William Nickols
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 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 2025-12-08 12:00 -0500 (Mon, 08 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| 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. |
| 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: 2025-12-05 01:23:23 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 01:45:03 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 1299.4 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 4.5.2 (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 24.04.3 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 43.781 0.338 44.086
maaslin_plot_results_from_output 43.185 0.413 43.601
maaslin3 19.249 0.545 19.796
maaslin_contrast_test 18.082 0.569 18.652
maaslin_write_results_lefse_format 15.084 0.120 15.205
maaslin_write_results 13.396 0.105 13.502
maaslin_fit 12.487 0.038 12.526
* 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")
2025-12-05 01:29:40.608193 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:29:40.700278 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:29:40.826453 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:29:40.848599 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:29:40.884397 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:29:40.969033 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:29:40.983127 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:29:40.996771 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:29:41.09577 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:29:41.101356 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:29:41.153528 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:29:41.205291 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:29:41.218497 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:29:41.2614 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:29:41.33534 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:29:56.782218 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:29:56.860625 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:29:56.935001 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:29:56.95662 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:29:56.99052 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:29:57.065027 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:29:57.070394 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:29:57.082207 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:29:57.178412 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:29:57.183696 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:29:57.232488 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:29:57.271891 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:29:57.283564 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:29:57.323768 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:29:57.405431 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:30:22.241571 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:30:22.318069 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:30:22.393807 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:30:22.415646 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:30:22.450191 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:30:22.528791 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:30:22.534735 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:30:22.547261 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:30:22.649667 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:30:22.656285 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:30:22.717661 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:30:22.7661 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:30:22.780227 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:30:22.855721 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:30:22.928326 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:30:36.019186 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:30:36.103861 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:30:36.183537 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:30:36.207121 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:30:36.242158 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:30:36.321436 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:30:36.327896 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:30:36.342133 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:30:36.445539 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:30:36.451158 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:30:36.502251 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:30:36.562684 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:30:36.574782 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:30:36.61602 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:30:36.68718 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:30:36.893695 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_linear.rds
2025-12-05 01:30:36.954734 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_linear.rds
2025-12-05 01:30:37.018377 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_logistic.rds
2025-12-05 01:30:37.318184 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_logistic.rds
2025-12-05 01:31:00.439159 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:31:00.524518 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:31:00.609276 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:31:00.634288 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:31:00.673037 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:31:00.769725 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:31:00.775192 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:31:00.786898 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:31:00.882802 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:31:00.888484 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:31:00.938536 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:31:00.980186 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:31:00.992008 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:31:01.032015 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:31:01.101884 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:31:12.957475 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:31:13.033143 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:31:13.108035 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:31:13.130467 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:31:13.165514 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:31:13.239474 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:31:13.244714 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:31:13.256276 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:31:13.350003 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:31:13.355531 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:31:13.405742 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:31:13.446217 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:31:13.458454 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:31:13.499066 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:31:13.569889 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:31:13.816966 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_linear.rds
2025-12-05 01:31:13.877944 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_linear.rds
2025-12-05 01:31:13.940944 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_logistic.rds
2025-12-05 01:31:14.239812 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_logistic.rds
2025-12-05 01:31:36.950075 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:31:37.030203 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:31:37.107244 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:31:37.130594 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:31:37.167941 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:31:37.244737 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:31:37.250272 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:31:37.262245 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:31:37.358203 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:31:37.363716 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:31:37.41392 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:31:37.454773 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:31:37.46749 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:31:37.50983 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:31:37.582154 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:31:48.480429 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:31:48.559915 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:31:48.636852 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:31:48.658911 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:31:48.717753 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:31:48.794494 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:31:48.799973 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:31:48.812091 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:31:48.953918 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:31:48.959779 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:31:49.010736 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:31:49.05114 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:31:49.063212 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:31:49.103712 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:31:49.172466 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:31:49.37758 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_linear.rds
2025-12-05 01:31:49.438816 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_linear.rds
2025-12-05 01:31:49.501678 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/residuals_logistic.rds
2025-12-05 01:31:49.800634 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba62e90b009/fits/fitted_logistic.rds
2025-12-05 01:32:12.675164 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:32:12.757626 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:32:12.837098 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:32:12.886529 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:32:12.924337 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:32:13.006063 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:32:13.011636 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:32:13.024933 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:32:13.12801 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:32:13.133838 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:32:13.184009 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:32:13.225931 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:32:13.238194 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:32:13.278799 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:32:13.349585 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:32:24.181134 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:32:24.256414 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:32:24.330323 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:32:24.35187 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:32:24.385931 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:32:24.490821 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:32:24.496364 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:32:24.508453 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:32:24.604595 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:32:24.610088 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:32:24.660215 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:32:24.700185 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:32:24.711998 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:32:24.752316 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:32:24.822213 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:32:49.502652 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:32:58.424959 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:33:23.745269 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:33:33.886433 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:33:34.549712 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_linear.rds
2025-12-05 01:33:34.611946 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_linear.rds
2025-12-05 01:33:34.651178 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_logistic.rds
2025-12-05 01:33:34.721985 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_logistic.rds
2025-12-05 01:33:57.618446 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:34:04.025884 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:34:04.370383 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_linear.rds
2025-12-05 01:34:04.432438 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_linear.rds
2025-12-05 01:34:04.471767 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_logistic.rds
2025-12-05 01:34:04.541273 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_logistic.rds
2025-12-05 01:34:23.415283 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:34:29.721949 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:34:30.025456 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_linear.rds
2025-12-05 01:34:30.088362 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_linear.rds
2025-12-05 01:34:30.128541 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_logistic.rds
2025-12-05 01:34:30.200424 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_logistic.rds
2025-12-05 01:34:49.430475 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:34:49.548531 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:34:49.626214 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:34:49.649295 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:34:49.685523 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:34:49.763633 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:34:49.769269 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:34:49.781529 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:34:49.882978 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:34:49.888666 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:34:49.940875 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:34:49.982762 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:34:49.995198 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:34:50.037707 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:34:50.109458 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:35:01.120149 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:35:01.200313 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:35:01.284455 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:35:01.307551 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:35:01.342302 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:35:01.418794 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:35:01.424226 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:35:01.436025 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:35:01.531313 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:35:01.536802 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:35:01.589103 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:35:01.630607 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:35:01.643026 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:35:01.68467 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:35:01.755106 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:35:02.036222 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_linear.rds
2025-12-05 01:35:02.096997 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_linear.rds
2025-12-05 01:35:02.15981 WARNING::Deleting existing residuals file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/residuals_logistic.rds
2025-12-05 01:35:02.458352 WARNING::Deleting existing fitted file: /tmp/Rtmp8FC5Qz/file343ba64e71f4ec/fits/fitted_logistic.rds
2025-12-05 01:35:23.587564 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-05 01:35:23.604892 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-05 01:35:23.616364 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-05 01:35:23.668299 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-05 01:35:23.685169 ERROR::Effect name not found in metadata: d
2025-12-05 01:35:23.696349 ERROR::No user formula provided
2025-12-05 01:35:23.728079 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-05 01:35:23.74086 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-05 01:35:26.646868 INFO::Writing function arguments to log file
2025-12-05 01:35:26.661695 INFO::Verifying options selected are valid
2025-12-05 01:35:29.07232 INFO::Writing function arguments to log file
2025-12-05 01:35:29.085722 INFO::Verifying options selected are valid
2025-12-05 01:35:29.086932 INFO::Determining format of input files
2025-12-05 01:35:29.088008 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:35:29.090545 INFO::Running selected normalization method: TSS
2025-12-05 01:35:29.092102 INFO::Creating output feature tables folder
2025-12-05 01:35:29.093135 INFO::Writing normalized data to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/features/data_norm.tsv
2025-12-05 01:35:29.094758 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-05 01:35:29.095723 INFO::Total samples in data: 16
2025-12-05 01:35:29.096679 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-05 01:35:29.097584 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-05 01:35:29.099694 INFO::Total filtered features: 0
2025-12-05 01:35:29.100705 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-05 01:35:29.101919 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-05 01:35:29.10289 INFO::Filtered feature names from variance filtering:
2025-12-05 01:35:29.103815 INFO::Writing filtered data to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/features/filtered_data.tsv
2025-12-05 01:35:29.105364 INFO::Running selected transform method: LOG
2025-12-05 01:35:29.106635 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/features/data_transformed.tsv
2025-12-05 01:35:29.108352 INFO::Applying z-score to standardize continuous metadata
2025-12-05 01:35:29.114331 INFO::Running the linear model component
2025-12-05 01:35:29.13083 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:29.135798 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:29.140435 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:29.148406 INFO::Counting total values for each feature
2025-12-05 01:35:29.150478 INFO::Running the logistic model component
2025-12-05 01:35:29.165486 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:29.172467 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:29.179195 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:29.189235 INFO::Counting total values for each feature
2025-12-05 01:35:29.191661 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:35:29.192688 INFO::Running selected normalization method: TSS
2025-12-05 01:35:29.194325 INFO::Running selected transform method: LOG
2025-12-05 01:35:29.209358 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:29.214664 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:29.219517 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:29.3131 INFO::Creating fits folder
2025-12-05 01:35:29.314456 INFO::Writing residuals to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/fits/residuals_linear.rds
2025-12-05 01:35:29.315704 INFO::Writing fitted values to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/fits/fitted_linear.rds
2025-12-05 01:35:29.317027 INFO::Writing residuals to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/fits/residuals_logistic.rds
2025-12-05 01:35:29.318283 INFO::Writing fitted values to file /tmp/Rtmp8FC5Qz/file343ba67ddb3467/fits/fitted_logistic.rds
2025-12-05 01:35:29.321156 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp8FC5Qz/file343ba67ddb3467/all_results.tsv
2025-12-05 01:35:29.322914 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/Rtmp8FC5Qz/file343ba67ddb3467/significant_results.tsv
2025-12-05 01:35:29.324347 INFO::Creating output figures folder
2025-12-05 01:35:29.325804 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp8FC5Qz/file343ba67ddb3467/figures/summary_plot.pdf
2025-12-05 01:35:30.971699 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp8FC5Qz/file343ba67ddb3467/figures
2025-12-05 01:35:30.973711 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:35:30.978791 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:35:31.501749 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp8FC5Qz/file343ba67ddb3467/figures/summary_plot.pdf
2025-12-05 01:35:33.130161 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp8FC5Qz/file343ba67ddb3467/figures
2025-12-05 01:35:33.131801 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:35:33.136783 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:35:33.661416 INFO::Running the linear model component
2025-12-05 01:35:33.670426 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:33.675066 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:33.679386 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:33.686503 INFO::Counting total values for each feature
2025-12-05 01:35:33.688184 INFO::Running the logistic model component
2025-12-05 01:35:33.696627 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:33.703283 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:33.709434 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:33.718574 INFO::Counting total values for each feature
2025-12-05 01:35:33.72066 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:35:33.721451 INFO::Running selected normalization method: TSS
2025-12-05 01:35:33.722793 INFO::Running selected transform method: LOG
2025-12-05 01:35:33.731372 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:33.735842 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:33.740114 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:33.827724 INFO::Creating output folder
2025-12-05 01:35:33.828687 INFO::Creating output figures folder
2025-12-05 01:35:33.829882 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp8FC5Qz/file343ba62bbe5995/figures/summary_plot.pdf
2025-12-05 01:35:35.444828 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp8FC5Qz/file343ba62bbe5995/figures
2025-12-05 01:35:35.446585 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:35:35.451483 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:35:36.50955 INFO::Applying z-score to standardize continuous metadata
2025-12-05 01:35:36.517394 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-05 01:35:36.518297 INFO::Bypass z-score application to metadata
2025-12-05 01:35:36.520838 INFO::Bypass z-score application to metadata
2025-12-05 01:35:36.539716 INFO::Determining format of input files
2025-12-05 01:35:36.540713 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:35:36.54158 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-05 01:35:36.549037 INFO::Determining format of input files
2025-12-05 01:35:36.550049 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-05 01:35:36.551345 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 01:35:36.559567 INFO::Determining format of input files
2025-12-05 01:35:36.560503 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:35:36.561543 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 01:35:36.563221 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-05 01:35:36.564012 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-05 01:35:36.575531 INFO::Running selected transform method: LOG
2025-12-05 01:35:36.576635 INFO::Creating output feature tables folder
2025-12-05 01:35:36.577479 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp8FC5Qz/file343ba644891439/features/data_transformed.tsv
2025-12-05 01:35:36.581277 INFO::Running selected transform method: LOG
2025-12-05 01:35:36.582286 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp8FC5Qz/file343ba644891439/features/data_transformed.tsv
2025-12-05 01:35:36.586162 INFO::Running selected transform method: PLOG
2025-12-05 01:35:36.587762 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp8FC5Qz/file343ba644891439/features/data_transformed.tsv
2025-12-05 01:35:36.590665 INFO::Running selected transform method: NONE
2025-12-05 01:35:36.591412 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp8FC5Qz/file343ba644891439/features/data_transformed.tsv
2025-12-05 01:35:36.599297 INFO::Running the linear model component
2025-12-05 01:35:36.608039 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:36.612424 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:36.616721 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:36.623959 INFO::Counting total values for each feature
2025-12-05 01:35:36.625697 INFO::Running the logistic model component
2025-12-05 01:35:36.634463 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:36.640736 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:36.660373 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:36.671265 INFO::Counting total values for each feature
2025-12-05 01:35:36.67394 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:35:36.674977 INFO::Running selected normalization method: TSS
2025-12-05 01:35:36.676652 INFO::Running selected transform method: LOG
2025-12-05 01:35:36.68821 INFO::Fitting model to feature number 1, a
2025-12-05 01:35:36.693869 INFO::Fitting model to feature number 2, b
2025-12-05 01:35:36.698818 INFO::Fitting model to feature number 3, c
2025-12-05 01:35:36.78958 INFO::Creating output folder
2025-12-05 01:35:36.790575 INFO::Creating fits folder
2025-12-05 01:35:36.791388 INFO::Writing residuals to file /tmp/Rtmp8FC5Qz/file343ba658652d7/fits/residuals_linear.rds
2025-12-05 01:35:36.792403 INFO::Writing fitted values to file /tmp/Rtmp8FC5Qz/file343ba658652d7/fits/fitted_linear.rds
2025-12-05 01:35:36.793445 INFO::Writing residuals to file /tmp/Rtmp8FC5Qz/file343ba658652d7/fits/residuals_logistic.rds
2025-12-05 01:35:36.794468 INFO::Writing fitted values to file /tmp/Rtmp8FC5Qz/file343ba658652d7/fits/fitted_logistic.rds
2025-12-05 01:35:36.796975 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp8FC5Qz/file343ba658652d7/all_results.tsv
2025-12-05 01:35:36.798489 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/Rtmp8FC5Qz/file343ba658652d7/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.676 6.312 368.977
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.249 | 0.545 | 19.796 | |
| maaslin_check_arguments | 0.140 | 0.001 | 0.140 | |
| maaslin_check_formula | 0.136 | 0.003 | 0.138 | |
| maaslin_compute_formula | 0.165 | 0.002 | 0.166 | |
| maaslin_contrast_test | 18.082 | 0.569 | 18.652 | |
| maaslin_filter | 0.438 | 0.005 | 0.444 | |
| maaslin_fit | 12.487 | 0.038 | 12.526 | |
| maaslin_log_arguments | 0.156 | 0.003 | 0.159 | |
| maaslin_normalize | 0.274 | 0.006 | 0.280 | |
| maaslin_plot_results | 43.781 | 0.338 | 44.086 | |
| maaslin_plot_results_from_output | 43.185 | 0.413 | 43.601 | |
| maaslin_process_metadata | 0.450 | 0.015 | 0.464 | |
| maaslin_read_data | 0.126 | 0.000 | 0.126 | |
| maaslin_reorder_data | 0.135 | 0.004 | 0.139 | |
| maaslin_transform | 0.601 | 0.018 | 0.619 | |
| maaslin_write_results | 13.396 | 0.105 | 13.502 | |
| maaslin_write_results_lefse_format | 15.084 | 0.120 | 15.205 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.004 | |