William Nickols
| Snapshot Date: 2025-11-11 13:40 -0500 (Tue, 11 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-12 11:32 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4823 |
| 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 1152/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-12 00:54:28 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 01:16:06 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 1298.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 43.597 0.519 44.118
maaslin_plot_results 43.141 0.416 43.528
maaslin3 20.829 0.611 21.451
maaslin_contrast_test 18.496 0.495 18.993
maaslin_write_results_lefse_format 14.469 0.082 14.551
maaslin_write_results 13.094 0.151 13.246
maaslin_fit 12.620 0.214 12.836
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-12 01:00:45.573618 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:00:45.646693 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:00:46.32201 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:00:46.344333 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:00:46.378404 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:00:46.464312 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:00:46.470028 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:00:46.482915 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:00:46.597862 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:00:46.603146 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:00:46.651742 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:00:46.690637 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:00:46.701984 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:00:46.740626 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:00:46.81363 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:01:02.575702 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:01:02.653034 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:01:02.72695 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:01:02.748683 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:01:02.782268 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:01:02.855461 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:01:02.860777 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:01:02.872829 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:01:02.971591 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:01:02.978261 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:01:03.046371 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:01:03.085439 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:01:03.096826 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:01:03.135866 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:01:03.203493 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:01:26.459919 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:01:26.555594 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:01:26.630256 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:01:26.653242 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:01:26.687263 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:01:26.762086 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:01:26.767664 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:01:26.779424 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:01:26.876256 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:01:26.881882 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:01:27.036415 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:01:27.085723 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:01:27.098309 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:01:27.140935 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:01:27.215426 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:01:40.692815 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:01:40.770265 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:01:40.844431 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:01:40.866925 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:01:40.901651 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:01:40.980195 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:01:40.985786 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:01:40.99837 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:01:41.09589 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:01:41.101334 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:01:41.152677 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:01:41.193174 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:01:41.204769 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:01:41.244276 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:01:41.311401 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:01:41.517252 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_linear.rds
2025-11-12 01:01:41.578199 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_linear.rds
2025-11-12 01:01:41.640902 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_logistic.rds
2025-11-12 01:01:41.940505 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_logistic.rds
2025-11-12 01:02:03.412229 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:02:03.492198 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:02:03.568171 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:02:03.590153 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:02:03.624427 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:02:03.699998 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:02:03.70542 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:02:03.717116 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:02:03.814756 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:02:03.820385 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:02:03.87312 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:02:03.917238 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:02:03.929379 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:02:03.971556 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:02:04.041986 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:02:16.969291 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:02:17.046565 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:02:17.128307 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:02:17.15206 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:02:17.18841 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:02:17.266992 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:02:17.272573 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:02:17.284707 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:02:17.381912 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:02:17.387598 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:02:17.441311 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:02:17.483592 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:02:17.495974 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:02:17.539049 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:02:17.612038 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:02:17.826429 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_linear.rds
2025-11-12 01:02:17.887818 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_linear.rds
2025-11-12 01:02:17.951198 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_logistic.rds
2025-11-12 01:02:18.2536 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_logistic.rds
2025-11-12 01:02:40.36043 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:02:40.438319 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:02:40.516617 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:02:40.538426 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:02:40.573063 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:02:40.64867 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:02:40.654304 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:02:40.666436 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:02:40.783996 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:02:40.789464 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:02:40.840167 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:02:40.880989 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:02:40.8934 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:02:40.933267 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:02:41.001457 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:02:52.7466 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:02:52.820195 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:02:52.894701 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:02:52.917452 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:02:52.952918 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:02:53.062753 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:02:53.068783 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:02:53.081089 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:02:53.179124 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:02:53.184738 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:02:53.237015 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:02:53.279521 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:02:53.291479 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:02:53.332855 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:02:53.40315 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:02:53.614678 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_linear.rds
2025-11-12 01:02:53.675631 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_linear.rds
2025-11-12 01:02:53.738943 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/residuals_logistic.rds
2025-11-12 01:02:54.039731 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c2fb8e19f/fits/fitted_logistic.rds
2025-11-12 01:03:15.407823 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:03:15.491242 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:03:15.570788 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:03:15.594702 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:03:15.630601 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:03:15.71157 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:03:15.718018 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:03:15.731692 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:03:15.847919 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:03:15.855557 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:03:15.914093 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:03:15.955928 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:03:15.969416 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:03:16.012422 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:03:16.084182 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:03:29.033803 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:03:29.115159 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:03:29.195142 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:03:29.217348 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:03:29.252615 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:03:29.329192 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:03:29.334595 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:03:29.346454 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:03:29.441919 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:03:29.44748 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:03:29.497516 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:03:29.539481 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:03:29.552067 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:03:29.594048 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:03:29.666505 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:03:53.39945 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:04:03.860244 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:04:29.913136 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:04:39.414754 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:04:40.033484 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_linear.rds
2025-11-12 01:04:40.095728 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_linear.rds
2025-11-12 01:04:40.135034 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_logistic.rds
2025-11-12 01:04:40.206027 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_logistic.rds
2025-11-12 01:05:02.5616 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:05:08.819319 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:05:09.138165 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_linear.rds
2025-11-12 01:05:09.200599 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_linear.rds
2025-11-12 01:05:09.240164 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_logistic.rds
2025-11-12 01:05:09.31037 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_logistic.rds
2025-11-12 01:05:28.09641 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:05:34.264232 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 01:05:34.563078 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_linear.rds
2025-11-12 01:05:34.624663 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_linear.rds
2025-11-12 01:05:34.663334 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_logistic.rds
2025-11-12 01:05:34.738758 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_logistic.rds
2025-11-12 01:05:52.614431 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:05:52.693317 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:05:52.771693 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:05:52.794825 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:05:52.83154 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:05:52.914787 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:05:52.920601 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:05:52.933338 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:05:53.038199 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:05:53.044076 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:05:53.096959 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:05:53.166434 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:05:53.17873 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:05:53.219565 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:05:53.290451 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:06:05.136653 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 01:06:05.25001 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 01:06:05.329 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 01:06:05.351882 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 01:06:05.388747 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 01:06:05.466539 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 01:06:05.472209 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 01:06:05.484223 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 01:06:05.580329 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 01:06:05.585931 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 01:06:05.636667 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 01:06:05.677895 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 01:06:05.690673 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 01:06:05.733356 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 01:06:05.807081 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 01:06:06.075735 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_linear.rds
2025-11-12 01:06:06.136811 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_linear.rds
2025-11-12 01:06:06.200019 WARNING::Deleting existing residuals file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/residuals_logistic.rds
2025-11-12 01:06:06.504434 WARNING::Deleting existing fitted file: /tmp/Rtmpu6WHLg/file2a9e7c6d3e278a/fits/fitted_logistic.rds
2025-11-12 01:06:26.53126 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-12 01:06:26.547938 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-12 01:06:26.559165 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-12 01:06:26.609144 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-12 01:06:26.625356 ERROR::Effect name not found in metadata: d
2025-11-12 01:06:26.636272 ERROR::No user formula provided
2025-11-12 01:06:26.664881 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-12 01:06:26.676472 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-12 01:06:29.58688 INFO::Writing function arguments to log file
2025-11-12 01:06:29.600554 INFO::Verifying options selected are valid
2025-11-12 01:06:32.093051 INFO::Writing function arguments to log file
2025-11-12 01:06:32.10591 INFO::Verifying options selected are valid
2025-11-12 01:06:32.107084 INFO::Determining format of input files
2025-11-12 01:06:32.10812 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 01:06:32.110574 INFO::Running selected normalization method: TSS
2025-11-12 01:06:32.112152 INFO::Creating output feature tables folder
2025-11-12 01:06:32.1132 INFO::Writing normalized data to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/features/data_norm.tsv
2025-11-12 01:06:32.114834 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-12 01:06:32.115812 INFO::Total samples in data: 16
2025-11-12 01:06:32.116728 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-12 01:06:32.117627 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-12 01:06:32.11966 INFO::Total filtered features: 0
2025-11-12 01:06:32.120659 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-12 01:06:32.121925 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-12 01:06:32.122915 INFO::Filtered feature names from variance filtering:
2025-11-12 01:06:32.123831 INFO::Writing filtered data to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/features/filtered_data.tsv
2025-11-12 01:06:32.125394 INFO::Running selected transform method: LOG
2025-11-12 01:06:32.126667 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/features/data_transformed.tsv
2025-11-12 01:06:32.128454 INFO::Applying z-score to standardize continuous metadata
2025-11-12 01:06:32.134302 INFO::Running the linear model component
2025-11-12 01:06:32.149043 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:32.154033 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:32.158497 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:32.166769 INFO::Counting total values for each feature
2025-11-12 01:06:32.168786 INFO::Running the logistic model component
2025-11-12 01:06:32.182882 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:32.189819 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:32.196276 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:32.205691 INFO::Counting total values for each feature
2025-11-12 01:06:32.208014 INFO::Re-running abundances for warn_prevalence
2025-11-12 01:06:32.209024 INFO::Running selected normalization method: TSS
2025-11-12 01:06:32.210557 INFO::Running selected transform method: LOG
2025-11-12 01:06:32.224408 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:32.24334 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:32.248902 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:32.348128 INFO::Creating fits folder
2025-11-12 01:06:32.349324 INFO::Writing residuals to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/fits/residuals_linear.rds
2025-11-12 01:06:32.350451 INFO::Writing fitted values to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/fits/fitted_linear.rds
2025-11-12 01:06:32.351635 INFO::Writing residuals to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/fits/residuals_logistic.rds
2025-11-12 01:06:32.352782 INFO::Writing fitted values to file /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/fits/fitted_logistic.rds
2025-11-12 01:06:32.355336 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/all_results.tsv
2025-11-12 01:06:32.356978 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/Rtmpu6WHLg/file2a9e7c66cdfef1/significant_results.tsv
2025-11-12 01:06:32.358314 INFO::Creating output figures folder
2025-11-12 01:06:32.359677 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/figures/summary_plot.pdf
2025-11-12 01:06:33.9625 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/figures
2025-11-12 01:06:33.964812 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 01:06:33.970563 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 01:06:34.498603 INFO::Writing summary plot of
significant results to file: /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/figures/summary_plot.pdf
2025-11-12 01:06:36.134683 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpu6WHLg/file2a9e7c66cdfef1/figures
2025-11-12 01:06:36.13629 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 01:06:36.141145 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 01:06:36.657011 INFO::Running the linear model component
2025-11-12 01:06:36.666386 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:36.67068 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:36.67467 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:36.681509 INFO::Counting total values for each feature
2025-11-12 01:06:36.683177 INFO::Running the logistic model component
2025-11-12 01:06:36.691634 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:36.697649 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:36.703189 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:36.711389 INFO::Counting total values for each feature
2025-11-12 01:06:36.713358 INFO::Re-running abundances for warn_prevalence
2025-11-12 01:06:36.714121 INFO::Running selected normalization method: TSS
2025-11-12 01:06:36.715421 INFO::Running selected transform method: LOG
2025-11-12 01:06:36.723609 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:36.727433 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:36.731106 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:36.816962 INFO::Creating output folder
2025-11-12 01:06:36.817956 INFO::Creating output figures folder
2025-11-12 01:06:36.819238 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpu6WHLg/file2a9e7c3dbdfc46/figures/summary_plot.pdf
2025-11-12 01:06:38.409766 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpu6WHLg/file2a9e7c3dbdfc46/figures
2025-11-12 01:06:38.411558 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 01:06:38.416551 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 01:06:39.42822 INFO::Applying z-score to standardize continuous metadata
2025-11-12 01:06:39.436991 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-12 01:06:39.438068 INFO::Bypass z-score application to metadata
2025-11-12 01:06:39.440997 INFO::Bypass z-score application to metadata
2025-11-12 01:06:39.46127 INFO::Determining format of input files
2025-11-12 01:06:39.462326 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 01:06:39.463289 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-12 01:06:39.471119 INFO::Determining format of input files
2025-11-12 01:06:39.472212 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-12 01:06:39.473618 INFO::Input format is feature_specific_covariate samples as columns
2025-11-12 01:06:39.482144 INFO::Determining format of input files
2025-11-12 01:06:39.483124 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 01:06:39.484233 INFO::Input format is feature_specific_covariate samples as columns
2025-11-12 01:06:39.485958 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-12 01:06:39.486751 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-12 01:06:39.498045 INFO::Running selected transform method: LOG
2025-11-12 01:06:39.499215 INFO::Creating output feature tables folder
2025-11-12 01:06:39.500112 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpu6WHLg/file2a9e7c4b9107f4/features/data_transformed.tsv
2025-11-12 01:06:39.503987 INFO::Running selected transform method: LOG
2025-11-12 01:06:39.505022 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpu6WHLg/file2a9e7c4b9107f4/features/data_transformed.tsv
2025-11-12 01:06:39.508599 INFO::Running selected transform method: PLOG
2025-11-12 01:06:39.510205 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpu6WHLg/file2a9e7c4b9107f4/features/data_transformed.tsv
2025-11-12 01:06:39.5129 INFO::Running selected transform method: NONE
2025-11-12 01:06:39.513634 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpu6WHLg/file2a9e7c4b9107f4/features/data_transformed.tsv
2025-11-12 01:06:39.521546 INFO::Running the linear model component
2025-11-12 01:06:39.530584 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:39.535043 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:39.539236 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:39.54668 INFO::Counting total values for each feature
2025-11-12 01:06:39.548491 INFO::Running the logistic model component
2025-11-12 01:06:39.557271 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:39.563925 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:39.570424 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:39.581057 INFO::Counting total values for each feature
2025-11-12 01:06:39.583552 INFO::Re-running abundances for warn_prevalence
2025-11-12 01:06:39.584574 INFO::Running selected normalization method: TSS
2025-11-12 01:06:39.586312 INFO::Running selected transform method: LOG
2025-11-12 01:06:39.595608 INFO::Fitting model to feature number 1, a
2025-11-12 01:06:39.600103 INFO::Fitting model to feature number 2, b
2025-11-12 01:06:39.60428 INFO::Fitting model to feature number 3, c
2025-11-12 01:06:39.706043 INFO::Creating output folder
2025-11-12 01:06:39.707068 INFO::Creating fits folder
2025-11-12 01:06:39.707936 INFO::Writing residuals to file /tmp/Rtmpu6WHLg/file2a9e7c144d8e43/fits/residuals_linear.rds
2025-11-12 01:06:39.708913 INFO::Writing fitted values to file /tmp/Rtmpu6WHLg/file2a9e7c144d8e43/fits/fitted_linear.rds
2025-11-12 01:06:39.709951 INFO::Writing residuals to file /tmp/Rtmpu6WHLg/file2a9e7c144d8e43/fits/residuals_logistic.rds
2025-11-12 01:06:39.710991 INFO::Writing fitted values to file /tmp/Rtmpu6WHLg/file2a9e7c144d8e43/fits/fitted_logistic.rds
2025-11-12 01:06:39.713482 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpu6WHLg/file2a9e7c144d8e43/all_results.tsv
2025-11-12 01:06:39.714982 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/Rtmpu6WHLg/file2a9e7c144d8e43/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
359.771 5.096 364.863
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.829 | 0.611 | 21.451 | |
| maaslin_check_arguments | 0.160 | 0.002 | 0.163 | |
| maaslin_check_formula | 0.138 | 0.005 | 0.143 | |
| maaslin_compute_formula | 0.162 | 0.005 | 0.168 | |
| maaslin_contrast_test | 18.496 | 0.495 | 18.993 | |
| maaslin_filter | 0.439 | 0.008 | 0.447 | |
| maaslin_fit | 12.620 | 0.214 | 12.836 | |
| maaslin_log_arguments | 0.136 | 0.001 | 0.136 | |
| maaslin_normalize | 0.294 | 0.010 | 0.304 | |
| maaslin_plot_results | 43.141 | 0.416 | 43.528 | |
| maaslin_plot_results_from_output | 43.597 | 0.519 | 44.118 | |
| maaslin_process_metadata | 0.441 | 0.015 | 0.457 | |
| maaslin_read_data | 0.118 | 0.007 | 0.126 | |
| maaslin_reorder_data | 0.132 | 0.002 | 0.135 | |
| maaslin_transform | 0.542 | 0.031 | 0.574 | |
| maaslin_write_results | 13.094 | 0.151 | 13.246 | |
| maaslin_write_results_lefse_format | 14.469 | 0.082 | 14.551 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.001 | 0.004 | |