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 12:00 -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. |
| 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: 2025-12-02 01:24:45 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 01:46:28 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 1303.4 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_from_output 43.789 0.489 44.419
maaslin_plot_results 43.508 0.328 43.808
maaslin3 19.150 0.486 19.639
maaslin_contrast_test 18.151 0.280 18.435
maaslin_write_results_lefse_format 14.596 0.093 14.690
maaslin_write_results 13.404 0.136 13.554
maaslin_fit 13.396 0.103 13.499
* 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")
2025-12-02 01:31:12.527891 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:31:12.617325 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:31:12.72361 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:31:12.746526 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:31:12.781241 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:31:12.859978 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:31:12.865569 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:31:12.877949 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:31:12.980255 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:31:12.985745 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:31:13.036185 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:31:13.090931 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:31:13.122768 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:31:13.163694 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:31:13.240032 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:31:27.922322 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:31:28.019032 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:31:28.099696 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:31:28.124226 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:31:28.162776 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:31:28.241947 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:31:28.247208 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:31:28.258746 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:31:28.364471 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:31:28.370381 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:31:28.420128 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:31:28.459379 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:31:28.470863 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:31:28.514646 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:31:28.603145 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:31:53.137438 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:31:53.216149 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:31:53.295523 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:31:53.318237 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:31:53.352258 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:31:53.42826 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:31:53.434384 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:31:53.446828 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:31:53.543931 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:31:53.549414 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:31:53.598981 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:31:53.638698 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:31:53.650416 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:31:53.691557 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:31:53.761247 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:32:06.390332 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:32:06.463985 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:32:06.537234 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:32:06.558667 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:32:06.592194 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:32:06.666347 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:32:06.671532 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:32:06.682922 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:32:06.795281 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:32:06.800655 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:32:06.849319 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:32:06.888859 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:32:06.901086 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:32:06.941267 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:32:07.00863 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:32:07.206172 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_linear.rds
2025-12-02 01:32:07.266993 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_linear.rds
2025-12-02 01:32:07.329751 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_logistic.rds
2025-12-02 01:32:07.62912 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_logistic.rds
2025-12-02 01:32:29.137631 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:32:29.212104 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:32:29.285445 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:32:29.307243 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:32:29.340705 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:32:29.414584 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:32:29.419817 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:32:29.431428 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:32:29.528352 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:32:29.534196 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:32:29.584327 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:32:30.637857 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:32:30.650178 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:32:30.691292 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:32:30.758815 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:32:42.269684 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:32:42.344573 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:32:42.418067 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:32:42.439774 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:32:42.474712 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:32:42.548522 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:32:42.553962 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:32:42.565896 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:32:42.659678 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:32:42.69069 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:32:42.740725 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:32:42.780775 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:32:42.792474 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:32:42.832465 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:32:42.899681 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:32:43.099557 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_linear.rds
2025-12-02 01:32:43.160604 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_linear.rds
2025-12-02 01:32:43.22346 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_logistic.rds
2025-12-02 01:32:43.522391 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_logistic.rds
2025-12-02 01:33:05.043057 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:33:05.126381 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:33:05.232146 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:33:05.254709 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:33:05.289987 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:33:05.36656 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:33:05.37198 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:33:05.383856 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:33:05.482759 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:33:05.488367 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:33:05.539599 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:33:05.581704 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:33:05.593778 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:33:05.6348 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:33:05.70731 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:33:17.758229 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:33:17.834187 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:33:17.909401 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:33:17.931176 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:33:17.965148 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:33:18.040776 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:33:18.046168 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:33:18.057986 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:33:18.158487 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:33:18.1648 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:33:18.215852 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:33:18.257671 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:33:18.269996 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:33:18.309787 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:33:18.378307 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:33:18.597687 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_linear.rds
2025-12-02 01:33:18.658545 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_linear.rds
2025-12-02 01:33:18.721522 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/residuals_logistic.rds
2025-12-02 01:33:19.020802 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e56345956a/fits/fitted_logistic.rds
2025-12-02 01:33:40.559741 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:33:40.635058 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:33:40.710589 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:33:40.732683 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:33:40.768633 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:33:40.843819 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:33:40.849306 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:33:40.861493 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:33:40.963732 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:33:40.969543 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:33:41.020893 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:33:41.097291 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:33:41.110054 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:33:41.151602 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:33:41.221092 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:33:52.977452 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:33:53.056592 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:33:53.134492 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:33:53.156878 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:33:53.190797 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:33:53.266926 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:33:53.272539 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:33:53.284246 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:33:53.377959 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:33:53.383458 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:33:53.433516 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:33:53.473627 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:33:53.485364 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:33:53.524994 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:33:53.592475 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:34:17.578045 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:34:27.381549 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:34:52.232965 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:02.423419 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:03.027691 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_linear.rds
2025-12-02 01:35:03.089758 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_linear.rds
2025-12-02 01:35:03.128212 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_logistic.rds
2025-12-02 01:35:03.19754 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_logistic.rds
2025-12-02 01:35:26.681353 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:32.758423 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:33.065036 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_linear.rds
2025-12-02 01:35:33.127136 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_linear.rds
2025-12-02 01:35:33.16627 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_logistic.rds
2025-12-02 01:35:33.237107 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_logistic.rds
2025-12-02 01:35:51.97599 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:58.161219 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 01:35:58.488537 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_linear.rds
2025-12-02 01:35:58.551291 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_linear.rds
2025-12-02 01:35:58.590614 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_logistic.rds
2025-12-02 01:35:58.662333 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_logistic.rds
2025-12-02 01:36:16.734529 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:36:16.812541 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:36:16.890418 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:36:16.913515 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:36:16.950566 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:36:17.058545 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:36:17.063973 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:36:17.07589 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:36:17.172273 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:36:17.177913 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:36:17.228977 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:36:17.269476 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:36:17.281687 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:36:17.322817 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:36:17.393213 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:36:29.204767 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 01:36:29.281785 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 01:36:29.356375 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 01:36:29.378453 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 01:36:29.41352 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 01:36:29.488768 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 01:36:29.49408 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 01:36:29.505769 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 01:36:29.599642 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 01:36:29.60518 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 01:36:29.654418 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 01:36:29.693962 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 01:36:29.706691 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 01:36:29.747194 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 01:36:29.814663 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 01:36:30.062163 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_linear.rds
2025-12-02 01:36:30.124576 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_linear.rds
2025-12-02 01:36:30.188358 WARNING::Deleting existing residuals file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/residuals_logistic.rds
2025-12-02 01:36:30.490685 WARNING::Deleting existing fitted file: /tmp/RtmpOwuhS9/filead4e5e3d4f29/fits/fitted_logistic.rds
2025-12-02 01:36:50.959469 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-02 01:36:50.976582 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-02 01:36:50.988108 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-02 01:36:51.037968 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-02 01:36:51.054235 ERROR::Effect name not found in metadata: d
2025-12-02 01:36:51.065246 ERROR::No user formula provided
2025-12-02 01:36:51.095903 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-02 01:36:51.107076 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-02 01:36:55.213016 INFO::Writing function arguments to log file
2025-12-02 01:36:55.228129 INFO::Verifying options selected are valid
2025-12-02 01:36:57.612491 INFO::Writing function arguments to log file
2025-12-02 01:36:57.624199 INFO::Verifying options selected are valid
2025-12-02 01:36:57.625272 INFO::Determining format of input files
2025-12-02 01:36:57.626243 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 01:36:57.62858 INFO::Running selected normalization method: TSS
2025-12-02 01:36:57.63007 INFO::Creating output feature tables folder
2025-12-02 01:36:57.63102 INFO::Writing normalized data to file /tmp/RtmpOwuhS9/filead4e556a47fb5/features/data_norm.tsv
2025-12-02 01:36:57.632472 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-02 01:36:57.633342 INFO::Total samples in data: 16
2025-12-02 01:36:57.63418 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-02 01:36:57.635016 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-02 01:36:57.636906 INFO::Total filtered features: 0
2025-12-02 01:36:57.637839 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-02 01:36:57.63896 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-02 01:36:57.639878 INFO::Filtered feature names from variance filtering:
2025-12-02 01:36:57.640726 INFO::Writing filtered data to file /tmp/RtmpOwuhS9/filead4e556a47fb5/features/filtered_data.tsv
2025-12-02 01:36:57.642167 INFO::Running selected transform method: LOG
2025-12-02 01:36:57.643325 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpOwuhS9/filead4e556a47fb5/features/data_transformed.tsv
2025-12-02 01:36:57.645002 INFO::Applying z-score to standardize continuous metadata
2025-12-02 01:36:57.650373 INFO::Running the linear model component
2025-12-02 01:36:57.663659 INFO::Fitting model to feature number 1, a
2025-12-02 01:36:57.668003 INFO::Fitting model to feature number 2, b
2025-12-02 01:36:57.672039 INFO::Fitting model to feature number 3, c
2025-12-02 01:36:57.679266 INFO::Counting total values for each feature
2025-12-02 01:36:57.681076 INFO::Running the logistic model component
2025-12-02 01:36:57.694243 INFO::Fitting model to feature number 1, a
2025-12-02 01:36:57.70068 INFO::Fitting model to feature number 2, b
2025-12-02 01:36:57.706712 INFO::Fitting model to feature number 3, c
2025-12-02 01:36:57.715538 INFO::Counting total values for each feature
2025-12-02 01:36:57.71764 INFO::Re-running abundances for warn_prevalence
2025-12-02 01:36:57.718545 INFO::Running selected normalization method: TSS
2025-12-02 01:36:57.719985 INFO::Running selected transform method: LOG
2025-12-02 01:36:57.733416 INFO::Fitting model to feature number 1, a
2025-12-02 01:36:57.737932 INFO::Fitting model to feature number 2, b
2025-12-02 01:36:57.742096 INFO::Fitting model to feature number 3, c
2025-12-02 01:36:57.826631 INFO::Creating fits folder
2025-12-02 01:36:57.827892 INFO::Writing residuals to file /tmp/RtmpOwuhS9/filead4e556a47fb5/fits/residuals_linear.rds
2025-12-02 01:36:57.829085 INFO::Writing fitted values to file /tmp/RtmpOwuhS9/filead4e556a47fb5/fits/fitted_linear.rds
2025-12-02 01:36:57.830419 INFO::Writing residuals to file /tmp/RtmpOwuhS9/filead4e556a47fb5/fits/residuals_logistic.rds
2025-12-02 01:36:57.831726 INFO::Writing fitted values to file /tmp/RtmpOwuhS9/filead4e556a47fb5/fits/fitted_logistic.rds
2025-12-02 01:36:57.834529 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpOwuhS9/filead4e556a47fb5/all_results.tsv
2025-12-02 01:36:57.83613 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/RtmpOwuhS9/filead4e556a47fb5/significant_results.tsv
2025-12-02 01:36:57.83742 INFO::Creating output figures folder
2025-12-02 01:36:57.838734 INFO::Writing summary plot of significant
results to file: /tmp/RtmpOwuhS9/filead4e556a47fb5/figures/summary_plot.pdf
2025-12-02 01:36:59.433266 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpOwuhS9/filead4e556a47fb5/figures
2025-12-02 01:36:59.435334 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 01:36:59.440299 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 01:36:59.974291 INFO::Writing summary plot of
significant results to file: /tmp/RtmpOwuhS9/filead4e556a47fb5/figures/summary_plot.pdf
2025-12-02 01:37:01.606682 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpOwuhS9/filead4e556a47fb5/figures
2025-12-02 01:37:01.608183 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 01:37:01.613109 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 01:37:02.16371 INFO::Running the linear model component
2025-12-02 01:37:02.172746 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:02.176886 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:02.180793 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:02.18766 INFO::Counting total values for each feature
2025-12-02 01:37:02.189295 INFO::Running the logistic model component
2025-12-02 01:37:02.197598 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:02.203884 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:02.209687 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:02.218353 INFO::Counting total values for each feature
2025-12-02 01:37:02.220336 INFO::Re-running abundances for warn_prevalence
2025-12-02 01:37:02.221096 INFO::Running selected normalization method: TSS
2025-12-02 01:37:02.222398 INFO::Running selected transform method: LOG
2025-12-02 01:37:02.230873 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:02.234908 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:02.238719 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:02.323242 INFO::Creating output folder
2025-12-02 01:37:02.324172 INFO::Creating output figures folder
2025-12-02 01:37:02.325361 INFO::Writing summary plot of significant
results to file: /tmp/RtmpOwuhS9/filead4e5fc0754b/figures/summary_plot.pdf
2025-12-02 01:37:03.898636 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpOwuhS9/filead4e5fc0754b/figures
2025-12-02 01:37:03.900437 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 01:37:03.905257 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 01:37:04.842794 INFO::Applying z-score to standardize continuous metadata
2025-12-02 01:37:04.850494 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-02 01:37:04.851345 INFO::Bypass z-score application to metadata
2025-12-02 01:37:04.853846 INFO::Bypass z-score application to metadata
2025-12-02 01:37:04.872254 INFO::Determining format of input files
2025-12-02 01:37:04.873158 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 01:37:04.873976 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-02 01:37:04.881087 INFO::Determining format of input files
2025-12-02 01:37:04.882063 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-02 01:37:04.88331 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 01:37:04.891044 INFO::Determining format of input files
2025-12-02 01:37:04.891981 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 01:37:04.892979 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 01:37:04.894594 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 01:37:04.895341 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 01:37:04.906717 INFO::Running selected transform method: LOG
2025-12-02 01:37:04.90787 INFO::Creating output feature tables folder
2025-12-02 01:37:04.90872 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpOwuhS9/filead4e5e02c67a/features/data_transformed.tsv
2025-12-02 01:37:04.912538 INFO::Running selected transform method: LOG
2025-12-02 01:37:04.913528 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpOwuhS9/filead4e5e02c67a/features/data_transformed.tsv
2025-12-02 01:37:04.919383 INFO::Running selected transform method: PLOG
2025-12-02 01:37:04.920989 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpOwuhS9/filead4e5e02c67a/features/data_transformed.tsv
2025-12-02 01:37:04.923883 INFO::Running selected transform method: NONE
2025-12-02 01:37:04.92462 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpOwuhS9/filead4e5e02c67a/features/data_transformed.tsv
2025-12-02 01:37:04.932234 INFO::Running the linear model component
2025-12-02 01:37:04.940548 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:04.94474 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:04.94871 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:04.955631 INFO::Counting total values for each feature
2025-12-02 01:37:04.957254 INFO::Running the logistic model component
2025-12-02 01:37:04.965485 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:04.971601 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:04.977435 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:04.986259 INFO::Counting total values for each feature
2025-12-02 01:37:04.988294 INFO::Re-running abundances for warn_prevalence
2025-12-02 01:37:04.989084 INFO::Running selected normalization method: TSS
2025-12-02 01:37:04.990452 INFO::Running selected transform method: LOG
2025-12-02 01:37:04.999175 INFO::Fitting model to feature number 1, a
2025-12-02 01:37:05.003524 INFO::Fitting model to feature number 2, b
2025-12-02 01:37:05.007654 INFO::Fitting model to feature number 3, c
2025-12-02 01:37:05.105402 INFO::Creating output folder
2025-12-02 01:37:05.106345 INFO::Creating fits folder
2025-12-02 01:37:05.107139 INFO::Writing residuals to file /tmp/RtmpOwuhS9/filead4e5669f34cd/fits/residuals_linear.rds
2025-12-02 01:37:05.108068 INFO::Writing fitted values to file /tmp/RtmpOwuhS9/filead4e5669f34cd/fits/fitted_linear.rds
2025-12-02 01:37:05.10916 INFO::Writing residuals to file /tmp/RtmpOwuhS9/filead4e5669f34cd/fits/residuals_logistic.rds
2025-12-02 01:37:05.110207 INFO::Writing fitted values to file /tmp/RtmpOwuhS9/filead4e5669f34cd/fits/fitted_logistic.rds
2025-12-02 01:37:05.112746 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpOwuhS9/filead4e5669f34cd/all_results.tsv
2025-12-02 01:37:05.114178 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/RtmpOwuhS9/filead4e5669f34cd/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
358.465 5.033 363.484
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.150 | 0.486 | 19.639 | |
| maaslin_check_arguments | 0.135 | 0.002 | 0.137 | |
| maaslin_check_formula | 0.132 | 0.002 | 0.134 | |
| maaslin_compute_formula | 0.134 | 0.003 | 0.137 | |
| maaslin_contrast_test | 18.151 | 0.280 | 18.435 | |
| maaslin_filter | 0.455 | 0.012 | 0.467 | |
| maaslin_fit | 13.396 | 0.103 | 13.499 | |
| maaslin_log_arguments | 0.139 | 0.001 | 0.140 | |
| maaslin_normalize | 0.262 | 0.007 | 0.269 | |
| maaslin_plot_results | 43.508 | 0.328 | 43.808 | |
| maaslin_plot_results_from_output | 43.789 | 0.489 | 44.419 | |
| maaslin_process_metadata | 0.467 | 0.010 | 0.477 | |
| maaslin_read_data | 0.135 | 0.002 | 0.137 | |
| maaslin_reorder_data | 0.136 | 0.003 | 0.138 | |
| maaslin_transform | 0.538 | 0.009 | 0.547 | |
| maaslin_write_results | 13.404 | 0.136 | 13.554 | |
| maaslin_write_results_lefse_format | 14.596 | 0.093 | 14.690 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.004 | |