William Nickols
| Snapshot Date: 2026-04-03 13:45 -0400 (Fri, 03 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-04 11:57 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-04-04 00:50:51 -0400 (Sat, 04 Apr 2026) |
| EndedAt: 2026-04-04 01:12:35 -0400 (Sat, 04 Apr 2026) |
| EllapsedTime: 1304.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 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 43.137 0.192 43.285
maaslin_plot_results_from_output 42.538 0.342 42.884
maaslin3 20.039 0.507 20.547
maaslin_contrast_test 18.920 0.446 19.367
maaslin_write_results 14.402 0.225 14.629
maaslin_write_results_lefse_format 14.333 0.046 14.379
maaslin_fit 12.747 0.109 12.857
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-04-04 00:57:07.567629 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:57:07.654228 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:57:07.747937 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:57:07.769635 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:57:07.804999 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:57:07.893536 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:57:07.915425 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:57:07.927735 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:57:08.02399 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:57:08.029514 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:57:08.079434 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:57:08.126515 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:57:08.13819 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:57:08.17829 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:57:08.248002 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:57:24.215885 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:57:24.289196 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:57:24.361283 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:57:24.382237 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:57:24.415996 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:57:24.503327 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:57:24.508568 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:57:24.520445 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:57:24.613564 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:57:24.618817 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:57:24.667642 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:57:24.707348 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:57:24.71879 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:57:24.758058 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:57:24.825476 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:57:48.825407 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:57:48.904807 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:57:48.98736 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:57:49.011514 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:57:49.047633 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:57:49.125362 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:57:49.13117 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:57:49.143588 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:57:49.242826 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:57:49.248909 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:57:49.303347 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:57:49.347109 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:57:49.359811 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:57:49.403507 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:57:49.482141 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:58:02.389938 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:58:02.495061 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:58:02.573359 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:58:02.596108 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:58:02.63348 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:58:02.709626 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:58:02.71507 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:58:02.727872 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:58:02.829869 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:58:02.835518 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:58:02.886475 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:58:02.930751 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:58:02.94432 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:58:02.98613 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:58:03.058424 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:58:03.265695 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_linear.rds
2026-04-04 00:58:03.329477 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_linear.rds
2026-04-04 00:58:03.392521 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_logistic.rds
2026-04-04 00:58:03.694012 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_logistic.rds
2026-04-04 00:58:26.074144 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:58:26.158953 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:58:26.266575 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:58:26.289556 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:58:26.325797 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:58:26.405869 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:58:26.411559 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:58:26.424312 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:58:26.523089 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:58:26.529307 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:58:26.581686 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:58:26.622672 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:58:26.634654 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:58:26.674935 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:58:26.745121 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:58:38.7133 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:58:38.794144 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:58:38.871993 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:58:38.894677 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:58:38.930913 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:58:39.007054 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:58:39.012429 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:58:39.024211 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:58:39.121926 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:58:39.127806 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:58:39.179202 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:58:39.220007 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:58:39.232001 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:58:39.274344 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:58:39.347151 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:58:39.559092 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_linear.rds
2026-04-04 00:58:39.620139 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_linear.rds
2026-04-04 00:58:39.682608 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_logistic.rds
2026-04-04 00:58:39.981426 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_logistic.rds
2026-04-04 00:59:01.610235 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:59:01.693953 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:59:01.774584 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:59:01.798984 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:59:01.835973 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:59:01.940503 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:59:01.946196 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:59:01.958434 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:59:02.055816 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:59:02.061406 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:59:02.112569 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:59:02.153734 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:59:02.166186 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:59:02.20818 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:59:02.279111 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:59:14.434712 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:59:14.514382 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:59:14.592113 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:59:14.614343 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:59:14.650269 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:59:14.733368 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:59:14.738764 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:59:14.750585 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:59:14.846982 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:59:14.852491 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:59:14.903684 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:59:14.946361 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:59:14.959192 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:59:15.002569 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:59:15.07703 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:59:15.275522 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_linear.rds
2026-04-04 00:59:15.337366 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_linear.rds
2026-04-04 00:59:15.400773 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/residuals_logistic.rds
2026-04-04 00:59:15.700052 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b459710603d97/fits/fitted_logistic.rds
2026-04-04 00:59:37.227014 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:59:37.303431 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:59:37.379257 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:59:37.401363 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:59:37.436237 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:59:37.513572 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:59:37.519305 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:59:37.531526 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:59:37.632036 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:59:37.637651 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:59:37.689285 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:59:37.731512 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:59:37.744126 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:59:37.786835 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:59:37.85958 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 00:59:49.750874 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 00:59:49.827117 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 00:59:49.901418 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 00:59:49.922941 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 00:59:49.95782 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 00:59:50.034185 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 00:59:50.039555 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 00:59:50.051425 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 00:59:50.147161 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 00:59:50.152712 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 00:59:50.202312 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 00:59:50.243956 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 00:59:50.256379 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 00:59:50.297631 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 00:59:50.368394 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 01:00:15.870394 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:00:26.107153 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:00:51.178764 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:01.774872 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:02.49122 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_linear.rds
2026-04-04 01:01:02.553573 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_linear.rds
2026-04-04 01:01:02.592707 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_logistic.rds
2026-04-04 01:01:02.665706 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_logistic.rds
2026-04-04 01:01:25.812659 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:31.259267 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:31.611842 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_linear.rds
2026-04-04 01:01:31.673377 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_linear.rds
2026-04-04 01:01:31.712071 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_logistic.rds
2026-04-04 01:01:31.781412 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_logistic.rds
2026-04-04 01:01:50.842253 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:57.541804 WARNING::Fitting problem for feature 124 returning NA
2026-04-04 01:01:57.937883 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_linear.rds
2026-04-04 01:01:57.999431 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_linear.rds
2026-04-04 01:01:58.038366 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_logistic.rds
2026-04-04 01:01:58.108403 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_logistic.rds
2026-04-04 01:02:16.52316 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 01:02:16.606627 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 01:02:16.686907 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 01:02:16.712557 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 01:02:16.753012 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 01:02:16.840266 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 01:02:16.846265 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 01:02:16.859797 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 01:02:16.998317 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 01:02:17.00514 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 01:02:17.059572 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 01:02:17.103008 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 01:02:17.116214 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 01:02:17.159539 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 01:02:17.232995 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 01:02:29.294021 WARNING::Fitting problem for feature 50 returning NA
2026-04-04 01:02:29.371301 WARNING::Fitting problem for feature 62 returning NA
2026-04-04 01:02:29.4483 WARNING::Fitting problem for feature 74 returning NA
2026-04-04 01:02:29.471044 WARNING::Fitting problem for feature 78 returning NA
2026-04-04 01:02:29.506191 WARNING::Fitting problem for feature 84 returning NA
2026-04-04 01:02:29.585408 WARNING::Fitting problem for feature 96 returning NA
2026-04-04 01:02:29.590983 WARNING::Fitting problem for feature 97 returning NA
2026-04-04 01:02:29.603543 WARNING::Fitting problem for feature 99 returning NA
2026-04-04 01:02:29.703309 WARNING::Fitting problem for feature 114 returning NA
2026-04-04 01:02:29.709044 WARNING::Fitting problem for feature 115 returning NA
2026-04-04 01:02:29.760003 WARNING::Fitting problem for feature 123 returning NA
2026-04-04 01:02:29.801342 WARNING::Fitting problem for feature 130 returning NA
2026-04-04 01:02:29.813461 WARNING::Fitting problem for feature 132 returning NA
2026-04-04 01:02:29.855263 WARNING::Fitting problem for feature 139 returning NA
2026-04-04 01:02:29.959533 WARNING::Fitting problem for feature 150 returning NA
2026-04-04 01:02:30.202429 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_linear.rds
2026-04-04 01:02:30.263206 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_linear.rds
2026-04-04 01:02:30.326065 WARNING::Deleting existing residuals file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/residuals_logistic.rds
2026-04-04 01:02:30.624738 WARNING::Deleting existing fitted file: /tmp/Rtmp9RntQi/file2b45972bd7c736/fits/fitted_logistic.rds
2026-04-04 01:02:50.946703 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-04-04 01:02:50.96371 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-04-04 01:02:50.975547 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-04-04 01:02:51.028463 ERROR::No fixed, group, or
ordered effects included in formula.
2026-04-04 01:02:51.045475 ERROR::Effect name not found in metadata: d
2026-04-04 01:02:51.056853 ERROR::No user formula provided
2026-04-04 01:02:51.087929 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-04-04 01:02:51.099744 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-04-04 01:02:53.969817 INFO::Writing function arguments to log file
2026-04-04 01:02:53.984757 INFO::Verifying options selected are valid
2026-04-04 01:02:56.311552 INFO::Writing function arguments to log file
2026-04-04 01:02:56.323848 INFO::Verifying options selected are valid
2026-04-04 01:02:56.324955 INFO::Determining format of input files
2026-04-04 01:02:56.325958 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-04 01:02:56.328334 INFO::Running selected normalization method: TSS
2026-04-04 01:02:56.329795 INFO::Creating output feature tables folder
2026-04-04 01:02:56.330776 INFO::Writing normalized data to file /tmp/Rtmp9RntQi/file2b459738396fe8/features/data_norm.tsv
2026-04-04 01:02:56.332336 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-04-04 01:02:56.333241 INFO::Total samples in data: 16
2026-04-04 01:02:56.334121 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-04-04 01:02:56.33499 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-04-04 01:02:56.336917 INFO::Total filtered features: 0
2026-04-04 01:02:56.337891 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-04-04 01:02:56.339052 INFO::Total features filtered by non-zero variance filtering: 0
2026-04-04 01:02:56.339993 INFO::Filtered feature names from variance filtering:
2026-04-04 01:02:56.340878 INFO::Writing filtered data to file /tmp/Rtmp9RntQi/file2b459738396fe8/features/filtered_data.tsv
2026-04-04 01:02:56.342366 INFO::Running selected transform method: LOG
2026-04-04 01:02:56.343548 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9RntQi/file2b459738396fe8/features/data_transformed.tsv
2026-04-04 01:02:56.345161 INFO::Applying z-score to standardize continuous metadata
2026-04-04 01:02:56.349623 INFO::Running the linear model component
2026-04-04 01:02:56.363774 INFO::Fitting model to feature number 1, a
2026-04-04 01:02:56.368312 INFO::Fitting model to feature number 2, b
2026-04-04 01:02:56.372693 INFO::Fitting model to feature number 3, c
2026-04-04 01:02:56.379982 INFO::Counting total values for each feature
2026-04-04 01:02:56.381849 INFO::Running the logistic model component
2026-04-04 01:02:56.395849 INFO::Fitting model to feature number 1, a
2026-04-04 01:02:56.402364 INFO::Fitting model to feature number 2, b
2026-04-04 01:02:56.408564 INFO::Fitting model to feature number 3, c
2026-04-04 01:02:56.417776 INFO::Counting total values for each feature
2026-04-04 01:02:56.420022 INFO::Re-running abundances for warn_prevalence
2026-04-04 01:02:56.420995 INFO::Running selected normalization method: TSS
2026-04-04 01:02:56.422527 INFO::Running selected transform method: LOG
2026-04-04 01:02:56.436799 INFO::Fitting model to feature number 1, a
2026-04-04 01:02:56.4414 INFO::Fitting model to feature number 2, b
2026-04-04 01:02:56.44577 INFO::Fitting model to feature number 3, c
2026-04-04 01:02:56.523316 INFO::Creating fits folder
2026-04-04 01:02:56.524517 INFO::Writing residuals to file /tmp/Rtmp9RntQi/file2b459738396fe8/fits/residuals_linear.rds
2026-04-04 01:02:56.525695 INFO::Writing fitted values to file /tmp/Rtmp9RntQi/file2b459738396fe8/fits/fitted_linear.rds
2026-04-04 01:02:56.526943 INFO::Writing residuals to file /tmp/Rtmp9RntQi/file2b459738396fe8/fits/residuals_logistic.rds
2026-04-04 01:02:56.528188 INFO::Writing fitted values to file /tmp/Rtmp9RntQi/file2b459738396fe8/fits/fitted_logistic.rds
2026-04-04 01:02:56.530712 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9RntQi/file2b459738396fe8/all_results.tsv
2026-04-04 01:02:56.532373 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/Rtmp9RntQi/file2b459738396fe8/significant_results.tsv
2026-04-04 01:02:56.533728 INFO::Creating output figures folder
2026-04-04 01:02:56.535105 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9RntQi/file2b459738396fe8/figures/summary_plot.pdf
2026-04-04 01:02:58.16292 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9RntQi/file2b459738396fe8/figures
2026-04-04 01:02:58.165095 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-04 01:02:58.170467 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-04 01:02:58.704209 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp9RntQi/file2b459738396fe8/figures/summary_plot.pdf
2026-04-04 01:03:00.346594 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9RntQi/file2b459738396fe8/figures
2026-04-04 01:03:00.348259 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-04 01:03:00.353702 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-04 01:03:00.882946 INFO::Running the linear model component
2026-04-04 01:03:00.892116 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:00.896592 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:00.90061 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:00.907644 INFO::Counting total values for each feature
2026-04-04 01:03:00.909338 INFO::Running the logistic model component
2026-04-04 01:03:00.917691 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:00.924036 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:00.930032 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:00.938786 INFO::Counting total values for each feature
2026-04-04 01:03:00.94084 INFO::Re-running abundances for warn_prevalence
2026-04-04 01:03:00.941625 INFO::Running selected normalization method: TSS
2026-04-04 01:03:00.942961 INFO::Running selected transform method: LOG
2026-04-04 01:03:00.951427 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:00.955559 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:00.959523 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:01.035621 INFO::Creating output folder
2026-04-04 01:03:01.03656 INFO::Creating output figures folder
2026-04-04 01:03:01.037771 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9RntQi/file2b459727644e0/figures/summary_plot.pdf
2026-04-04 01:03:02.61019 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9RntQi/file2b459727644e0/figures
2026-04-04 01:03:02.611931 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-04 01:03:02.616759 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-04 01:03:03.577091 INFO::Applying z-score to standardize continuous metadata
2026-04-04 01:03:03.584186 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-04-04 01:03:03.585069 INFO::Bypass z-score application to metadata
2026-04-04 01:03:03.587661 INFO::Bypass z-score application to metadata
2026-04-04 01:03:03.606309 INFO::Determining format of input files
2026-04-04 01:03:03.607219 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-04 01:03:03.608065 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-04-04 01:03:03.615458 INFO::Determining format of input files
2026-04-04 01:03:03.616433 INFO::Input format is data samples as columns and metadata samples as rows
2026-04-04 01:03:03.617689 INFO::Input format is feature_specific_covariate samples as columns
2026-04-04 01:03:03.625867 INFO::Determining format of input files
2026-04-04 01:03:03.626802 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-04 01:03:03.627829 INFO::Input format is feature_specific_covariate samples as columns
2026-04-04 01:03:03.629481 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-04-04 01:03:03.630256 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-04-04 01:03:03.64229 INFO::Running selected transform method: LOG
2026-04-04 01:03:03.6434 INFO::Creating output feature tables folder
2026-04-04 01:03:03.644226 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9RntQi/file2b459722021523/features/data_transformed.tsv
2026-04-04 01:03:03.648008 INFO::Running selected transform method: LOG
2026-04-04 01:03:03.649019 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9RntQi/file2b459722021523/features/data_transformed.tsv
2026-04-04 01:03:03.652888 INFO::Running selected transform method: PLOG
2026-04-04 01:03:03.654522 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9RntQi/file2b459722021523/features/data_transformed.tsv
2026-04-04 01:03:03.657393 INFO::Running selected transform method: NONE
2026-04-04 01:03:03.658119 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9RntQi/file2b459722021523/features/data_transformed.tsv
2026-04-04 01:03:03.665647 INFO::Running the linear model component
2026-04-04 01:03:03.674168 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:03.678404 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:03.682424 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:03.689434 INFO::Counting total values for each feature
2026-04-04 01:03:03.691037 INFO::Running the logistic model component
2026-04-04 01:03:03.699468 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:03.705669 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:03.711555 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:03.720506 INFO::Counting total values for each feature
2026-04-04 01:03:03.72259 INFO::Re-running abundances for warn_prevalence
2026-04-04 01:03:03.723373 INFO::Running selected normalization method: TSS
2026-04-04 01:03:03.724712 INFO::Running selected transform method: LOG
2026-04-04 01:03:03.733346 INFO::Fitting model to feature number 1, a
2026-04-04 01:03:03.737469 INFO::Fitting model to feature number 2, b
2026-04-04 01:03:03.741394 INFO::Fitting model to feature number 3, c
2026-04-04 01:03:03.833177 INFO::Creating output folder
2026-04-04 01:03:03.834194 INFO::Creating fits folder
2026-04-04 01:03:03.835076 INFO::Writing residuals to file /tmp/Rtmp9RntQi/file2b45973b81fd6a/fits/residuals_linear.rds
2026-04-04 01:03:03.836097 INFO::Writing fitted values to file /tmp/Rtmp9RntQi/file2b45973b81fd6a/fits/fitted_linear.rds
2026-04-04 01:03:03.837217 INFO::Writing residuals to file /tmp/Rtmp9RntQi/file2b45973b81fd6a/fits/residuals_logistic.rds
2026-04-04 01:03:03.838314 INFO::Writing fitted values to file /tmp/Rtmp9RntQi/file2b45973b81fd6a/fits/fitted_logistic.rds
2026-04-04 01:03:03.84068 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9RntQi/file2b45973b81fd6a/all_results.tsv
2026-04-04 01:03:03.842189 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/Rtmp9RntQi/file2b45973b81fd6a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.578 4.887 367.448
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.039 | 0.507 | 20.547 | |
| maaslin_check_arguments | 0.137 | 0.004 | 0.140 | |
| maaslin_check_formula | 0.168 | 0.003 | 0.172 | |
| maaslin_compute_formula | 0.144 | 0.001 | 0.146 | |
| maaslin_contrast_test | 18.920 | 0.446 | 19.367 | |
| maaslin_filter | 0.435 | 0.041 | 0.476 | |
| maaslin_fit | 12.747 | 0.109 | 12.857 | |
| maaslin_log_arguments | 0.126 | 0.002 | 0.128 | |
| maaslin_normalize | 0.256 | 0.006 | 0.262 | |
| maaslin_plot_results | 43.137 | 0.192 | 43.285 | |
| maaslin_plot_results_from_output | 42.538 | 0.342 | 42.884 | |
| maaslin_process_metadata | 0.472 | 0.023 | 0.495 | |
| maaslin_read_data | 0.139 | 0.003 | 0.142 | |
| maaslin_reorder_data | 0.139 | 0.001 | 0.140 | |
| maaslin_transform | 0.569 | 0.011 | 0.580 | |
| maaslin_write_results | 14.402 | 0.225 | 14.629 | |
| maaslin_write_results_lefse_format | 14.333 | 0.046 | 14.379 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |