William Nickols
| Snapshot Date: 2025-11-06 13:45 -0500 (Thu, 06 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 2025-11-07 12:00 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| 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: 1.2.0 |
| 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: 2025-11-07 00:58:20 -0500 (Fri, 07 Nov 2025) |
| EndedAt: 2025-11-07 01:20:10 -0500 (Fri, 07 Nov 2025) |
| EllapsedTime: 1310.4 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 4.5.1 Patched (2025-08-23 r88802)
* 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 44.815 0.496 45.315
maaslin_plot_results 43.347 0.312 43.641
maaslin3 19.519 0.436 19.957
maaslin_contrast_test 18.215 0.338 18.582
maaslin_write_results_lefse_format 13.969 0.079 14.052
maaslin_write_results 12.804 0.095 12.916
maaslin_fit 12.679 0.095 12.774
* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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")
2025-11-07 01:04:39.630109 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:04:39.70532 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:04:39.799113 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:04:39.82124 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:04:39.855494 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:04:39.940094 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:04:39.945947 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:04:39.95782 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:04:40.070821 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:04:40.076267 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:04:40.126083 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:04:40.166579 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:04:40.17877 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:04:40.219946 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:04:40.295737 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:04:57.2887 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:04:57.363684 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:04:57.438704 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:04:57.460802 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:04:57.496763 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:04:57.590234 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:04:57.59561 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:04:57.607511 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:04:57.70249 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:04:57.707745 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:04:57.756232 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:04:57.795886 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:04:57.807601 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:04:57.847128 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:04:57.916331 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:05:22.915644 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:05:22.995643 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:05:23.076441 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:05:23.1017 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:05:23.141438 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:05:23.221921 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:05:23.227328 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:05:23.239413 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:05:23.340907 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:05:23.346749 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:05:23.399037 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:05:23.441895 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:05:23.454375 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:05:23.515304 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:05:23.588915 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:05:36.573897 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:05:36.650824 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:05:36.733403 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:05:36.758048 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:05:36.796815 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:05:36.881852 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:05:36.888263 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:05:36.901548 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:05:37.004894 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:05:37.010833 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:05:37.083977 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:05:37.125316 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:05:37.137527 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:05:37.179808 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:05:37.250235 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:05:37.459684 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_linear.rds
2025-11-07 01:05:37.520407 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_linear.rds
2025-11-07 01:05:37.582956 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_logistic.rds
2025-11-07 01:05:37.881546 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_logistic.rds
2025-11-07 01:06:01.081532 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:06:01.177054 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:06:01.266093 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:06:01.291164 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:06:01.33152 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:06:01.419467 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:06:01.425699 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:06:01.440014 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:06:01.552975 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:06:01.559235 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:06:01.618704 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:06:01.665407 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:06:01.679233 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:06:01.727957 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:06:01.834151 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:06:13.867236 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:06:13.947092 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:06:14.025159 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:06:14.047801 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:06:14.084691 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:06:14.162598 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:06:14.168306 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:06:14.18054 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:06:14.279494 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:06:14.285196 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:06:14.339273 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:06:14.384104 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:06:14.396541 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:06:14.440823 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:06:14.514467 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:06:14.728435 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_linear.rds
2025-11-07 01:06:14.789209 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_linear.rds
2025-11-07 01:06:14.851526 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_logistic.rds
2025-11-07 01:06:15.149225 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_logistic.rds
2025-11-07 01:06:37.269173 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:06:37.349334 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:06:37.427069 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:06:37.449916 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:06:37.48654 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:06:37.565283 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:06:37.571133 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:06:37.58397 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:06:37.687609 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:06:37.693356 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:06:37.746228 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:06:37.788982 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:06:37.801746 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:06:37.84399 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:06:37.920672 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:06:49.853217 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:06:49.930858 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:06:50.004668 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:06:50.026535 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:06:50.060194 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:06:50.160594 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:06:50.166033 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:06:50.177984 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:06:50.275739 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:06:50.281409 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:06:50.331251 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:06:50.371 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:06:50.382896 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:06:50.422932 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:06:50.491951 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:06:50.693273 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_linear.rds
2025-11-07 01:06:50.753757 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_linear.rds
2025-11-07 01:06:50.816872 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/residuals_logistic.rds
2025-11-07 01:06:51.114079 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca5e1c39e7/fits/fitted_logistic.rds
2025-11-07 01:07:12.993856 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:07:13.082659 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:07:13.167894 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:07:13.192628 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:07:13.231227 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:07:13.349364 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:07:13.356066 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:07:13.370409 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:07:13.47403 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:07:13.479969 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:07:13.531206 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:07:13.573598 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:07:13.586301 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:07:13.630375 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:07:13.705583 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:07:26.888671 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:07:26.966537 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:07:27.043944 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:07:27.06905 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:07:27.106991 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:07:27.187048 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:07:27.192682 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:07:27.205915 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:07:27.313216 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:07:27.319455 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:07:27.377 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:07:27.422241 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:07:27.435105 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:07:27.478727 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:07:27.553426 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:07:52.513255 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:08:02.784356 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:08:28.264371 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:08:39.17007 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:08:39.820448 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_linear.rds
2025-11-07 01:08:39.881845 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_linear.rds
2025-11-07 01:08:39.93816 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_logistic.rds
2025-11-07 01:08:40.006165 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_logistic.rds
2025-11-07 01:09:02.670801 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:09:09.144079 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:09:09.462212 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_linear.rds
2025-11-07 01:09:09.523739 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_linear.rds
2025-11-07 01:09:09.562212 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_logistic.rds
2025-11-07 01:09:09.630302 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_logistic.rds
2025-11-07 01:09:28.607109 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:09:34.918137 WARNING::Fitting problem for feature 124 returning NA
2025-11-07 01:09:35.227488 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_linear.rds
2025-11-07 01:09:35.288696 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_linear.rds
2025-11-07 01:09:35.326917 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_logistic.rds
2025-11-07 01:09:35.397803 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_logistic.rds
2025-11-07 01:09:53.836838 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:09:53.923054 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:09:54.004189 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:09:54.028386 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:09:54.064721 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:09:54.146727 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:09:54.152428 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:09:54.16504 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:09:54.269516 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:09:54.275513 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:09:54.330235 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:09:54.374577 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:09:54.387607 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:09:54.430703 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:09:54.509749 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:10:07.547622 WARNING::Fitting problem for feature 50 returning NA
2025-11-07 01:10:07.624153 WARNING::Fitting problem for feature 62 returning NA
2025-11-07 01:10:07.699791 WARNING::Fitting problem for feature 74 returning NA
2025-11-07 01:10:07.721994 WARNING::Fitting problem for feature 78 returning NA
2025-11-07 01:10:07.7573 WARNING::Fitting problem for feature 84 returning NA
2025-11-07 01:10:07.834471 WARNING::Fitting problem for feature 96 returning NA
2025-11-07 01:10:07.840019 WARNING::Fitting problem for feature 97 returning NA
2025-11-07 01:10:07.852015 WARNING::Fitting problem for feature 99 returning NA
2025-11-07 01:10:07.947736 WARNING::Fitting problem for feature 114 returning NA
2025-11-07 01:10:07.953348 WARNING::Fitting problem for feature 115 returning NA
2025-11-07 01:10:08.00404 WARNING::Fitting problem for feature 123 returning NA
2025-11-07 01:10:08.045767 WARNING::Fitting problem for feature 130 returning NA
2025-11-07 01:10:08.058285 WARNING::Fitting problem for feature 132 returning NA
2025-11-07 01:10:08.100917 WARNING::Fitting problem for feature 139 returning NA
2025-11-07 01:10:08.175715 WARNING::Fitting problem for feature 150 returning NA
2025-11-07 01:10:08.477318 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_linear.rds
2025-11-07 01:10:08.53917 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_linear.rds
2025-11-07 01:10:08.60228 WARNING::Deleting existing residuals file: /tmp/RtmpTDen0K/file62aca185b8728/fits/residuals_logistic.rds
2025-11-07 01:10:08.901139 WARNING::Deleting existing fitted file: /tmp/RtmpTDen0K/file62aca185b8728/fits/fitted_logistic.rds
2025-11-07 01:10:29.561168 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-07 01:10:29.578648 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-07 01:10:29.590544 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-07 01:10:29.643331 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-07 01:10:29.660464 ERROR::Effect name not found in metadata: d
2025-11-07 01:10:29.672158 ERROR::No user formula provided
2025-11-07 01:10:29.702144 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-07 01:10:29.714053 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-07 01:10:32.623727 INFO::Writing function arguments to log file
2025-11-07 01:10:32.638807 INFO::Verifying options selected are valid
2025-11-07 01:10:35.084088 INFO::Writing function arguments to log file
2025-11-07 01:10:35.09649 INFO::Verifying options selected are valid
2025-11-07 01:10:35.09765 INFO::Determining format of input files
2025-11-07 01:10:35.098687 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-07 01:10:35.101185 INFO::Running selected normalization method: TSS
2025-11-07 01:10:35.102764 INFO::Creating output feature tables folder
2025-11-07 01:10:35.10378 INFO::Writing normalized data to file /tmp/RtmpTDen0K/file62aca337a9fa3/features/data_norm.tsv
2025-11-07 01:10:35.10538 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-07 01:10:35.106297 INFO::Total samples in data: 16
2025-11-07 01:10:35.107159 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-07 01:10:35.108032 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-07 01:10:35.110058 INFO::Total filtered features: 0
2025-11-07 01:10:35.111054 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-07 01:10:35.112291 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-07 01:10:35.113283 INFO::Filtered feature names from variance filtering:
2025-11-07 01:10:35.114193 INFO::Writing filtered data to file /tmp/RtmpTDen0K/file62aca337a9fa3/features/filtered_data.tsv
2025-11-07 01:10:35.115851 INFO::Running selected transform method: LOG
2025-11-07 01:10:35.117159 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTDen0K/file62aca337a9fa3/features/data_transformed.tsv
2025-11-07 01:10:35.118977 INFO::Applying z-score to standardize continuous metadata
2025-11-07 01:10:35.12524 INFO::Running the linear model component
2025-11-07 01:10:35.13966 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:35.144629 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:35.149061 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:35.156749 INFO::Counting total values for each feature
2025-11-07 01:10:35.158634 INFO::Running the logistic model component
2025-11-07 01:10:35.172687 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:35.17958 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:35.186077 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:35.196604 INFO::Counting total values for each feature
2025-11-07 01:10:35.199198 INFO::Re-running abundances for warn_prevalence
2025-11-07 01:10:35.200342 INFO::Running selected normalization method: TSS
2025-11-07 01:10:35.20207 INFO::Running selected transform method: LOG
2025-11-07 01:10:35.2172 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:35.22258 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:35.227216 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:35.317201 INFO::Creating fits folder
2025-11-07 01:10:35.31839 INFO::Writing residuals to file /tmp/RtmpTDen0K/file62aca337a9fa3/fits/residuals_linear.rds
2025-11-07 01:10:35.31953 INFO::Writing fitted values to file /tmp/RtmpTDen0K/file62aca337a9fa3/fits/fitted_linear.rds
2025-11-07 01:10:35.320764 INFO::Writing residuals to file /tmp/RtmpTDen0K/file62aca337a9fa3/fits/residuals_logistic.rds
2025-11-07 01:10:35.321973 INFO::Writing fitted values to file /tmp/RtmpTDen0K/file62aca337a9fa3/fits/fitted_logistic.rds
2025-11-07 01:10:35.324631 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpTDen0K/file62aca337a9fa3/all_results.tsv
2025-11-07 01:10:35.326373 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/RtmpTDen0K/file62aca337a9fa3/significant_results.tsv
2025-11-07 01:10:35.327764 INFO::Creating output figures folder
2025-11-07 01:10:35.329161 INFO::Writing summary plot of significant
results to file: /tmp/RtmpTDen0K/file62aca337a9fa3/figures/summary_plot.pdf
2025-11-07 01:10:37.171968 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTDen0K/file62aca337a9fa3/figures
2025-11-07 01:10:37.174016 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-07 01:10:37.17983 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-07 01:10:37.75156 INFO::Writing summary plot of
significant results to file: /tmp/RtmpTDen0K/file62aca337a9fa3/figures/summary_plot.pdf
2025-11-07 01:10:39.432099 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTDen0K/file62aca337a9fa3/figures
2025-11-07 01:10:39.434012 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-07 01:10:39.439726 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-07 01:10:39.99793 INFO::Running the linear model component
2025-11-07 01:10:40.007935 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:40.01306 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:40.017751 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:40.026593 INFO::Counting total values for each feature
2025-11-07 01:10:40.028574 INFO::Running the logistic model component
2025-11-07 01:10:40.038136 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:40.045744 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:40.052795 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:40.063025 INFO::Counting total values for each feature
2025-11-07 01:10:40.065152 INFO::Re-running abundances for warn_prevalence
2025-11-07 01:10:40.065926 INFO::Running selected normalization method: TSS
2025-11-07 01:10:40.067345 INFO::Running selected transform method: LOG
2025-11-07 01:10:40.076243 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:40.08047 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:40.084842 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:40.179682 INFO::Creating output folder
2025-11-07 01:10:40.180855 INFO::Creating output figures folder
2025-11-07 01:10:40.18218 INFO::Writing summary plot of significant
results to file: /tmp/RtmpTDen0K/file62aca7c839b0/figures/summary_plot.pdf
2025-11-07 01:10:41.865547 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTDen0K/file62aca7c839b0/figures
2025-11-07 01:10:41.867317 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-07 01:10:41.872309 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-07 01:10:42.835548 INFO::Applying z-score to standardize continuous metadata
2025-11-07 01:10:42.843627 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-07 01:10:42.844519 INFO::Bypass z-score application to metadata
2025-11-07 01:10:42.846924 INFO::Bypass z-score application to metadata
2025-11-07 01:10:42.864084 INFO::Determining format of input files
2025-11-07 01:10:42.865061 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-07 01:10:42.865908 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-07 01:10:42.873015 INFO::Determining format of input files
2025-11-07 01:10:42.874072 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-07 01:10:42.875397 INFO::Input format is feature_specific_covariate samples as columns
2025-11-07 01:10:42.883111 INFO::Determining format of input files
2025-11-07 01:10:42.884046 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-07 01:10:42.885044 INFO::Input format is feature_specific_covariate samples as columns
2025-11-07 01:10:42.886667 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-07 01:10:42.88744 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-07 01:10:42.897927 INFO::Running selected transform method: LOG
2025-11-07 01:10:42.899085 INFO::Creating output feature tables folder
2025-11-07 01:10:42.899953 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTDen0K/file62aca22a9acff/features/data_transformed.tsv
2025-11-07 01:10:42.903726 INFO::Running selected transform method: LOG
2025-11-07 01:10:42.904753 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTDen0K/file62aca22a9acff/features/data_transformed.tsv
2025-11-07 01:10:42.908559 INFO::Running selected transform method: PLOG
2025-11-07 01:10:42.910111 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTDen0K/file62aca22a9acff/features/data_transformed.tsv
2025-11-07 01:10:42.912885 INFO::Running selected transform method: NONE
2025-11-07 01:10:42.913648 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTDen0K/file62aca22a9acff/features/data_transformed.tsv
2025-11-07 01:10:42.920637 INFO::Running the linear model component
2025-11-07 01:10:42.929215 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:42.933605 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:42.937691 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:42.944885 INFO::Counting total values for each feature
2025-11-07 01:10:42.946591 INFO::Running the logistic model component
2025-11-07 01:10:42.9552 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:42.973721 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:42.980985 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:42.991536 INFO::Counting total values for each feature
2025-11-07 01:10:42.993858 INFO::Re-running abundances for warn_prevalence
2025-11-07 01:10:42.994835 INFO::Running selected normalization method: TSS
2025-11-07 01:10:42.996443 INFO::Running selected transform method: LOG
2025-11-07 01:10:43.006586 INFO::Fitting model to feature number 1, a
2025-11-07 01:10:43.01149 INFO::Fitting model to feature number 2, b
2025-11-07 01:10:43.016316 INFO::Fitting model to feature number 3, c
2025-11-07 01:10:43.114203 INFO::Creating output folder
2025-11-07 01:10:43.115194 INFO::Creating fits folder
2025-11-07 01:10:43.116038 INFO::Writing residuals to file /tmp/RtmpTDen0K/file62aca4848298/fits/residuals_linear.rds
2025-11-07 01:10:43.117019 INFO::Writing fitted values to file /tmp/RtmpTDen0K/file62aca4848298/fits/fitted_linear.rds
2025-11-07 01:10:43.118054 INFO::Writing residuals to file /tmp/RtmpTDen0K/file62aca4848298/fits/residuals_logistic.rds
2025-11-07 01:10:43.119069 INFO::Writing fitted values to file /tmp/RtmpTDen0K/file62aca4848298/fits/fitted_logistic.rds
2025-11-07 01:10:43.121596 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpTDen0K/file62aca4848298/all_results.tsv
2025-11-07 01:10:43.123095 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/RtmpTDen0K/file62aca4848298/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
369.522 5.822 375.336
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.519 | 0.436 | 19.957 | |
| maaslin_check_arguments | 0.148 | 0.001 | 0.149 | |
| maaslin_check_formula | 0.137 | 0.001 | 0.138 | |
| maaslin_compute_formula | 0.156 | 0.004 | 0.160 | |
| maaslin_contrast_test | 18.215 | 0.338 | 18.582 | |
| maaslin_filter | 0.444 | 0.016 | 0.460 | |
| maaslin_fit | 12.679 | 0.095 | 12.774 | |
| maaslin_log_arguments | 0.131 | 0.001 | 0.132 | |
| maaslin_normalize | 0.262 | 0.004 | 0.266 | |
| maaslin_plot_results | 43.347 | 0.312 | 43.641 | |
| maaslin_plot_results_from_output | 44.815 | 0.496 | 45.315 | |
| maaslin_process_metadata | 0.444 | 0.012 | 0.456 | |
| maaslin_read_data | 0.122 | 0.001 | 0.123 | |
| maaslin_reorder_data | 0.126 | 0.005 | 0.131 | |
| maaslin_transform | 0.561 | 0.017 | 0.578 | |
| maaslin_write_results | 12.804 | 0.095 | 12.916 | |
| maaslin_write_results_lefse_format | 13.969 | 0.079 | 14.052 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.003 | |