William Nickols
| Snapshot Date: 2025-12-10 13:40 -0500 (Wed, 10 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-11 11:35 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| 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 1157/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-12-11 02:22:55 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 02:44:31 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 1296.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.3.0’
* 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 43.927 0.334 44.264
maaslin_plot_results 43.555 0.293 43.830
maaslin3 19.272 0.520 19.797
maaslin_contrast_test 18.433 0.388 18.825
maaslin_write_results 14.339 0.090 14.430
maaslin_fit 13.934 0.120 14.057
maaslin_write_results_lefse_format 13.916 0.083 14.000
* 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-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-12-11 02:29:10.784926 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:29:10.861295 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:29:10.959063 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:29:10.985618 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:29:11.031148 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:29:11.105446 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:29:11.110807 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:29:11.12277 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:29:11.227275 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:29:11.232959 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:29:11.282063 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:29:11.322002 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:29:11.334252 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:29:11.375333 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:29:11.454335 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:29:27.108481 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:29:27.182498 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:29:27.255696 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:29:27.277519 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:29:27.311172 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:29:27.401432 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:29:27.406867 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:29:27.41879 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:29:27.513111 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:29:27.518582 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:29:27.569321 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:29:27.623607 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:29:27.636178 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:29:27.675927 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:29:27.74314 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:29:51.962329 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:29:52.041441 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:29:52.119753 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:29:52.142467 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:29:52.1776 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:29:52.254874 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:29:52.260761 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:29:52.273285 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:29:52.369702 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:29:52.375232 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:29:52.425456 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:29:52.465908 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:29:52.477764 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:29:52.519303 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:29:52.592333 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:30:05.3421 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:30:05.42428 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:30:05.500659 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:30:05.532555 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:30:05.567037 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:30:05.64293 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:30:05.648329 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:30:05.660257 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:30:05.758451 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:30:05.764254 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:30:05.815378 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:30:05.856058 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:30:05.868022 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:30:05.908366 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:30:06.010999 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:30:06.207761 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_linear.rds
2025-12-11 02:30:06.26852 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_linear.rds
2025-12-11 02:30:06.331347 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_logistic.rds
2025-12-11 02:30:06.633541 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_logistic.rds
2025-12-11 02:30:28.199031 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:30:28.275641 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:30:28.351545 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:30:28.373326 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:30:28.407729 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:30:28.48312 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:30:28.488606 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:30:28.500351 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:30:28.594521 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:30:28.600236 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:30:28.650105 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:30:28.690634 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:30:28.702974 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:30:28.743337 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:30:28.814214 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:30:41.784748 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:30:41.863844 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:30:41.942833 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:30:41.966798 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:30:42.002928 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:30:42.08175 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:30:42.087459 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:30:42.099834 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:30:42.199743 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:30:42.205481 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:30:42.298596 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:30:42.34263 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:30:42.35588 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:30:42.400426 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:30:42.47512 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:30:42.684713 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_linear.rds
2025-12-11 02:30:42.746546 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_linear.rds
2025-12-11 02:30:42.809609 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_logistic.rds
2025-12-11 02:30:43.109651 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_logistic.rds
2025-12-11 02:31:05.467352 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:31:05.544065 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:31:05.62024 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:31:05.642617 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:31:05.678591 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:31:05.755254 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:31:05.760651 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:31:05.772551 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:31:05.869336 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:31:05.874919 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:31:05.925776 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:31:05.966815 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:31:05.978939 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:31:06.019542 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:31:06.089727 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:31:17.999194 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:31:18.078935 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:31:18.157739 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:31:18.181361 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:31:18.218597 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:31:18.301165 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:31:18.307157 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:31:18.320032 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:31:18.42644 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:31:18.43253 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:31:18.536 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:31:18.580703 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:31:18.593497 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:31:18.635331 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:31:18.707599 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:31:18.914847 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_linear.rds
2025-12-11 02:31:18.975726 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_linear.rds
2025-12-11 02:31:19.038963 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/residuals_logistic.rds
2025-12-11 02:31:19.338579 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e36421b9c/fits/fitted_logistic.rds
2025-12-11 02:31:40.703281 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:31:40.787996 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:31:40.872596 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:31:40.89666 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:31:40.935888 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:31:41.022978 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:31:41.029374 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:31:41.043516 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:31:41.180737 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:31:41.18647 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:31:41.239727 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:31:41.282583 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:31:41.296315 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:31:41.340593 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:31:41.412365 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:31:53.28731 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:31:53.366915 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:31:53.442672 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:31:53.465058 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:31:53.500049 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:31:53.579313 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:31:53.584818 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:31:53.596727 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:31:53.694234 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:31:53.699906 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:31:53.749576 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:31:53.790017 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:31:53.802325 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:31:53.843229 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:31:53.913777 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:32:17.568433 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:32:26.353221 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:32:51.380868 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:01.479741 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:02.118649 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_linear.rds
2025-12-11 02:33:02.180024 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_linear.rds
2025-12-11 02:33:02.218757 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_logistic.rds
2025-12-11 02:33:02.289314 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_logistic.rds
2025-12-11 02:33:24.962049 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:31.157147 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:31.484461 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_linear.rds
2025-12-11 02:33:31.545947 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_linear.rds
2025-12-11 02:33:31.584367 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_logistic.rds
2025-12-11 02:33:31.653171 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_logistic.rds
2025-12-11 02:33:50.236148 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:56.77729 WARNING::Fitting problem for feature 124 returning NA
2025-12-11 02:33:57.10801 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_linear.rds
2025-12-11 02:33:57.170174 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_linear.rds
2025-12-11 02:33:57.209428 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_logistic.rds
2025-12-11 02:33:57.279309 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_logistic.rds
2025-12-11 02:34:15.391984 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:34:15.468349 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:34:15.542226 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:34:15.563618 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:34:15.597355 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:34:15.674264 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:34:15.679652 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:34:15.691562 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:34:15.785935 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:34:15.791359 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:34:15.840292 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:34:15.879436 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:34:15.891029 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:34:15.930211 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:34:15.998226 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:34:28.19835 WARNING::Fitting problem for feature 50 returning NA
2025-12-11 02:34:28.274428 WARNING::Fitting problem for feature 62 returning NA
2025-12-11 02:34:28.349048 WARNING::Fitting problem for feature 74 returning NA
2025-12-11 02:34:28.371134 WARNING::Fitting problem for feature 78 returning NA
2025-12-11 02:34:28.405856 WARNING::Fitting problem for feature 84 returning NA
2025-12-11 02:34:28.483208 WARNING::Fitting problem for feature 96 returning NA
2025-12-11 02:34:28.488729 WARNING::Fitting problem for feature 97 returning NA
2025-12-11 02:34:28.500979 WARNING::Fitting problem for feature 99 returning NA
2025-12-11 02:34:28.598547 WARNING::Fitting problem for feature 114 returning NA
2025-12-11 02:34:28.604259 WARNING::Fitting problem for feature 115 returning NA
2025-12-11 02:34:28.656284 WARNING::Fitting problem for feature 123 returning NA
2025-12-11 02:34:28.697859 WARNING::Fitting problem for feature 130 returning NA
2025-12-11 02:34:28.710749 WARNING::Fitting problem for feature 132 returning NA
2025-12-11 02:34:28.754182 WARNING::Fitting problem for feature 139 returning NA
2025-12-11 02:34:28.82742 WARNING::Fitting problem for feature 150 returning NA
2025-12-11 02:34:29.130574 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_linear.rds
2025-12-11 02:34:29.19172 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_linear.rds
2025-12-11 02:34:29.255123 WARNING::Deleting existing residuals file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/residuals_logistic.rds
2025-12-11 02:34:29.555685 WARNING::Deleting existing fitted file: /tmp/RtmpwO0pBt/file3c3d1e1b594925/fits/fitted_logistic.rds
2025-12-11 02:34:49.802895 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-11 02:34:49.820384 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-11 02:34:49.832125 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-11 02:34:49.884413 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-11 02:34:49.901179 ERROR::Effect name not found in metadata: d
2025-12-11 02:34:49.912726 ERROR::No user formula provided
2025-12-11 02:34:49.944295 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-11 02:34:49.95584 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-11 02:34:52.880269 INFO::Writing function arguments to log file
2025-12-11 02:34:52.89458 INFO::Verifying options selected are valid
2025-12-11 02:34:56.328737 INFO::Writing function arguments to log file
2025-12-11 02:34:56.341008 INFO::Verifying options selected are valid
2025-12-11 02:34:56.342121 INFO::Determining format of input files
2025-12-11 02:34:56.343125 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-11 02:34:56.345452 INFO::Running selected normalization method: TSS
2025-12-11 02:34:56.346925 INFO::Creating output feature tables folder
2025-12-11 02:34:56.347925 INFO::Writing normalized data to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/features/data_norm.tsv
2025-12-11 02:34:56.349434 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-11 02:34:56.350358 INFO::Total samples in data: 16
2025-12-11 02:34:56.351243 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-11 02:34:56.352132 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-11 02:34:56.35408 INFO::Total filtered features: 0
2025-12-11 02:34:56.355049 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-11 02:34:56.356233 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-11 02:34:56.357191 INFO::Filtered feature names from variance filtering:
2025-12-11 02:34:56.35808 INFO::Writing filtered data to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/features/filtered_data.tsv
2025-12-11 02:34:56.359553 INFO::Running selected transform method: LOG
2025-12-11 02:34:56.36075 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/features/data_transformed.tsv
2025-12-11 02:34:56.362404 INFO::Applying z-score to standardize continuous metadata
2025-12-11 02:34:56.368003 INFO::Running the linear model component
2025-12-11 02:34:56.382042 INFO::Fitting model to feature number 1, a
2025-12-11 02:34:56.386614 INFO::Fitting model to feature number 2, b
2025-12-11 02:34:56.390996 INFO::Fitting model to feature number 3, c
2025-12-11 02:34:56.398687 INFO::Counting total values for each feature
2025-12-11 02:34:56.400624 INFO::Running the logistic model component
2025-12-11 02:34:56.415107 INFO::Fitting model to feature number 1, a
2025-12-11 02:34:56.421954 INFO::Fitting model to feature number 2, b
2025-12-11 02:34:56.428325 INFO::Fitting model to feature number 3, c
2025-12-11 02:34:56.437478 INFO::Counting total values for each feature
2025-12-11 02:34:56.439677 INFO::Re-running abundances for warn_prevalence
2025-12-11 02:34:56.440639 INFO::Running selected normalization method: TSS
2025-12-11 02:34:56.442177 INFO::Running selected transform method: LOG
2025-12-11 02:34:56.456547 INFO::Fitting model to feature number 1, a
2025-12-11 02:34:56.461205 INFO::Fitting model to feature number 2, b
2025-12-11 02:34:56.465705 INFO::Fitting model to feature number 3, c
2025-12-11 02:34:56.555246 INFO::Creating fits folder
2025-12-11 02:34:56.556461 INFO::Writing residuals to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/fits/residuals_linear.rds
2025-12-11 02:34:56.557796 INFO::Writing fitted values to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/fits/fitted_linear.rds
2025-12-11 02:34:56.559001 INFO::Writing residuals to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/fits/residuals_logistic.rds
2025-12-11 02:34:56.560196 INFO::Writing fitted values to file /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/fits/fitted_logistic.rds
2025-12-11 02:34:56.562747 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/all_results.tsv
2025-12-11 02:34:56.564366 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/RtmpwO0pBt/file3c3d1e22e6a73e/significant_results.tsv
2025-12-11 02:34:56.565713 INFO::Creating output figures folder
2025-12-11 02:34:56.567099 INFO::Writing summary plot of significant
results to file: /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/figures/summary_plot.pdf
2025-12-11 02:34:58.165636 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/figures
2025-12-11 02:34:58.167774 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-11 02:34:58.173049 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-11 02:34:58.705683 INFO::Writing summary plot of
significant results to file: /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/figures/summary_plot.pdf
2025-12-11 02:35:00.262343 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwO0pBt/file3c3d1e22e6a73e/figures
2025-12-11 02:35:00.263897 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-11 02:35:00.268683 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-11 02:35:00.787239 INFO::Running the linear model component
2025-12-11 02:35:00.79602 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:00.800226 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:00.804182 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:00.811001 INFO::Counting total values for each feature
2025-12-11 02:35:00.812621 INFO::Running the logistic model component
2025-12-11 02:35:00.820689 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:00.826362 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:00.831831 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:00.839888 INFO::Counting total values for each feature
2025-12-11 02:35:00.84181 INFO::Re-running abundances for warn_prevalence
2025-12-11 02:35:00.842532 INFO::Running selected normalization method: TSS
2025-12-11 02:35:00.843805 INFO::Running selected transform method: LOG
2025-12-11 02:35:00.851857 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:00.855616 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:00.859215 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:00.940827 INFO::Creating output folder
2025-12-11 02:35:00.941776 INFO::Creating output figures folder
2025-12-11 02:35:00.943034 INFO::Writing summary plot of significant
results to file: /tmp/RtmpwO0pBt/file3c3d1e9003ca1/figures/summary_plot.pdf
2025-12-11 02:35:02.49362 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwO0pBt/file3c3d1e9003ca1/figures
2025-12-11 02:35:02.495384 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-11 02:35:02.500139 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-11 02:35:03.456195 INFO::Applying z-score to standardize continuous metadata
2025-12-11 02:35:03.464737 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-11 02:35:03.465716 INFO::Bypass z-score application to metadata
2025-12-11 02:35:03.468433 INFO::Bypass z-score application to metadata
2025-12-11 02:35:03.487653 INFO::Determining format of input files
2025-12-11 02:35:03.488597 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-11 02:35:03.489435 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-11 02:35:03.496557 INFO::Determining format of input files
2025-12-11 02:35:03.497521 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-11 02:35:03.49876 INFO::Input format is feature_specific_covariate samples as columns
2025-12-11 02:35:03.506523 INFO::Determining format of input files
2025-12-11 02:35:03.507397 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-11 02:35:03.508391 INFO::Input format is feature_specific_covariate samples as columns
2025-12-11 02:35:03.509999 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-11 02:35:03.510737 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-11 02:35:03.522204 INFO::Running selected transform method: LOG
2025-12-11 02:35:03.523435 INFO::Creating output feature tables folder
2025-12-11 02:35:03.524336 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwO0pBt/file3c3d1e10045ba1/features/data_transformed.tsv
2025-12-11 02:35:03.528242 INFO::Running selected transform method: LOG
2025-12-11 02:35:03.529261 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwO0pBt/file3c3d1e10045ba1/features/data_transformed.tsv
2025-12-11 02:35:03.533079 INFO::Running selected transform method: PLOG
2025-12-11 02:35:03.534583 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwO0pBt/file3c3d1e10045ba1/features/data_transformed.tsv
2025-12-11 02:35:03.537452 INFO::Running selected transform method: NONE
2025-12-11 02:35:03.538204 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwO0pBt/file3c3d1e10045ba1/features/data_transformed.tsv
2025-12-11 02:35:03.545861 INFO::Running the linear model component
2025-12-11 02:35:03.554305 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:03.558482 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:03.562465 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:03.569389 INFO::Counting total values for each feature
2025-12-11 02:35:03.57102 INFO::Running the logistic model component
2025-12-11 02:35:03.579289 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:03.585037 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:03.590539 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:03.598921 INFO::Counting total values for each feature
2025-12-11 02:35:03.600833 INFO::Re-running abundances for warn_prevalence
2025-12-11 02:35:03.601588 INFO::Running selected normalization method: TSS
2025-12-11 02:35:03.602917 INFO::Running selected transform method: LOG
2025-12-11 02:35:03.611235 INFO::Fitting model to feature number 1, a
2025-12-11 02:35:03.615206 INFO::Fitting model to feature number 2, b
2025-12-11 02:35:03.618969 INFO::Fitting model to feature number 3, c
2025-12-11 02:35:03.704428 INFO::Creating output folder
2025-12-11 02:35:03.705471 INFO::Creating fits folder
2025-12-11 02:35:03.706352 INFO::Writing residuals to file /tmp/RtmpwO0pBt/file3c3d1ea9e0/fits/residuals_linear.rds
2025-12-11 02:35:03.707319 INFO::Writing fitted values to file /tmp/RtmpwO0pBt/file3c3d1ea9e0/fits/fitted_linear.rds
2025-12-11 02:35:03.708411 INFO::Writing residuals to file /tmp/RtmpwO0pBt/file3c3d1ea9e0/fits/residuals_logistic.rds
2025-12-11 02:35:03.709465 INFO::Writing fitted values to file /tmp/RtmpwO0pBt/file3c3d1ea9e0/fits/fitted_logistic.rds
2025-12-11 02:35:03.711942 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpwO0pBt/file3c3d1ea9e0/all_results.tsv
2025-12-11 02:35:03.713413 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/RtmpwO0pBt/file3c3d1ea9e0/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
358.661 5.236 364.185
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.272 | 0.520 | 19.797 | |
| maaslin_check_arguments | 0.154 | 0.002 | 0.156 | |
| maaslin_check_formula | 0.140 | 0.004 | 0.144 | |
| maaslin_compute_formula | 0.141 | 0.005 | 0.146 | |
| maaslin_contrast_test | 18.433 | 0.388 | 18.825 | |
| maaslin_filter | 0.444 | 0.022 | 0.466 | |
| maaslin_fit | 13.934 | 0.120 | 14.057 | |
| maaslin_log_arguments | 0.124 | 0.006 | 0.130 | |
| maaslin_normalize | 0.251 | 0.007 | 0.258 | |
| maaslin_plot_results | 43.555 | 0.293 | 43.830 | |
| maaslin_plot_results_from_output | 43.927 | 0.334 | 44.264 | |
| maaslin_process_metadata | 0.452 | 0.005 | 0.457 | |
| maaslin_read_data | 0.121 | 0.006 | 0.127 | |
| maaslin_reorder_data | 0.127 | 0.004 | 0.132 | |
| maaslin_transform | 0.542 | 0.010 | 0.552 | |
| maaslin_write_results | 14.339 | 0.090 | 14.430 | |
| maaslin_write_results_lefse_format | 13.916 | 0.083 | 14.000 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.005 | |