William Nickols
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).
| 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" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-12-02 11:07:02 -0000 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 11:24:37 -0000 (Tue, 02 Dec 2025) |
| EllapsedTime: 1055.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 65.439 0.379 66.010
maaslin_plot_results 64.689 0.279 65.131
maaslin_contrast_test 28.859 0.320 29.253
maaslin3 28.153 0.556 28.774
maaslin_write_results_lefse_format 24.133 0.063 24.268
maaslin_write_results 22.189 0.208 22.467
maaslin_fit 21.520 0.110 21.683
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-12-02 11:15:44.560544 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:15:44.704147 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:15:44.8617 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:15:44.896826 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:15:44.955181 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:15:45.078339 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:15:45.086576 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:15:45.10555 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:15:45.274967 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:15:45.283365 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:15:45.36516 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:15:45.43329 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:15:45.466783 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:15:45.534961 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:15:45.648291 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:16:09.306398 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:16:09.435954 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:16:09.560046 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:16:09.595963 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:16:09.653226 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:16:09.811869 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:16:09.820925 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:16:09.84135 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:16:10.008938 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:16:10.017986 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:16:10.100185 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:16:10.16656 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:16:10.186573 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:16:10.253998 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:16:10.368565 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:16:44.414515 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:16:44.552231 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:16:44.692809 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:16:44.735124 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:16:44.799345 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:16:44.947545 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:16:44.957011 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:16:44.978493 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:16:45.153854 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:16:45.163758 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:16:45.25603 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:16:45.34015 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:16:45.3624 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:16:45.4369 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:16:45.572837 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:17:06.996964 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:17:07.130969 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:17:07.295789 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:17:07.336128 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:17:07.400534 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:17:07.534836 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:17:07.543978 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:17:07.565077 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:17:07.7377 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:17:07.746767 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:17:07.835175 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:17:07.907343 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:17:07.929225 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:17:08.002471 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:17:08.123054 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:17:08.427682 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_linear.rds
2025-12-02 11:17:08.49646 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_linear.rds
2025-12-02 11:17:08.566995 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_logistic.rds
2025-12-02 11:17:08.912475 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_logistic.rds
2025-12-02 11:17:39.031931 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:17:39.163349 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:17:39.2952 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:17:39.333659 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:17:39.392983 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:17:39.526996 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:17:39.536013 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:17:39.556732 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:17:39.715942 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:17:39.724546 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:17:39.810046 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:17:40.918117 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:17:40.937927 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:17:41.006331 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:17:41.124864 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:18:01.003624 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:18:01.133176 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:18:01.261599 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:18:01.298377 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:18:01.357893 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:18:01.492585 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:18:01.501816 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:18:01.522852 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:18:01.690933 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:18:01.700052 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:18:01.790323 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:18:01.862796 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:18:01.88483 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:18:01.95921 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:18:02.08754 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:18:02.393217 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_linear.rds
2025-12-02 11:18:02.458599 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_linear.rds
2025-12-02 11:18:02.529325 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_logistic.rds
2025-12-02 11:18:02.856562 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_logistic.rds
2025-12-02 11:18:32.098565 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:18:32.233148 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:18:32.368978 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:18:32.409822 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:18:32.475351 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:18:32.622254 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:18:32.632247 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:18:32.654835 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:18:32.838873 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:18:32.848537 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:18:32.974467 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:18:33.046241 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:18:33.067461 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:18:33.145501 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:18:33.283083 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:18:55.083107 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:18:55.236366 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:18:55.387485 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:18:55.432237 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:18:55.504875 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:18:55.670267 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:18:55.681492 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:18:55.706117 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:18:55.878029 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:18:55.887617 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:18:55.976999 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:18:56.055184 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:18:56.076712 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:18:56.148291 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:18:56.272583 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:18:56.57326 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_linear.rds
2025-12-02 11:18:56.642852 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_linear.rds
2025-12-02 11:18:56.71361 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/residuals_logistic.rds
2025-12-02 11:18:57.064677 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c91e6f1892/fits/fitted_logistic.rds
2025-12-02 11:19:28.554955 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:19:28.698988 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:19:28.850703 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:19:28.894819 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:19:28.964718 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:19:29.120284 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:19:29.130454 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:19:29.153493 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:19:29.347249 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:19:29.357921 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:19:29.506701 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:19:29.601666 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:19:29.627462 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:19:29.709147 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:19:29.842836 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:19:52.201351 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:19:52.340367 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:19:52.473999 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:19:52.513458 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:19:52.577664 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:19:52.718896 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:19:52.728997 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:19:52.752939 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:19:52.932461 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:19:52.942343 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:19:53.03862 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:19:53.11935 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:19:53.143897 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:19:53.234803 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:19:53.384246 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:20:29.538844 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:20:45.509133 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:21:20.533824 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:21:35.818527 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:21:36.821083 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_linear.rds
2025-12-02 11:21:36.89067 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_linear.rds
2025-12-02 11:21:36.934088 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_logistic.rds
2025-12-02 11:21:37.011675 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_logistic.rds
2025-12-02 11:22:09.513926 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:22:19.041867 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:22:19.560843 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_linear.rds
2025-12-02 11:22:19.62941 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_linear.rds
2025-12-02 11:22:19.672526 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_logistic.rds
2025-12-02 11:22:19.750393 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_logistic.rds
2025-12-02 11:22:46.249334 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:22:55.647225 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 11:22:56.129135 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_linear.rds
2025-12-02 11:22:56.197825 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_linear.rds
2025-12-02 11:22:56.241185 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_logistic.rds
2025-12-02 11:22:56.319548 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_logistic.rds
2025-12-02 11:23:21.626042 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:23:21.792658 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:23:21.925373 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:23:21.963916 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:23:22.024208 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:23:22.166327 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:23:22.175304 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:23:22.195551 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:23:22.370975 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:23:22.380584 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:23:22.469564 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:23:22.541213 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:23:22.562019 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:23:22.636909 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:23:22.761035 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:23:43.217679 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 11:23:43.348685 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 11:23:43.479596 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 11:23:43.517605 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 11:23:43.576786 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 11:23:43.712617 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 11:23:43.721814 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 11:23:43.742786 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 11:23:43.910463 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 11:23:43.919712 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 11:23:44.003443 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 11:23:44.071548 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 11:23:44.091649 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 11:23:44.158684 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 11:23:44.271602 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 11:23:44.625075 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_linear.rds
2025-12-02 11:23:44.694149 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_linear.rds
2025-12-02 11:23:44.764462 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/residuals_logistic.rds
2025-12-02 11:23:45.10649 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c948fcab78/fits/fitted_logistic.rds
2025-12-02 11:24:13.279618 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-02 11:24:13.307392 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-02 11:24:13.326051 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-02 11:24:13.404332 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-02 11:24:13.429988 ERROR::Effect name not found in metadata: d
2025-12-02 11:24:13.447901 ERROR::No user formula provided
2025-12-02 11:24:13.497032 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-02 11:24:13.516115 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-02 11:24:18.585936 INFO::Writing function arguments to log file
2025-12-02 11:24:18.609067 INFO::Verifying options selected are valid
2025-12-02 11:24:22.068558 INFO::Writing function arguments to log file
2025-12-02 11:24:22.087566 INFO::Verifying options selected are valid
2025-12-02 11:24:22.0892 INFO::Determining format of input files
2025-12-02 11:24:22.090614 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 11:24:22.0941 INFO::Running selected normalization method: TSS
2025-12-02 11:24:22.096364 INFO::Creating output feature tables folder
2025-12-02 11:24:22.097926 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/features/data_norm.tsv
2025-12-02 11:24:22.100133 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-02 11:24:22.101587 INFO::Total samples in data: 16
2025-12-02 11:24:22.102947 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-02 11:24:22.10436 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-02 11:24:22.107377 INFO::Total filtered features: 0
2025-12-02 11:24:22.109001 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-02 11:24:22.110806 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-02 11:24:22.112317 INFO::Filtered feature names from variance filtering:
2025-12-02 11:24:22.113755 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/features/filtered_data.tsv
2025-12-02 11:24:22.115972 INFO::Running selected transform method: LOG
2025-12-02 11:24:22.117953 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/features/data_transformed.tsv
2025-12-02 11:24:22.120645 INFO::Applying z-score to standardize continuous metadata
2025-12-02 11:24:22.128894 INFO::Running the linear model component
2025-12-02 11:24:22.15223 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:22.159101 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:22.166044 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:22.177104 INFO::Counting total values for each feature
2025-12-02 11:24:22.179998 INFO::Running the logistic model component
2025-12-02 11:24:22.20271 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:22.212846 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:22.222979 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:22.237201 INFO::Counting total values for each feature
2025-12-02 11:24:22.240801 INFO::Re-running abundances for warn_prevalence
2025-12-02 11:24:22.242362 INFO::Running selected normalization method: TSS
2025-12-02 11:24:22.244789 INFO::Running selected transform method: LOG
2025-12-02 11:24:22.268124 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:22.275023 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:22.282182 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:22.422704 INFO::Creating fits folder
2025-12-02 11:24:22.4246 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/fits/residuals_linear.rds
2025-12-02 11:24:22.426351 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/fits/fitted_linear.rds
2025-12-02 11:24:22.42827 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/fits/residuals_logistic.rds
2025-12-02 11:24:22.430118 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/fits/fitted_logistic.rds
2025-12-02 11:24:22.43432 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/all_results.tsv
2025-12-02 11:24:22.437177 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): /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/significant_results.tsv
2025-12-02 11:24:22.439398 INFO::Creating output figures folder
2025-12-02 11:24:22.441656 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/figures/summary_plot.pdf
2025-12-02 11:24:24.840884 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/figures
2025-12-02 11:24:24.843926 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 11:24:24.852104 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 11:24:25.597446 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/figures/summary_plot.pdf
2025-12-02 11:24:27.940942 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c97ab775e6/figures
2025-12-02 11:24:27.942996 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 11:24:27.950014 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 11:24:28.674301 INFO::Running the linear model component
2025-12-02 11:24:28.687934 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:28.694416 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:28.700883 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:28.711365 INFO::Counting total values for each feature
2025-12-02 11:24:28.714051 INFO::Running the logistic model component
2025-12-02 11:24:28.72767 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:28.737017 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:28.746501 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:28.760659 INFO::Counting total values for each feature
2025-12-02 11:24:28.763893 INFO::Re-running abundances for warn_prevalence
2025-12-02 11:24:28.76525 INFO::Running selected normalization method: TSS
2025-12-02 11:24:28.767453 INFO::Running selected transform method: LOG
2025-12-02 11:24:28.781853 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:28.789006 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:28.795929 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:28.956696 INFO::Creating output folder
2025-12-02 11:24:28.958203 INFO::Creating output figures folder
2025-12-02 11:24:28.96029 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c939039ef9/figures/summary_plot.pdf
2025-12-02 11:24:31.329238 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpJsBESJ/file2e97c939039ef9/figures
2025-12-02 11:24:31.331672 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 11:24:31.338865 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 11:24:32.695976 INFO::Applying z-score to standardize continuous metadata
2025-12-02 11:24:32.707412 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-02 11:24:32.70876 INFO::Bypass z-score application to metadata
2025-12-02 11:24:32.71258 INFO::Bypass z-score application to metadata
2025-12-02 11:24:32.761046 INFO::Determining format of input files
2025-12-02 11:24:32.76271 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 11:24:32.764379 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-02 11:24:32.77771 INFO::Determining format of input files
2025-12-02 11:24:32.779413 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-02 11:24:32.781667 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 11:24:32.795081 INFO::Determining format of input files
2025-12-02 11:24:32.796712 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 11:24:32.798488 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 11:24:32.801388 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-02 11:24:32.802826 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-02 11:24:32.818742 INFO::Running selected transform method: LOG
2025-12-02 11:24:32.820421 INFO::Creating output feature tables folder
2025-12-02 11:24:32.821662 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c947859be3/features/data_transformed.tsv
2025-12-02 11:24:32.82736 INFO::Running selected transform method: LOG
2025-12-02 11:24:32.829043 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c947859be3/features/data_transformed.tsv
2025-12-02 11:24:32.834692 INFO::Running selected transform method: PLOG
2025-12-02 11:24:32.837325 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c947859be3/features/data_transformed.tsv
2025-12-02 11:24:32.841599 INFO::Running selected transform method: NONE
2025-12-02 11:24:32.842911 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c947859be3/features/data_transformed.tsv
2025-12-02 11:24:32.854939 INFO::Running the linear model component
2025-12-02 11:24:32.869777 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:32.87641 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:32.882903 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:32.893625 INFO::Counting total values for each feature
2025-12-02 11:24:32.896237 INFO::Running the logistic model component
2025-12-02 11:24:32.910259 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:32.919734 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:32.929121 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:32.942627 INFO::Counting total values for each feature
2025-12-02 11:24:32.94586 INFO::Re-running abundances for warn_prevalence
2025-12-02 11:24:32.947175 INFO::Running selected normalization method: TSS
2025-12-02 11:24:32.949486 INFO::Running selected transform method: LOG
2025-12-02 11:24:32.964067 INFO::Fitting model to feature number 1, a
2025-12-02 11:24:32.970877 INFO::Fitting model to feature number 2, b
2025-12-02 11:24:32.977718 INFO::Fitting model to feature number 3, c
2025-12-02 11:24:33.115092 INFO::Creating output folder
2025-12-02 11:24:33.116575 INFO::Creating fits folder
2025-12-02 11:24:33.117821 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/fits/residuals_linear.rds
2025-12-02 11:24:33.119202 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/fits/fitted_linear.rds
2025-12-02 11:24:33.120736 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/fits/residuals_logistic.rds
2025-12-02 11:24:33.122256 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/fits/fitted_logistic.rds
2025-12-02 11:24:33.125934 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/all_results.tsv
2025-12-02 11:24:33.128206 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): /home/biocbuild/tmp/RtmpJsBESJ/file2e97c950344ec2/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
536.024 5.293 542.913
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.153 | 0.556 | 28.774 | |
| maaslin_check_arguments | 0.207 | 0.000 | 0.208 | |
| maaslin_check_formula | 0.195 | 0.008 | 0.203 | |
| maaslin_compute_formula | 0.224 | 0.007 | 0.233 | |
| maaslin_contrast_test | 28.859 | 0.320 | 29.253 | |
| maaslin_filter | 0.630 | 0.020 | 0.652 | |
| maaslin_fit | 21.520 | 0.110 | 21.683 | |
| maaslin_log_arguments | 0.203 | 0.000 | 0.205 | |
| maaslin_normalize | 0.405 | 0.012 | 0.418 | |
| maaslin_plot_results | 64.689 | 0.279 | 65.131 | |
| maaslin_plot_results_from_output | 65.439 | 0.379 | 66.010 | |
| maaslin_process_metadata | 0.696 | 0.011 | 0.709 | |
| maaslin_read_data | 0.203 | 0.004 | 0.208 | |
| maaslin_reorder_data | 0.204 | 0.008 | 0.213 | |
| maaslin_transform | 0.742 | 0.036 | 0.780 | |
| maaslin_write_results | 22.189 | 0.208 | 22.467 | |
| maaslin_write_results_lefse_format | 24.133 | 0.063 | 24.268 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |