William Nickols
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-11 12:02 -0500 (Tue, 11 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-11-11 01:11:38 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 01:33:24 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 1306.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 43.331 0.315 43.609
maaslin_plot_results_from_output 43.219 0.369 43.592
maaslin3 19.565 0.509 20.275
maaslin_contrast_test 18.447 0.348 18.796
maaslin_write_results_lefse_format 14.758 0.062 14.822
maaslin_write_results 14.119 0.208 14.338
maaslin_fit 12.859 0.084 12.954
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-11 01:17:54.944971 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:17:55.022779 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:17:55.125537 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:17:55.14909 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:17:55.186044 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:17:55.283074 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:17:55.288516 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:17:55.30064 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:17:55.425724 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:17:55.431813 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:17:55.484035 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:17:55.525857 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:17:55.538064 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:17:55.57939 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:17:55.658926 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:18:12.734101 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:18:12.811698 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:18:12.888645 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:18:12.911557 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:18:12.947883 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:18:13.040287 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:18:13.045902 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:18:13.058022 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:18:13.153363 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:18:13.15877 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:18:13.209197 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:18:13.249759 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:18:13.261671 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:18:13.303387 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:18:13.372734 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:18:38.52489 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:18:38.60797 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:18:38.683352 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:18:38.706342 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:18:38.740187 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:18:38.815984 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:18:38.821788 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:18:38.836457 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:18:38.935419 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:18:38.941127 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:18:38.99732 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:18:39.042429 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:18:39.056189 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:18:39.121578 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:18:39.192592 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:18:52.155128 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:18:52.233334 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:18:52.312804 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:18:52.336911 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:18:52.37432 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:18:52.452918 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:18:52.458436 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:18:52.470588 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:18:52.570475 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:18:52.576299 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:18:52.647727 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:18:52.688706 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:18:52.701001 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:18:52.744036 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:18:52.815382 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:18:53.018742 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_linear.rds
2025-11-11 01:18:53.080473 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_linear.rds
2025-11-11 01:18:53.143777 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_logistic.rds
2025-11-11 01:18:53.442602 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_logistic.rds
2025-11-11 01:19:15.957935 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:19:16.04739 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:19:16.141582 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:19:16.167441 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:19:16.209334 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:19:16.301124 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:19:16.307443 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:19:16.322273 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:19:16.437205 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:19:16.443488 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:19:16.503859 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:19:16.551005 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:19:16.564786 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:19:16.611538 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:19:16.712709 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:19:28.745523 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:19:28.819752 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:19:28.892846 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:19:28.914397 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:19:28.94829 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:19:29.024487 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:19:29.030102 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:19:29.042603 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:19:29.142942 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:19:29.149145 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:19:29.203082 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:19:29.248583 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:19:29.261163 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:19:29.304829 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:19:29.375981 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:19:29.59564 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_linear.rds
2025-11-11 01:19:29.656379 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_linear.rds
2025-11-11 01:19:29.718999 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_logistic.rds
2025-11-11 01:19:30.018205 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_logistic.rds
2025-11-11 01:19:51.963161 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:19:52.050386 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:19:52.138377 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:19:52.16448 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:19:52.20259 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:19:52.287871 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:19:52.293925 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:19:52.307894 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:19:52.418634 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:19:52.425183 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:19:52.48448 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:19:52.527737 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:19:52.541194 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:19:52.585394 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:19:52.659351 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:20:04.844202 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:20:04.922713 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:20:04.99905 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:20:05.020544 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:20:05.054056 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:20:05.15473 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:20:05.16044 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:20:05.173176 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:20:05.271063 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:20:05.276667 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:20:05.327157 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:20:05.367868 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:20:05.380224 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:20:05.421893 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:20:05.49366 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:20:05.694945 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_linear.rds
2025-11-11 01:20:05.756224 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_linear.rds
2025-11-11 01:20:05.819231 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/residuals_logistic.rds
2025-11-11 01:20:06.118469 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d7c798a94/fits/fitted_logistic.rds
2025-11-11 01:20:27.979 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:20:28.063926 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:20:28.149934 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:20:28.175134 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:20:28.215011 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:20:28.329815 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:20:28.336018 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:20:28.348561 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:20:28.445052 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:20:28.450568 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:20:28.500833 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:20:28.5416 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:20:28.553809 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:20:28.597406 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:20:28.670203 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:20:41.669936 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:20:41.755874 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:20:41.842011 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:20:41.867031 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:20:41.905853 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:20:41.993516 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:20:42.000099 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:20:42.013884 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:20:42.121874 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:20:42.128507 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:20:42.184993 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:20:42.229221 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:20:42.242808 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:20:42.290426 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:20:42.371202 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:21:07.513222 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:21:17.763698 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:21:42.733694 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:21:52.721214 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:21:53.365536 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_linear.rds
2025-11-11 01:21:53.444992 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_linear.rds
2025-11-11 01:21:53.483273 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_logistic.rds
2025-11-11 01:21:53.551223 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_logistic.rds
2025-11-11 01:22:16.7619 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:22:24.079976 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:22:24.437656 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_linear.rds
2025-11-11 01:22:24.499232 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_linear.rds
2025-11-11 01:22:24.537593 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_logistic.rds
2025-11-11 01:22:24.608498 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_logistic.rds
2025-11-11 01:22:43.215183 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:22:49.578972 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 01:22:49.894108 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_linear.rds
2025-11-11 01:22:49.95578 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_linear.rds
2025-11-11 01:22:49.993967 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_logistic.rds
2025-11-11 01:22:50.06221 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_logistic.rds
2025-11-11 01:23:08.556519 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:23:08.637128 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:23:08.716325 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:23:08.739317 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:23:08.775444 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:23:08.8565 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:23:08.861865 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:23:08.874061 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:23:08.982666 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:23:08.990767 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:23:09.048144 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:23:09.08937 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:23:09.101492 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:23:09.143168 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:23:09.214134 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:23:22.271948 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 01:23:22.349216 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 01:23:22.426482 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 01:23:22.44924 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 01:23:22.486165 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 01:23:22.56703 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 01:23:22.572909 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 01:23:22.585715 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 01:23:22.686425 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 01:23:22.692036 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 01:23:22.745349 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 01:23:22.791599 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 01:23:22.804725 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 01:23:22.848903 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 01:23:22.92253 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 01:23:23.237188 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_linear.rds
2025-11-11 01:23:23.298018 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_linear.rds
2025-11-11 01:23:23.360865 WARNING::Deleting existing residuals file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/residuals_logistic.rds
2025-11-11 01:23:23.663091 WARNING::Deleting existing fitted file: /tmp/RtmpH1BBSE/file71b1d64b32133/fits/fitted_logistic.rds
2025-11-11 01:23:44.310537 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-11 01:23:44.32706 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-11 01:23:44.338353 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-11 01:23:44.388562 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-11 01:23:44.404558 ERROR::Effect name not found in metadata: d
2025-11-11 01:23:44.415564 ERROR::No user formula provided
2025-11-11 01:23:44.444447 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-11 01:23:44.456069 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-11 01:23:47.335486 INFO::Writing function arguments to log file
2025-11-11 01:23:47.349899 INFO::Verifying options selected are valid
2025-11-11 01:23:49.735343 INFO::Writing function arguments to log file
2025-11-11 01:23:49.747525 INFO::Verifying options selected are valid
2025-11-11 01:23:49.748611 INFO::Determining format of input files
2025-11-11 01:23:49.749586 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 01:23:49.7519 INFO::Running selected normalization method: TSS
2025-11-11 01:23:49.753362 INFO::Creating output feature tables folder
2025-11-11 01:23:49.754303 INFO::Writing normalized data to file /tmp/RtmpH1BBSE/file71b1d2580e833/features/data_norm.tsv
2025-11-11 01:23:49.755751 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-11 01:23:49.756639 INFO::Total samples in data: 16
2025-11-11 01:23:49.757492 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-11 01:23:49.758336 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-11 01:23:49.76021 INFO::Total filtered features: 0
2025-11-11 01:23:49.761157 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-11 01:23:49.762324 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-11 01:23:49.763297 INFO::Filtered feature names from variance filtering:
2025-11-11 01:23:49.764172 INFO::Writing filtered data to file /tmp/RtmpH1BBSE/file71b1d2580e833/features/filtered_data.tsv
2025-11-11 01:23:49.765638 INFO::Running selected transform method: LOG
2025-11-11 01:23:49.766843 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpH1BBSE/file71b1d2580e833/features/data_transformed.tsv
2025-11-11 01:23:49.768503 INFO::Applying z-score to standardize continuous metadata
2025-11-11 01:23:49.77398 INFO::Running the linear model component
2025-11-11 01:23:49.787779 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:49.792391 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:49.7967 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:49.804105 INFO::Counting total values for each feature
2025-11-11 01:23:49.806113 INFO::Running the logistic model component
2025-11-11 01:23:49.820743 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:49.828485 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:49.83533 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:49.84537 INFO::Counting total values for each feature
2025-11-11 01:23:49.847629 INFO::Re-running abundances for warn_prevalence
2025-11-11 01:23:49.848586 INFO::Running selected normalization method: TSS
2025-11-11 01:23:49.850113 INFO::Running selected transform method: LOG
2025-11-11 01:23:49.864368 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:49.868874 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:49.873248 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:49.963059 INFO::Creating fits folder
2025-11-11 01:23:49.964414 INFO::Writing residuals to file /tmp/RtmpH1BBSE/file71b1d2580e833/fits/residuals_linear.rds
2025-11-11 01:23:49.965668 INFO::Writing fitted values to file /tmp/RtmpH1BBSE/file71b1d2580e833/fits/fitted_linear.rds
2025-11-11 01:23:49.966966 INFO::Writing residuals to file /tmp/RtmpH1BBSE/file71b1d2580e833/fits/residuals_logistic.rds
2025-11-11 01:23:49.968204 INFO::Writing fitted values to file /tmp/RtmpH1BBSE/file71b1d2580e833/fits/fitted_logistic.rds
2025-11-11 01:23:49.970858 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpH1BBSE/file71b1d2580e833/all_results.tsv
2025-11-11 01:23:49.972495 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/RtmpH1BBSE/file71b1d2580e833/significant_results.tsv
2025-11-11 01:23:49.973814 INFO::Creating output figures folder
2025-11-11 01:23:49.975152 INFO::Writing summary plot of significant
results to file: /tmp/RtmpH1BBSE/file71b1d2580e833/figures/summary_plot.pdf
2025-11-11 01:23:51.73691 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpH1BBSE/file71b1d2580e833/figures
2025-11-11 01:23:51.738828 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 01:23:51.744146 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 01:23:52.310357 INFO::Writing summary plot of
significant results to file: /tmp/RtmpH1BBSE/file71b1d2580e833/figures/summary_plot.pdf
2025-11-11 01:23:54.019085 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpH1BBSE/file71b1d2580e833/figures
2025-11-11 01:23:54.021086 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 01:23:54.026789 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 01:23:54.600736 INFO::Running the linear model component
2025-11-11 01:23:54.610996 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:54.616954 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:54.622433 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:54.631038 INFO::Counting total values for each feature
2025-11-11 01:23:54.633031 INFO::Running the logistic model component
2025-11-11 01:23:54.642192 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:54.6495 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:54.656125 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:54.665813 INFO::Counting total values for each feature
2025-11-11 01:23:54.668111 INFO::Re-running abundances for warn_prevalence
2025-11-11 01:23:54.668988 INFO::Running selected normalization method: TSS
2025-11-11 01:23:54.670492 INFO::Running selected transform method: LOG
2025-11-11 01:23:54.679599 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:54.684052 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:54.688419 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:54.787786 INFO::Creating output folder
2025-11-11 01:23:54.78896 INFO::Creating output figures folder
2025-11-11 01:23:54.790318 INFO::Writing summary plot of significant
results to file: /tmp/RtmpH1BBSE/file71b1d50eeea1a/figures/summary_plot.pdf
2025-11-11 01:23:56.447851 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpH1BBSE/file71b1d50eeea1a/figures
2025-11-11 01:23:56.450081 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 01:23:56.456014 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 01:23:57.412106 INFO::Applying z-score to standardize continuous metadata
2025-11-11 01:23:57.419706 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-11 01:23:57.420549 INFO::Bypass z-score application to metadata
2025-11-11 01:23:57.422865 INFO::Bypass z-score application to metadata
2025-11-11 01:23:57.439294 INFO::Determining format of input files
2025-11-11 01:23:57.440197 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 01:23:57.441009 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-11 01:23:57.447688 INFO::Determining format of input files
2025-11-11 01:23:57.448649 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-11 01:23:57.449899 INFO::Input format is feature_specific_covariate samples as columns
2025-11-11 01:23:57.457354 INFO::Determining format of input files
2025-11-11 01:23:57.458235 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 01:23:57.459211 INFO::Input format is feature_specific_covariate samples as columns
2025-11-11 01:23:57.460806 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-11 01:23:57.461558 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-11 01:23:57.471543 INFO::Running selected transform method: LOG
2025-11-11 01:23:57.472582 INFO::Creating output feature tables folder
2025-11-11 01:23:57.473391 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpH1BBSE/file71b1d2f0f1bd7/features/data_transformed.tsv
2025-11-11 01:23:57.476886 INFO::Running selected transform method: LOG
2025-11-11 01:23:57.47786 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpH1BBSE/file71b1d2f0f1bd7/features/data_transformed.tsv
2025-11-11 01:23:57.481452 INFO::Running selected transform method: PLOG
2025-11-11 01:23:57.482975 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpH1BBSE/file71b1d2f0f1bd7/features/data_transformed.tsv
2025-11-11 01:23:57.485637 INFO::Running selected transform method: NONE
2025-11-11 01:23:57.486368 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpH1BBSE/file71b1d2f0f1bd7/features/data_transformed.tsv
2025-11-11 01:23:57.492994 INFO::Running the linear model component
2025-11-11 01:23:57.501437 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:57.505645 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:57.509586 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:57.516592 INFO::Counting total values for each feature
2025-11-11 01:23:57.518198 INFO::Running the logistic model component
2025-11-11 01:23:57.526501 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:57.53261 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:57.538398 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:57.547083 INFO::Counting total values for each feature
2025-11-11 01:23:57.54903 INFO::Re-running abundances for warn_prevalence
2025-11-11 01:23:57.560327 INFO::Running selected normalization method: TSS
2025-11-11 01:23:57.562673 INFO::Running selected transform method: LOG
2025-11-11 01:23:57.572753 INFO::Fitting model to feature number 1, a
2025-11-11 01:23:57.577318 INFO::Fitting model to feature number 2, b
2025-11-11 01:23:57.581734 INFO::Fitting model to feature number 3, c
2025-11-11 01:23:57.674792 INFO::Creating output folder
2025-11-11 01:23:57.675778 INFO::Creating fits folder
2025-11-11 01:23:57.676632 INFO::Writing residuals to file /tmp/RtmpH1BBSE/file71b1d310e53eb/fits/residuals_linear.rds
2025-11-11 01:23:57.677619 INFO::Writing fitted values to file /tmp/RtmpH1BBSE/file71b1d310e53eb/fits/fitted_linear.rds
2025-11-11 01:23:57.678651 INFO::Writing residuals to file /tmp/RtmpH1BBSE/file71b1d310e53eb/fits/residuals_logistic.rds
2025-11-11 01:23:57.679664 INFO::Writing fitted values to file /tmp/RtmpH1BBSE/file71b1d310e53eb/fits/fitted_logistic.rds
2025-11-11 01:23:57.682191 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpH1BBSE/file71b1d310e53eb/all_results.tsv
2025-11-11 01:23:57.683673 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/RtmpH1BBSE/file71b1d310e53eb/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
368.931 6.216 375.119
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.565 | 0.509 | 20.275 | |
| maaslin_check_arguments | 0.139 | 0.001 | 0.139 | |
| maaslin_check_formula | 0.132 | 0.003 | 0.135 | |
| maaslin_compute_formula | 0.155 | 0.000 | 0.155 | |
| maaslin_contrast_test | 18.447 | 0.348 | 18.796 | |
| maaslin_filter | 0.445 | 0.020 | 0.465 | |
| maaslin_fit | 12.859 | 0.084 | 12.954 | |
| maaslin_log_arguments | 0.126 | 0.002 | 0.129 | |
| maaslin_normalize | 0.259 | 0.004 | 0.264 | |
| maaslin_plot_results | 43.331 | 0.315 | 43.609 | |
| maaslin_plot_results_from_output | 43.219 | 0.369 | 43.592 | |
| maaslin_process_metadata | 0.462 | 0.012 | 0.474 | |
| maaslin_read_data | 0.127 | 0.004 | 0.130 | |
| maaslin_reorder_data | 0.129 | 0.003 | 0.131 | |
| maaslin_transform | 0.553 | 0.022 | 0.574 | |
| maaslin_write_results | 14.119 | 0.208 | 14.338 | |
| maaslin_write_results_lefse_format | 14.758 | 0.062 | 14.822 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |