William Nickols
| Snapshot Date: 2025-09-08 13:40 -0400 (Mon, 08 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7584c46 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-11 11:38 -0400 (Thu, 11 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| 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 1155/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.0.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.0.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.0.tar.gz |
| StartedAt: 2025-09-11 01:16:13 -0400 (Thu, 11 Sep 2025) |
| EndedAt: 2025-09-11 01:35:33 -0400 (Thu, 11 Sep 2025) |
| EllapsedTime: 1160.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.0.0’
* 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 36.227 0.414 36.607
maaslin_plot_results_from_output 35.199 0.275 35.478
maaslin3 19.278 0.646 19.929
maaslin_contrast_test 18.724 0.477 19.206
maaslin_write_results_lefse_format 14.406 0.183 14.593
maaslin_write_results 12.862 0.232 13.094
maaslin_fit 12.586 0.071 12.659
* 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-3.21-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.0.0’ ** 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 (2025-06-13) -- "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")
2025-09-11 01:22:07.692585 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:22:07.76653 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:22:07.84765 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:22:07.868426 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:22:07.908352 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:22:07.982333 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:22:07.987444 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:22:07.998805 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:22:08.099524 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:22:08.104762 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:22:08.152807 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:22:08.191728 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:22:08.2032 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:22:08.242907 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:22:08.316787 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:22:24.086136 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:22:24.165701 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:22:24.239761 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:22:24.263167 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:22:24.302212 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:22:24.390361 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:22:24.396724 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:22:24.411359 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:22:24.543266 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:22:24.548917 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:22:24.599645 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:22:24.64008 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:22:24.65166 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:22:24.691158 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:22:24.760451 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:22:43.106556 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:22:43.210466 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:22:43.286238 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:22:43.308612 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:22:43.342515 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:22:43.416141 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:22:43.421348 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:22:43.43279 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:22:43.525082 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:22:43.530686 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:22:43.617041 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:22:43.662605 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:22:43.674602 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:22:43.714581 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:22:43.782086 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:22:56.633313 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:22:56.707366 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:22:56.78136 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:22:56.803408 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:22:56.837454 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:22:56.911139 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:22:56.916394 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:22:56.928162 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:22:57.022767 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:22:57.028211 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:22:57.077101 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:22:57.118499 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:22:57.130747 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:22:57.171687 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:22:57.241849 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:22:57.479413 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_linear.rds
2025-09-11 01:22:57.541592 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_linear.rds
2025-09-11 01:22:57.60566 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_logistic.rds
2025-09-11 01:22:57.906522 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_logistic.rds
2025-09-11 01:23:14.60533 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:23:14.697451 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:23:14.773463 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:23:14.795142 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:23:14.830576 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:23:14.905953 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:23:14.911342 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:23:14.923159 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:23:15.016409 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:23:15.022033 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:23:15.072161 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:23:15.11284 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:23:15.124535 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:23:15.165164 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:23:15.237376 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:23:27.395284 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:23:27.467984 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:23:27.540243 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:23:27.56168 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:23:27.595215 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:23:27.669736 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:23:27.675059 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:23:27.686769 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:23:27.806818 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:23:27.812491 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:23:27.862147 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:23:27.901518 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:23:27.913319 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:23:27.953568 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:23:28.022875 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:23:28.221213 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_linear.rds
2025-09-11 01:23:28.281761 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_linear.rds
2025-09-11 01:23:28.344392 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_logistic.rds
2025-09-11 01:23:28.643772 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_logistic.rds
2025-09-11 01:23:45.14079 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:23:45.237559 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:23:45.314862 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:23:45.336819 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:23:45.37225 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:23:45.449661 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:23:45.455736 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:23:45.468601 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:23:45.565426 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:23:45.571095 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:23:45.621094 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:23:45.660806 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:23:45.673073 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:23:45.713693 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:23:45.783247 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:23:57.430532 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:23:57.506153 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:23:57.57887 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:23:57.600224 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:23:57.633844 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:23:57.707795 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:23:57.713096 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:23:57.724846 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:23:57.82153 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:23:57.827083 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:23:57.876974 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:23:57.917234 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:23:57.929176 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:23:57.969787 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:23:58.03806 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:23:58.275067 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_linear.rds
2025-09-11 01:23:58.335699 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_linear.rds
2025-09-11 01:23:58.398512 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40376dca743/fits/residuals_logistic.rds
2025-09-11 01:23:58.698179 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40376dca743/fits/fitted_logistic.rds
2025-09-11 01:24:15.114419 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:24:15.193426 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:24:15.271741 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:24:15.294178 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:24:15.330194 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:24:15.409451 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:24:15.415118 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:24:15.427449 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:24:15.525415 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:24:15.530985 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:24:15.581756 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:24:15.653158 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:24:15.666898 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:24:15.710522 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:24:15.781186 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:24:27.343079 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:24:27.42026 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:24:27.493843 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:24:27.515331 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:24:27.549513 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:24:27.624806 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:24:27.630172 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:24:27.642121 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:24:27.739714 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:24:27.745695 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:24:27.797527 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:24:27.837727 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:24:27.849366 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:24:27.889097 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:24:27.958194 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:24:46.798946 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:24:56.317456 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:25:15.936256 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:25:25.413299 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:25:26.052702 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_linear.rds
2025-09-11 01:25:26.114534 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_linear.rds
2025-09-11 01:25:26.153585 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_logistic.rds
2025-09-11 01:25:26.222224 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_logistic.rds
2025-09-11 01:25:44.888249 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:25:50.209632 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:25:50.532753 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_linear.rds
2025-09-11 01:25:50.594324 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_linear.rds
2025-09-11 01:25:50.632965 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_logistic.rds
2025-09-11 01:25:50.701592 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_logistic.rds
2025-09-11 01:26:05.349437 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:26:12.503887 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 01:26:12.820727 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_linear.rds
2025-09-11 01:26:12.882648 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_linear.rds
2025-09-11 01:26:12.921354 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_logistic.rds
2025-09-11 01:26:12.990134 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_logistic.rds
2025-09-11 01:26:26.991958 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:26:27.067764 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:26:27.14132 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:26:27.162929 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:26:27.197191 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:26:27.273449 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:26:27.279136 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:26:27.291551 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:26:27.388074 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:26:27.39351 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:26:27.443022 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:26:27.482141 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:26:27.493745 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:26:27.533469 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:26:27.601931 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:26:39.216108 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 01:26:39.291608 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 01:26:39.367138 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 01:26:39.389213 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 01:26:39.424216 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 01:26:39.499465 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 01:26:39.504783 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 01:26:39.516394 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 01:26:39.610558 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 01:26:39.616215 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 01:26:39.666257 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 01:26:39.707125 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 01:26:39.719162 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 01:26:39.760541 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 01:26:39.832195 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 01:26:41.006725 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_linear.rds
2025-09-11 01:26:41.067283 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_linear.rds
2025-09-11 01:26:41.130346 WARNING::Deleting existing residuals file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/residuals_logistic.rds
2025-09-11 01:26:41.429059 WARNING::Deleting existing fitted file: /tmp/RtmpvkSogm/file3f40312b1224f/fits/fitted_logistic.rds
2025-09-11 01:26:56.970166 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-11 01:26:56.986354 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-11 01:26:56.997474 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-11 01:26:57.048527 ERROR::No fixed, group, or
ordered effects included in formula.
2025-09-11 01:26:57.065379 ERROR::Effect name not found in metadata: d
2025-09-11 01:26:57.076987 ERROR::No user formula provided
2025-09-11 01:26:57.10692 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-11 01:26:57.1186 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-09-11 01:26:59.989075 INFO::Writing function arguments to log file
2025-09-11 01:27:00.002946 INFO::Verifying options selected are valid
2025-09-11 01:27:01.846724 INFO::Writing function arguments to log file
2025-09-11 01:27:01.858418 INFO::Verifying options selected are valid
2025-09-11 01:27:01.859561 INFO::Determining format of input files
2025-09-11 01:27:01.860579 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 01:27:01.862978 INFO::Running selected normalization method: TSS
2025-09-11 01:27:01.864429 INFO::Creating output feature tables folder
2025-09-11 01:27:01.865415 INFO::Writing normalized data to file /tmp/RtmpvkSogm/file3f4034c24058c/features/data_norm.tsv
2025-09-11 01:27:01.86688 INFO::Filter data based on min abundance and min prevalence
2025-09-11 01:27:01.867803 INFO::Total samples in data: 16
2025-09-11 01:27:01.868678 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-11 01:27:01.870498 INFO::Total filtered features: 0
2025-09-11 01:27:01.871456 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 01:27:01.872617 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-11 01:27:01.873575 INFO::Filtered feature names from variance filtering:
2025-09-11 01:27:01.874495 INFO::Writing filtered data to file /tmp/RtmpvkSogm/file3f4034c24058c/features/filtered_data.tsv
2025-09-11 01:27:01.875986 INFO::Running selected transform method: LOG
2025-09-11 01:27:01.877203 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvkSogm/file3f4034c24058c/features/data_transformed.tsv
2025-09-11 01:27:01.878819 INFO::Applying z-score to standardize continuous metadata
2025-09-11 01:27:01.884074 INFO::Running the linear model component
2025-09-11 01:27:01.897806 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:01.902255 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:01.906414 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:01.913572 INFO::Counting total values for each feature
2025-09-11 01:27:01.915394 INFO::Running the logistic model component
2025-09-11 01:27:01.928912 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:01.935194 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:01.941317 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:01.950324 INFO::Counting total values for each feature
2025-09-11 01:27:01.952494 INFO::Re-running abundances for warn_prevalence
2025-09-11 01:27:01.95344 INFO::Running selected normalization method: TSS
2025-09-11 01:27:01.954938 INFO::Running selected transform method: LOG
2025-09-11 01:27:01.968734 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:01.973055 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:01.977167 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:02.062873 INFO::Creating fits folder
2025-09-11 01:27:02.064113 INFO::Writing residuals to file /tmp/RtmpvkSogm/file3f4034c24058c/fits/residuals_linear.rds
2025-09-11 01:27:02.065272 INFO::Writing fitted values to file /tmp/RtmpvkSogm/file3f4034c24058c/fits/fitted_linear.rds
2025-09-11 01:27:02.066477 INFO::Writing residuals to file /tmp/RtmpvkSogm/file3f4034c24058c/fits/residuals_logistic.rds
2025-09-11 01:27:02.067721 INFO::Writing fitted values to file /tmp/RtmpvkSogm/file3f4034c24058c/fits/fitted_logistic.rds
2025-09-11 01:27:02.07046 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpvkSogm/file3f4034c24058c/all_results.tsv
2025-09-11 01:27:02.072229 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/RtmpvkSogm/file3f4034c24058c/significant_results.tsv
2025-09-11 01:27:02.073644 INFO::Creating output figures folder
2025-09-11 01:27:02.075088 INFO::Writing summary plot of significant
results to file: /tmp/RtmpvkSogm/file3f4034c24058c/figures/summary_plot.pdf
2025-09-11 01:27:03.305983 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvkSogm/file3f4034c24058c/figures
2025-09-11 01:27:03.307998 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 01:27:03.313035 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 01:27:03.704419 INFO::Writing summary plot of
significant results to file: /tmp/RtmpvkSogm/file3f4034c24058c/figures/summary_plot.pdf
2025-09-11 01:27:04.927498 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvkSogm/file3f4034c24058c/figures
2025-09-11 01:27:04.929093 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 01:27:04.934051 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 01:27:05.32534 INFO::Running the linear model component
2025-09-11 01:27:05.334424 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:05.338858 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:05.342965 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:05.350085 INFO::Counting total values for each feature
2025-09-11 01:27:05.351781 INFO::Running the logistic model component
2025-09-11 01:27:05.360203 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:05.366318 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:05.372176 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:05.380959 INFO::Counting total values for each feature
2025-09-11 01:27:05.382989 INFO::Re-running abundances for warn_prevalence
2025-09-11 01:27:05.383781 INFO::Running selected normalization method: TSS
2025-09-11 01:27:05.385153 INFO::Running selected transform method: LOG
2025-09-11 01:27:05.393739 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:05.397914 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:05.401882 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:05.50768 INFO::Creating output folder
2025-09-11 01:27:05.508873 INFO::Creating output figures folder
2025-09-11 01:27:05.510237 INFO::Writing summary plot of significant
results to file: /tmp/RtmpvkSogm/file3f40348700e5/figures/summary_plot.pdf
2025-09-11 01:27:06.762189 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvkSogm/file3f40348700e5/figures
2025-09-11 01:27:06.764135 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 01:27:06.769341 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 01:27:07.616511 INFO::Applying z-score to standardize continuous metadata
2025-09-11 01:27:07.624716 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-11 01:27:07.62575 INFO::Bypass z-score application to metadata
2025-09-11 01:27:07.62844 INFO::Bypass z-score application to metadata
2025-09-11 01:27:07.645848 INFO::Determining format of input files
2025-09-11 01:27:07.64684 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 01:27:07.647714 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-11 01:27:07.654487 INFO::Determining format of input files
2025-09-11 01:27:07.655527 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-11 01:27:07.656842 INFO::Input format is feature_specific_covariate samples as columns
2025-09-11 01:27:07.664197 INFO::Determining format of input files
2025-09-11 01:27:07.665083 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 01:27:07.666064 INFO::Input format is feature_specific_covariate samples as columns
2025-09-11 01:27:07.66767 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-11 01:27:07.668453 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-11 01:27:07.678786 INFO::Running selected transform method: LOG
2025-09-11 01:27:07.679929 INFO::Creating output feature tables folder
2025-09-11 01:27:07.680814 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvkSogm/file3f4036fc5e246/features/data_transformed.tsv
2025-09-11 01:27:07.684583 INFO::Running selected transform method: LOG
2025-09-11 01:27:07.685638 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvkSogm/file3f4036fc5e246/features/data_transformed.tsv
2025-09-11 01:27:07.689221 INFO::Running selected transform method: PLOG
2025-09-11 01:27:07.690807 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvkSogm/file3f4036fc5e246/features/data_transformed.tsv
2025-09-11 01:27:07.693779 INFO::Running selected transform method: NONE
2025-09-11 01:27:07.694579 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvkSogm/file3f4036fc5e246/features/data_transformed.tsv
2025-09-11 01:27:07.701784 INFO::Running the linear model component
2025-09-11 01:27:07.710304 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:07.714672 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:07.718719 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:07.725613 INFO::Counting total values for each feature
2025-09-11 01:27:07.72725 INFO::Running the logistic model component
2025-09-11 01:27:07.735516 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:07.741482 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:07.747262 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:07.755807 INFO::Counting total values for each feature
2025-09-11 01:27:07.757741 INFO::Re-running abundances for warn_prevalence
2025-09-11 01:27:07.758511 INFO::Running selected normalization method: TSS
2025-09-11 01:27:07.759894 INFO::Running selected transform method: LOG
2025-09-11 01:27:07.768456 INFO::Fitting model to feature number 1, a
2025-09-11 01:27:07.77248 INFO::Fitting model to feature number 2, b
2025-09-11 01:27:07.776401 INFO::Fitting model to feature number 3, c
2025-09-11 01:27:07.863804 INFO::Creating output folder
2025-09-11 01:27:07.864933 INFO::Creating fits folder
2025-09-11 01:27:07.865886 INFO::Writing residuals to file /tmp/RtmpvkSogm/file3f40346165810/fits/residuals_linear.rds
2025-09-11 01:27:07.866965 INFO::Writing fitted values to file /tmp/RtmpvkSogm/file3f40346165810/fits/fitted_linear.rds
2025-09-11 01:27:07.868084 INFO::Writing residuals to file /tmp/RtmpvkSogm/file3f40346165810/fits/residuals_logistic.rds
2025-09-11 01:27:07.869163 INFO::Writing fitted values to file /tmp/RtmpvkSogm/file3f40346165810/fits/fitted_logistic.rds
2025-09-11 01:27:07.871853 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpvkSogm/file3f40346165810/all_results.tsv
2025-09-11 01:27:07.873418 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/RtmpvkSogm/file3f40346165810/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
307.970 3.415 311.401
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.278 | 0.646 | 19.929 | |
| maaslin_check_arguments | 0.141 | 0.008 | 0.150 | |
| maaslin_check_formula | 0.143 | 0.006 | 0.149 | |
| maaslin_compute_formula | 0.139 | 0.003 | 0.142 | |
| maaslin_contrast_test | 18.724 | 0.477 | 19.206 | |
| maaslin_filter | 0.445 | 0.018 | 0.463 | |
| maaslin_fit | 12.586 | 0.071 | 12.659 | |
| maaslin_log_arguments | 0.142 | 0.002 | 0.144 | |
| maaslin_normalize | 0.257 | 0.013 | 0.270 | |
| maaslin_plot_results | 36.227 | 0.414 | 36.607 | |
| maaslin_plot_results_from_output | 35.199 | 0.275 | 35.478 | |
| maaslin_process_metadata | 0.435 | 0.012 | 0.447 | |
| maaslin_read_data | 0.122 | 0.006 | 0.128 | |
| maaslin_reorder_data | 0.130 | 0.003 | 0.133 | |
| maaslin_transform | 0.531 | 0.033 | 0.564 | |
| maaslin_write_results | 12.862 | 0.232 | 13.094 | |
| maaslin_write_results_lefse_format | 14.406 | 0.183 | 14.593 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |