18 05:45:19.840991 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUkO7bN/file1980d43bf44fb8/features/data_transformed.tsv
2025-11-18 05:45:19.848907 INFO::Running the linear model component
2025-11-18 05:45:19.857593 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:19.862177 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:19.866382 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:19.873996 INFO::Counting total values for each feature
2025-11-18 05:45:19.875756 INFO::Running the logistic model component
2025-11-18 05:45:19.884227 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:19.890808 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:19.897088 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:19.906214 INFO::Counting total values for each feature
2025-11-18 05:45:19.908253 INFO::Re-running abundances for warn_prevalence
2025-11-18 05:45:19.909075 INFO::Running selected normalization method: TSS
2025-11-18 05:45:19.910473 INFO::Running selected transform method: LOG
2025-11-18 05:45:19.919 INFO::Fitting model to feature number 1, a
2025-11-18 05:45:19.92324 INFO::Fitting model to feature number 2, b
2025-11-18 05:45:19.927229 INFO::Fitting model to feature number 3, c
2025-11-18 05:45:20.015465 INFO::Creating output folder
2025-11-18 05:45:20.016462 INFO::Creating fits folder
2025-11-18 05:45:20.017302 INFO::Writing residuals to file /tmp/RtmpUkO7bN/file1980d439fe5293/fits/residuals_linear.rds
2025-11-18 05:45:20.018306 INFO::Writing fitted values to file /tmp/RtmpUkO7bN/file1980d439fe5293/fits/fitted_linear.rds
2025-11-18 05:45:20.019466 INFO::Writing residuals to file /tmp/RtmpUkO7bN/file1980d439fe5293/fits/residuals_logistic.rds
2025-11-18 05:45:20.020602 INFO::Writing fitted values to file /tmp/RtmpUkO7bN/file1980d439fe5293/fits/fitted_logistic.rds
2025-11-18 05:45:20.023355 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpUkO7bN/file1980d439fe5293/all_results.tsv
2025-11-18 05:45:20.024864 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/RtmpUkO7bN/file1980d439fe5293/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
366.447 5.680 372.099
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.461 | 0.505 | 19.967 | |
| maaslin_check_arguments | 0.137 | 0.000 | 0.137 | |
| maaslin_check_formula | 0.135 | 0.001 | 0.136 | |
| maaslin_compute_formula | 0.157 | 0.001 | 0.158 | |
| maaslin_contrast_test | 18.205 | 0.323 | 18.528 | |
| maaslin_filter | 0.441 | 0.018 | 0.459 | |
| maaslin_fit | 12.747 | 0.089 | 12.837 | |
| maaslin_log_arguments | 0.129 | 0.001 | 0.130 | |
| maaslin_normalize | 0.259 | 0.003 | 0.262 | |
| maaslin_plot_results | 43.814 | 0.331 | 44.106 | |
| maaslin_plot_results_from_output | 44.159 | 0.405 | 44.569 | |
| maaslin_process_metadata | 0.493 | 0.018 | 0.511 | |
| maaslin_read_data | 0.129 | 0.000 | 0.129 | |
| maaslin_reorder_data | 0.133 | 0.003 | 0.135 | |
| maaslin_transform | 0.572 | 0.010 | 0.582 | |
| maaslin_write_results | 13.708 | 0.077 | 13.787 | |
| maaslin_write_results_lefse_format | 14.959 | 0.132 | 15.092 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |