William Nickols
| Snapshot Date: 2026-03-04 13:45 -0500 (Wed, 04 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-05 11:57 -0500 (Thu, 05 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4894 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-03-05 01:05:47 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 01:27:36 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 1309.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 44.278 0.346 44.629
maaslin_plot_results 44.129 0.255 44.345
maaslin3 20.355 0.544 20.902
maaslin_contrast_test 19.383 0.380 19.763
maaslin_write_results_lefse_format 15.221 0.120 15.342
maaslin_write_results 13.118 0.124 13.243
maaslin_fit 13.067 0.086 13.154
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-03-05 01:12:10.257595 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:12:10.344979 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:12:10.443659 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:12:10.466176 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:12:10.500662 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:12:10.575529 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:12:10.587847 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:12:10.599816 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:12:10.692516 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:12:10.697754 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:12:10.746804 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:12:10.794722 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:12:10.806847 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:12:10.847817 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:12:10.917327 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:12:27.364926 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:12:27.43988 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:12:27.516411 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:12:27.539181 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:12:27.576222 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:12:27.674035 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:12:27.679572 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:12:27.691492 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:12:27.789105 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:12:27.794382 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:12:27.843022 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:12:27.882254 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:12:27.893787 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:12:27.933084 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:12:28.001772 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:12:53.039296 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:12:53.120975 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:12:53.20046 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:12:53.224516 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:12:53.264677 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:12:53.344791 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:12:53.350237 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:12:53.362471 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:12:53.460604 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:12:53.466288 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:12:53.518847 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:12:53.561395 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:12:53.57409 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:12:53.617192 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:12:53.691847 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:13:07.214207 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:13:07.322047 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:13:07.399846 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:13:07.422709 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:13:07.459703 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:13:07.540554 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:13:07.546247 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:13:07.559027 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:13:07.656717 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:13:07.662259 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:13:07.714644 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:13:07.758354 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:13:07.771238 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:13:07.814836 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:13:07.890332 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:13:08.110744 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_linear.rds
2026-03-05 01:13:08.172905 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_linear.rds
2026-03-05 01:13:08.237284 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_logistic.rds
2026-03-05 01:13:08.542987 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_logistic.rds
2026-03-05 01:13:31.338551 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:13:31.425544 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:13:31.53261 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:13:31.555182 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:13:31.590801 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:13:31.668657 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:13:31.674344 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:13:31.686793 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:13:31.783986 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:13:31.789457 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:13:31.840049 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:13:31.879989 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:13:31.891862 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:13:31.932517 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:13:32.001968 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:13:43.976169 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:13:44.056658 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:13:44.132465 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:13:44.154294 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:13:44.189813 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:13:44.266919 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:13:44.272501 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:13:44.285101 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:13:44.384011 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:13:44.389966 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:13:44.441313 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:13:44.484188 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:13:44.498399 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:13:44.54375 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:13:44.617433 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:13:44.824159 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_linear.rds
2026-03-05 01:13:44.885843 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_linear.rds
2026-03-05 01:13:44.949905 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_logistic.rds
2026-03-05 01:13:45.250332 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_logistic.rds
2026-03-05 01:14:06.888356 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:14:06.970673 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:14:07.050491 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:14:07.074421 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:14:07.110603 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:14:07.209092 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:14:07.214707 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:14:07.227175 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:14:07.327171 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:14:07.33295 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:14:07.384848 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:14:07.426909 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:14:07.439417 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:14:07.48196 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:14:07.553905 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:14:19.763762 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:14:19.84168 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:14:19.916342 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:14:19.93804 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:14:19.972395 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:14:20.048683 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:14:20.053992 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:14:20.065807 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:14:20.161191 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:14:20.166738 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:14:20.21684 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:14:20.257678 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:14:20.269636 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:14:20.310778 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:14:20.381238 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:14:20.580038 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_linear.rds
2026-03-05 01:14:20.641146 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_linear.rds
2026-03-05 01:14:20.704528 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/residuals_logistic.rds
2026-03-05 01:14:21.003912 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a85533e90a8/fits/fitted_logistic.rds
2026-03-05 01:14:42.608966 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:14:42.693357 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:14:42.773323 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:14:42.797744 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:14:42.835156 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:14:42.918264 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:14:42.924244 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:14:42.938096 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:14:43.043072 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:14:43.049262 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:14:43.102251 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:14:43.144782 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:14:43.157777 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:14:43.201404 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:14:43.275045 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:14:55.196277 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:14:55.279228 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:14:55.363013 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:14:55.385921 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:14:55.421846 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:14:55.502008 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:14:55.507591 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:14:55.519931 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:14:55.621566 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:14:55.627967 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:14:55.681734 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:14:55.724642 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:14:55.738285 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:14:55.780759 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:14:55.855924 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:15:20.218891 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:15:30.676425 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:15:56.046859 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:16:06.122896 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:16:06.791042 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_linear.rds
2026-03-05 01:16:06.853472 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_linear.rds
2026-03-05 01:16:06.892834 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_logistic.rds
2026-03-05 01:16:06.962442 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_logistic.rds
2026-03-05 01:16:30.776966 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:16:37.209399 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:16:37.518258 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_linear.rds
2026-03-05 01:16:37.581331 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_linear.rds
2026-03-05 01:16:37.620782 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_logistic.rds
2026-03-05 01:16:37.693333 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_logistic.rds
2026-03-05 01:16:56.322577 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:17:02.872158 WARNING::Fitting problem for feature 124 returning NA
2026-03-05 01:17:03.21524 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_linear.rds
2026-03-05 01:17:03.276945 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_linear.rds
2026-03-05 01:17:03.315442 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_logistic.rds
2026-03-05 01:17:03.386772 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_logistic.rds
2026-03-05 01:17:21.722343 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:17:21.811481 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:17:21.894414 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:17:21.918666 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:17:21.957097 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:17:22.074488 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:17:22.080246 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:17:22.092822 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:17:22.197032 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:17:22.202685 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:17:22.254181 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:17:22.296527 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:17:22.309074 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:17:22.351635 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:17:22.422648 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:17:34.42358 WARNING::Fitting problem for feature 50 returning NA
2026-03-05 01:17:34.500299 WARNING::Fitting problem for feature 62 returning NA
2026-03-05 01:17:34.575848 WARNING::Fitting problem for feature 74 returning NA
2026-03-05 01:17:34.598009 WARNING::Fitting problem for feature 78 returning NA
2026-03-05 01:17:34.633552 WARNING::Fitting problem for feature 84 returning NA
2026-03-05 01:17:34.710885 WARNING::Fitting problem for feature 96 returning NA
2026-03-05 01:17:34.716465 WARNING::Fitting problem for feature 97 returning NA
2026-03-05 01:17:34.729353 WARNING::Fitting problem for feature 99 returning NA
2026-03-05 01:17:34.828256 WARNING::Fitting problem for feature 114 returning NA
2026-03-05 01:17:34.83396 WARNING::Fitting problem for feature 115 returning NA
2026-03-05 01:17:34.885787 WARNING::Fitting problem for feature 123 returning NA
2026-03-05 01:17:34.928456 WARNING::Fitting problem for feature 130 returning NA
2026-03-05 01:17:34.940987 WARNING::Fitting problem for feature 132 returning NA
2026-03-05 01:17:34.98388 WARNING::Fitting problem for feature 139 returning NA
2026-03-05 01:17:35.088563 WARNING::Fitting problem for feature 150 returning NA
2026-03-05 01:17:35.327341 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_linear.rds
2026-03-05 01:17:35.388248 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_linear.rds
2026-03-05 01:17:35.45144 WARNING::Deleting existing residuals file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/residuals_logistic.rds
2026-03-05 01:17:35.751727 WARNING::Deleting existing fitted file: /tmp/RtmpvNhLrg/file353a8570fe6349/fits/fitted_logistic.rds
2026-03-05 01:17:57.182262 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-05 01:17:57.198885 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-05 01:17:57.210049 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-05 01:17:57.26085 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-05 01:17:57.276748 ERROR::Effect name not found in metadata: d
2026-03-05 01:17:57.287671 ERROR::No user formula provided
2026-03-05 01:17:57.320812 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-05 01:17:57.332222 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-05 01:18:00.118286 INFO::Writing function arguments to log file
2026-03-05 01:18:00.132761 INFO::Verifying options selected are valid
2026-03-05 01:18:02.450072 INFO::Writing function arguments to log file
2026-03-05 01:18:02.46274 INFO::Verifying options selected are valid
2026-03-05 01:18:02.46387 INFO::Determining format of input files
2026-03-05 01:18:02.46488 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-05 01:18:02.467327 INFO::Running selected normalization method: TSS
2026-03-05 01:18:02.46886 INFO::Creating output feature tables folder
2026-03-05 01:18:02.46987 INFO::Writing normalized data to file /tmp/RtmpvNhLrg/file353a85249a5277/features/data_norm.tsv
2026-03-05 01:18:02.471477 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-05 01:18:02.47241 INFO::Total samples in data: 16
2026-03-05 01:18:02.473291 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-05 01:18:02.474143 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-05 01:18:02.476101 INFO::Total filtered features: 0
2026-03-05 01:18:02.477072 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-05 01:18:02.478257 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-05 01:18:02.47922 INFO::Filtered feature names from variance filtering:
2026-03-05 01:18:02.480113 INFO::Writing filtered data to file /tmp/RtmpvNhLrg/file353a85249a5277/features/filtered_data.tsv
2026-03-05 01:18:02.481633 INFO::Running selected transform method: LOG
2026-03-05 01:18:02.482841 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvNhLrg/file353a85249a5277/features/data_transformed.tsv
2026-03-05 01:18:02.484664 INFO::Applying z-score to standardize continuous metadata
2026-03-05 01:18:02.490009 INFO::Running the linear model component
2026-03-05 01:18:02.504939 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:02.510295 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:02.515131 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:02.523766 INFO::Counting total values for each feature
2026-03-05 01:18:02.525769 INFO::Running the logistic model component
2026-03-05 01:18:02.539949 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:02.547016 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:02.553414 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:02.562693 INFO::Counting total values for each feature
2026-03-05 01:18:02.565003 INFO::Re-running abundances for warn_prevalence
2026-03-05 01:18:02.566014 INFO::Running selected normalization method: TSS
2026-03-05 01:18:02.567651 INFO::Running selected transform method: LOG
2026-03-05 01:18:02.582064 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:02.58675 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:02.591234 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:02.672349 INFO::Creating fits folder
2026-03-05 01:18:02.673766 INFO::Writing residuals to file /tmp/RtmpvNhLrg/file353a85249a5277/fits/residuals_linear.rds
2026-03-05 01:18:02.675118 INFO::Writing fitted values to file /tmp/RtmpvNhLrg/file353a85249a5277/fits/fitted_linear.rds
2026-03-05 01:18:02.676423 INFO::Writing residuals to file /tmp/RtmpvNhLrg/file353a85249a5277/fits/residuals_logistic.rds
2026-03-05 01:18:02.677675 INFO::Writing fitted values to file /tmp/RtmpvNhLrg/file353a85249a5277/fits/fitted_logistic.rds
2026-03-05 01:18:02.680315 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpvNhLrg/file353a85249a5277/all_results.tsv
2026-03-05 01:18:02.682106 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/RtmpvNhLrg/file353a85249a5277/significant_results.tsv
2026-03-05 01:18:02.683599 INFO::Creating output figures folder
2026-03-05 01:18:02.685133 INFO::Writing summary plot of significant
results to file: /tmp/RtmpvNhLrg/file353a85249a5277/figures/summary_plot.pdf
2026-03-05 01:18:04.315 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvNhLrg/file353a85249a5277/figures
2026-03-05 01:18:04.316964 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-05 01:18:04.322607 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-05 01:18:04.881727 INFO::Writing summary plot of
significant results to file: /tmp/RtmpvNhLrg/file353a85249a5277/figures/summary_plot.pdf
2026-03-05 01:18:06.493044 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvNhLrg/file353a85249a5277/figures
2026-03-05 01:18:06.494643 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-05 01:18:06.499599 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-05 01:18:07.022539 INFO::Running the linear model component
2026-03-05 01:18:07.03156 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:07.036086 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:07.040476 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:07.04784 INFO::Counting total values for each feature
2026-03-05 01:18:07.049625 INFO::Running the logistic model component
2026-03-05 01:18:07.058079 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:07.064373 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:07.070178 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:07.078831 INFO::Counting total values for each feature
2026-03-05 01:18:07.080863 INFO::Re-running abundances for warn_prevalence
2026-03-05 01:18:07.081666 INFO::Running selected normalization method: TSS
2026-03-05 01:18:07.08299 INFO::Running selected transform method: LOG
2026-03-05 01:18:07.091502 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:07.095972 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:07.099958 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:07.177206 INFO::Creating output folder
2026-03-05 01:18:07.178182 INFO::Creating output figures folder
2026-03-05 01:18:07.179397 INFO::Writing summary plot of significant
results to file: /tmp/RtmpvNhLrg/file353a857c350c2e/figures/summary_plot.pdf
2026-03-05 01:18:08.804361 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvNhLrg/file353a857c350c2e/figures
2026-03-05 01:18:08.806015 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-05 01:18:08.810955 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-05 01:18:09.745868 INFO::Applying z-score to standardize continuous metadata
2026-03-05 01:18:09.753055 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-05 01:18:09.753981 INFO::Bypass z-score application to metadata
2026-03-05 01:18:09.756664 INFO::Bypass z-score application to metadata
2026-03-05 01:18:09.776119 INFO::Determining format of input files
2026-03-05 01:18:09.777139 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-05 01:18:09.778007 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-05 01:18:09.785715 INFO::Determining format of input files
2026-03-05 01:18:09.786782 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-05 01:18:09.788067 INFO::Input format is feature_specific_covariate samples as columns
2026-03-05 01:18:09.796451 INFO::Determining format of input files
2026-03-05 01:18:09.797514 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-05 01:18:09.798572 INFO::Input format is feature_specific_covariate samples as columns
2026-03-05 01:18:09.800215 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-05 01:18:09.800994 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-05 01:18:09.81306 INFO::Running selected transform method: LOG
2026-03-05 01:18:09.814277 INFO::Creating output feature tables folder
2026-03-05 01:18:09.815181 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvNhLrg/file353a855a51a13b/features/data_transformed.tsv
2026-03-05 01:18:09.819256 INFO::Running selected transform method: LOG
2026-03-05 01:18:09.820327 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvNhLrg/file353a855a51a13b/features/data_transformed.tsv
2026-03-05 01:18:09.824571 INFO::Running selected transform method: PLOG
2026-03-05 01:18:09.837558 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvNhLrg/file353a855a51a13b/features/data_transformed.tsv
2026-03-05 01:18:09.842111 INFO::Running selected transform method: NONE
2026-03-05 01:18:09.843064 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvNhLrg/file353a855a51a13b/features/data_transformed.tsv
2026-03-05 01:18:09.851525 INFO::Running the linear model component
2026-03-05 01:18:09.860409 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:09.865253 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:09.869499 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:09.876707 INFO::Counting total values for each feature
2026-03-05 01:18:09.878473 INFO::Running the logistic model component
2026-03-05 01:18:09.887183 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:09.893674 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:09.899726 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:09.908713 INFO::Counting total values for each feature
2026-03-05 01:18:09.910708 INFO::Re-running abundances for warn_prevalence
2026-03-05 01:18:09.911478 INFO::Running selected normalization method: TSS
2026-03-05 01:18:09.912806 INFO::Running selected transform method: LOG
2026-03-05 01:18:09.921303 INFO::Fitting model to feature number 1, a
2026-03-05 01:18:09.925592 INFO::Fitting model to feature number 2, b
2026-03-05 01:18:09.929593 INFO::Fitting model to feature number 3, c
2026-03-05 01:18:10.007216 INFO::Creating output folder
2026-03-05 01:18:10.008275 INFO::Creating fits folder
2026-03-05 01:18:10.00916 INFO::Writing residuals to file /tmp/RtmpvNhLrg/file353a856b558d7d/fits/residuals_linear.rds
2026-03-05 01:18:10.010165 INFO::Writing fitted values to file /tmp/RtmpvNhLrg/file353a856b558d7d/fits/fitted_linear.rds
2026-03-05 01:18:10.011226 INFO::Writing residuals to file /tmp/RtmpvNhLrg/file353a856b558d7d/fits/residuals_logistic.rds
2026-03-05 01:18:10.01225 INFO::Writing fitted values to file /tmp/RtmpvNhLrg/file353a856b558d7d/fits/fitted_logistic.rds
2026-03-05 01:18:10.014631 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpvNhLrg/file353a856b558d7d/all_results.tsv
2026-03-05 01:18:10.01618 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/RtmpvNhLrg/file353a856b558d7d/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
366.302 6.347 372.630
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.355 | 0.544 | 20.902 | |
| maaslin_check_arguments | 0.141 | 0.003 | 0.144 | |
| maaslin_check_formula | 0.161 | 0.003 | 0.164 | |
| maaslin_compute_formula | 0.151 | 0.001 | 0.153 | |
| maaslin_contrast_test | 19.383 | 0.380 | 19.763 | |
| maaslin_filter | 0.473 | 0.020 | 0.493 | |
| maaslin_fit | 13.067 | 0.086 | 13.154 | |
| maaslin_log_arguments | 0.129 | 0.002 | 0.132 | |
| maaslin_normalize | 0.261 | 0.006 | 0.267 | |
| maaslin_plot_results | 44.129 | 0.255 | 44.345 | |
| maaslin_plot_results_from_output | 44.278 | 0.346 | 44.629 | |
| maaslin_process_metadata | 0.467 | 0.008 | 0.475 | |
| maaslin_read_data | 0.132 | 0.000 | 0.132 | |
| maaslin_reorder_data | 0.13 | 0.00 | 0.13 | |
| maaslin_transform | 0.529 | 0.008 | 0.537 | |
| maaslin_write_results | 13.118 | 0.124 | 13.243 | |
| maaslin_write_results_lefse_format | 15.221 | 0.120 | 15.342 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |