William Nickols
| Snapshot Date: 2025-11-13 13:45 -0500 (Thu, 13 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 2025-11-14 11:58 -0500 (Fri, 14 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" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| 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: 2025-11-14 01:08:19 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 01:30:08 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 1308.4 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_from_output 43.974 0.340 44.320
maaslin_plot_results 43.894 0.295 44.164
maaslin3 19.979 0.446 20.427
maaslin_contrast_test 18.194 0.338 18.533
maaslin_write_results_lefse_format 15.048 0.661 15.710
maaslin_write_results 13.804 0.809 14.614
maaslin_fit 12.818 0.155 12.974
* 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")
2025-11-14 01:14:40.423341 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:14:40.508335 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:14:40.619825 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:14:40.644557 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:14:40.680126 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:14:40.760871 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:14:40.766443 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:14:40.7786 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:14:40.894343 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:14:40.899646 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:14:40.949568 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:14:40.989938 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:14:41.001954 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:14:41.051202 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:14:41.119014 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:14:57.187422 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:14:57.262671 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:14:57.337367 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:14:57.359136 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:14:57.393814 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:14:57.469345 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:14:57.474636 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:14:57.486628 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:14:57.583786 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:14:57.589225 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:14:57.656224 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:14:57.696388 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:14:57.708182 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:14:57.748616 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:14:57.815977 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:15:22.528238 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:15:22.605421 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:15:22.679533 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:15:22.701571 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:15:22.737364 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:15:22.814456 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:15:22.819736 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:15:22.831435 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:15:22.926751 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:15:22.932188 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:15:22.981911 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:15:23.022589 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:15:23.034759 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:15:23.076705 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:15:23.147274 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:15:36.303463 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:15:36.400712 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:15:36.477085 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:15:36.499154 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:15:36.533879 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:15:36.612453 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:15:36.617855 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:15:36.6298 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:15:36.726319 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:15:36.731946 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:15:36.78327 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:15:36.825053 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:15:36.837888 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:15:36.880333 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:15:36.953191 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:15:37.167068 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_linear.rds
2025-11-14 01:15:37.22848 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_linear.rds
2025-11-14 01:15:37.291691 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_logistic.rds
2025-11-14 01:15:37.595027 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_logistic.rds
2025-11-14 01:15:59.520617 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:15:59.601349 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:15:59.677631 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:15:59.699726 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:15:59.734711 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:15:59.814836 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:15:59.820744 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:15:59.833348 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:15:59.931772 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:15:59.937471 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:15:59.990234 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:16:00.034943 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:16:00.048145 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:16:00.194393 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:16:00.265325 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:16:13.184897 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:16:13.264585 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:16:13.345142 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:16:13.369642 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:16:13.406763 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:16:13.487252 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:16:13.492737 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:16:13.505018 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:16:13.604001 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:16:13.609591 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:16:13.660475 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:16:13.702328 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:16:13.714709 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:16:13.756617 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:16:13.826211 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:16:14.036331 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_linear.rds
2025-11-14 01:16:14.097191 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_linear.rds
2025-11-14 01:16:14.160073 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_logistic.rds
2025-11-14 01:16:14.459677 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_logistic.rds
2025-11-14 01:16:37.226899 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:16:37.307882 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:16:37.386552 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:16:37.409451 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:16:37.446936 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:16:37.525279 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:16:37.530926 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:16:37.543942 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:16:37.642393 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:16:37.648367 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:16:37.704319 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:16:37.750368 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:16:37.764102 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:16:37.809845 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:16:37.888305 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:16:48.742399 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:16:48.818533 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:16:48.895946 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:16:48.918747 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:16:48.954726 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:16:49.0343 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:16:49.039929 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:16:49.052369 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:16:49.184326 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:16:49.190007 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:16:49.241292 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:16:49.283141 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:16:49.29596 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:16:49.338744 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:16:49.412501 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:16:49.629295 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_linear.rds
2025-11-14 01:16:49.690853 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_linear.rds
2025-11-14 01:16:49.754903 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/residuals_logistic.rds
2025-11-14 01:16:50.053706 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdccdc445f/fits/fitted_logistic.rds
2025-11-14 01:17:11.451653 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:17:11.531259 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:17:11.611904 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:17:11.636433 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:17:11.672372 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:17:11.750272 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:17:11.755878 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:17:11.768392 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:17:11.86601 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:17:11.871428 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:17:11.921813 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:17:11.961782 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:17:11.973411 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:17:12.013667 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:17:12.083705 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:17:24.118042 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:17:24.195918 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:17:24.274397 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:17:24.296913 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:17:24.331379 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:17:24.411196 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:17:24.416914 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:17:24.429262 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:17:24.53486 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:17:24.54098 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:17:24.593334 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:17:24.635109 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:17:24.648425 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:17:24.691711 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:17:24.763954 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:17:49.292932 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:17:59.471439 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:18:24.690208 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:18:33.746307 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:18:34.435187 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_linear.rds
2025-11-14 01:18:34.497018 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_linear.rds
2025-11-14 01:18:34.535912 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_logistic.rds
2025-11-14 01:18:34.607341 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_logistic.rds
2025-11-14 01:18:57.791523 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:19:04.143987 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:19:04.474061 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_linear.rds
2025-11-14 01:19:04.535655 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_linear.rds
2025-11-14 01:19:04.573899 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_logistic.rds
2025-11-14 01:19:04.64176 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_logistic.rds
2025-11-14 01:19:23.375255 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:19:29.70718 WARNING::Fitting problem for feature 124 returning NA
2025-11-14 01:19:30.078367 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_linear.rds
2025-11-14 01:19:30.140359 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_linear.rds
2025-11-14 01:19:30.179304 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_logistic.rds
2025-11-14 01:19:30.247451 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_logistic.rds
2025-11-14 01:19:48.508825 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:19:48.585238 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:19:48.661735 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:19:48.683824 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:19:48.71856 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:19:48.821011 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:19:48.826672 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:19:48.839021 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:19:48.938049 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:19:48.943611 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:19:48.993645 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:19:49.03362 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:19:49.045525 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:19:49.086397 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:19:49.156842 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:20:01.185545 WARNING::Fitting problem for feature 50 returning NA
2025-11-14 01:20:01.263916 WARNING::Fitting problem for feature 62 returning NA
2025-11-14 01:20:01.341625 WARNING::Fitting problem for feature 74 returning NA
2025-11-14 01:20:01.364088 WARNING::Fitting problem for feature 78 returning NA
2025-11-14 01:20:01.398887 WARNING::Fitting problem for feature 84 returning NA
2025-11-14 01:20:01.47625 WARNING::Fitting problem for feature 96 returning NA
2025-11-14 01:20:01.481575 WARNING::Fitting problem for feature 97 returning NA
2025-11-14 01:20:01.493711 WARNING::Fitting problem for feature 99 returning NA
2025-11-14 01:20:01.591881 WARNING::Fitting problem for feature 114 returning NA
2025-11-14 01:20:01.597514 WARNING::Fitting problem for feature 115 returning NA
2025-11-14 01:20:01.647724 WARNING::Fitting problem for feature 123 returning NA
2025-11-14 01:20:01.688169 WARNING::Fitting problem for feature 130 returning NA
2025-11-14 01:20:01.700813 WARNING::Fitting problem for feature 132 returning NA
2025-11-14 01:20:01.741695 WARNING::Fitting problem for feature 139 returning NA
2025-11-14 01:20:01.811226 WARNING::Fitting problem for feature 150 returning NA
2025-11-14 01:20:02.111287 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_linear.rds
2025-11-14 01:20:02.172301 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_linear.rds
2025-11-14 01:20:02.235319 WARNING::Deleting existing residuals file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/residuals_logistic.rds
2025-11-14 01:20:02.533017 WARNING::Deleting existing fitted file: /tmp/RtmpZWmh1n/file247bdc4ad8f653/fits/fitted_logistic.rds
2025-11-14 01:20:23.201186 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-14 01:20:23.217889 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-14 01:20:23.229393 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-14 01:20:23.280725 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-14 01:20:23.296805 ERROR::Effect name not found in metadata: d
2025-11-14 01:20:23.307671 ERROR::No user formula provided
2025-11-14 01:20:23.338087 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-14 01:20:23.350257 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-14 01:20:26.428899 INFO::Writing function arguments to log file
2025-11-14 01:20:26.443846 INFO::Verifying options selected are valid
2025-11-14 01:20:28.88451 INFO::Writing function arguments to log file
2025-11-14 01:20:28.896626 INFO::Verifying options selected are valid
2025-11-14 01:20:28.897689 INFO::Determining format of input files
2025-11-14 01:20:28.898654 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 01:20:28.900919 INFO::Running selected normalization method: TSS
2025-11-14 01:20:28.90234 INFO::Creating output feature tables folder
2025-11-14 01:20:28.903281 INFO::Writing normalized data to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/features/data_norm.tsv
2025-11-14 01:20:28.904712 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-14 01:20:28.905583 INFO::Total samples in data: 16
2025-11-14 01:20:28.906434 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-14 01:20:28.907278 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-14 01:20:28.909159 INFO::Total filtered features: 0
2025-11-14 01:20:28.910164 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-14 01:20:28.91132 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-14 01:20:28.912277 INFO::Filtered feature names from variance filtering:
2025-11-14 01:20:28.913156 INFO::Writing filtered data to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/features/filtered_data.tsv
2025-11-14 01:20:28.914603 INFO::Running selected transform method: LOG
2025-11-14 01:20:28.915765 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/features/data_transformed.tsv
2025-11-14 01:20:28.917367 INFO::Applying z-score to standardize continuous metadata
2025-11-14 01:20:28.922497 INFO::Running the linear model component
2025-11-14 01:20:28.936564 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:28.941084 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:28.945389 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:28.952489 INFO::Counting total values for each feature
2025-11-14 01:20:28.954323 INFO::Running the logistic model component
2025-11-14 01:20:28.968165 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:28.974738 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:28.980887 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:28.9903 INFO::Counting total values for each feature
2025-11-14 01:20:28.992501 INFO::Re-running abundances for warn_prevalence
2025-11-14 01:20:28.993435 INFO::Running selected normalization method: TSS
2025-11-14 01:20:28.994904 INFO::Running selected transform method: LOG
2025-11-14 01:20:29.00886 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:29.013285 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:29.017453 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:29.104193 INFO::Creating fits folder
2025-11-14 01:20:29.105403 INFO::Writing residuals to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/fits/residuals_linear.rds
2025-11-14 01:20:29.106553 INFO::Writing fitted values to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/fits/fitted_linear.rds
2025-11-14 01:20:29.107724 INFO::Writing residuals to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/fits/residuals_logistic.rds
2025-11-14 01:20:29.108879 INFO::Writing fitted values to file /tmp/RtmpZWmh1n/file247bdc34ee36b5/fits/fitted_logistic.rds
2025-11-14 01:20:29.111582 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpZWmh1n/file247bdc34ee36b5/all_results.tsv
2025-11-14 01:20:29.113282 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/RtmpZWmh1n/file247bdc34ee36b5/significant_results.tsv
2025-11-14 01:20:29.114657 INFO::Creating output figures folder
2025-11-14 01:20:29.11605 INFO::Writing summary plot of significant
results to file: /tmp/RtmpZWmh1n/file247bdc34ee36b5/figures/summary_plot.pdf
2025-11-14 01:20:30.778057 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZWmh1n/file247bdc34ee36b5/figures
2025-11-14 01:20:30.779963 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 01:20:30.784995 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 01:20:31.326907 INFO::Writing summary plot of
significant results to file: /tmp/RtmpZWmh1n/file247bdc34ee36b5/figures/summary_plot.pdf
2025-11-14 01:20:32.997572 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZWmh1n/file247bdc34ee36b5/figures
2025-11-14 01:20:32.999199 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 01:20:33.004236 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 01:20:33.568993 INFO::Running the linear model component
2025-11-14 01:20:33.578315 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:33.582891 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:33.586905 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:33.59386 INFO::Counting total values for each feature
2025-11-14 01:20:33.595483 INFO::Running the logistic model component
2025-11-14 01:20:33.603809 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:33.609948 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:33.615717 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:33.624814 INFO::Counting total values for each feature
2025-11-14 01:20:33.626883 INFO::Re-running abundances for warn_prevalence
2025-11-14 01:20:33.627652 INFO::Running selected normalization method: TSS
2025-11-14 01:20:33.629018 INFO::Running selected transform method: LOG
2025-11-14 01:20:33.637727 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:33.642361 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:33.646428 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:33.731881 INFO::Creating output folder
2025-11-14 01:20:33.732888 INFO::Creating output figures folder
2025-11-14 01:20:33.734071 INFO::Writing summary plot of significant
results to file: /tmp/RtmpZWmh1n/file247bdc443e0b38/figures/summary_plot.pdf
2025-11-14 01:20:35.335357 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZWmh1n/file247bdc443e0b38/figures
2025-11-14 01:20:35.337133 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-14 01:20:35.341934 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-14 01:20:36.314235 INFO::Applying z-score to standardize continuous metadata
2025-11-14 01:20:36.322042 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-14 01:20:36.322909 INFO::Bypass z-score application to metadata
2025-11-14 01:20:36.325408 INFO::Bypass z-score application to metadata
2025-11-14 01:20:36.3435 INFO::Determining format of input files
2025-11-14 01:20:36.344444 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 01:20:36.345282 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-14 01:20:36.352699 INFO::Determining format of input files
2025-11-14 01:20:36.353712 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-14 01:20:36.35499 INFO::Input format is feature_specific_covariate samples as columns
2025-11-14 01:20:36.363201 INFO::Determining format of input files
2025-11-14 01:20:36.36411 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-14 01:20:36.365136 INFO::Input format is feature_specific_covariate samples as columns
2025-11-14 01:20:36.36687 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-14 01:20:36.367678 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-14 01:20:36.379271 INFO::Running selected transform method: LOG
2025-11-14 01:20:36.380356 INFO::Creating output feature tables folder
2025-11-14 01:20:36.381217 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZWmh1n/file247bdc7c3d5653/features/data_transformed.tsv
2025-11-14 01:20:36.385057 INFO::Running selected transform method: LOG
2025-11-14 01:20:36.386095 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZWmh1n/file247bdc7c3d5653/features/data_transformed.tsv
2025-11-14 01:20:36.390058 INFO::Running selected transform method: PLOG
2025-11-14 01:20:36.391625 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZWmh1n/file247bdc7c3d5653/features/data_transformed.tsv
2025-11-14 01:20:36.394595 INFO::Running selected transform method: NONE
2025-11-14 01:20:36.395358 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZWmh1n/file247bdc7c3d5653/features/data_transformed.tsv
2025-11-14 01:20:36.403064 INFO::Running the linear model component
2025-11-14 01:20:36.411739 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:36.41589 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:36.419969 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:36.427113 INFO::Counting total values for each feature
2025-11-14 01:20:36.428799 INFO::Running the logistic model component
2025-11-14 01:20:36.437362 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:36.443387 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:36.449063 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:36.457797 INFO::Counting total values for each feature
2025-11-14 01:20:36.459855 INFO::Re-running abundances for warn_prevalence
2025-11-14 01:20:36.460649 INFO::Running selected normalization method: TSS
2025-11-14 01:20:36.46199 INFO::Running selected transform method: LOG
2025-11-14 01:20:36.470702 INFO::Fitting model to feature number 1, a
2025-11-14 01:20:36.47491 INFO::Fitting model to feature number 2, b
2025-11-14 01:20:36.478873 INFO::Fitting model to feature number 3, c
2025-11-14 01:20:36.572395 INFO::Creating output folder
2025-11-14 01:20:36.573426 INFO::Creating fits folder
2025-11-14 01:20:36.574276 INFO::Writing residuals to file /tmp/RtmpZWmh1n/file247bdc41a364d0/fits/residuals_linear.rds
2025-11-14 01:20:36.57526 INFO::Writing fitted values to file /tmp/RtmpZWmh1n/file247bdc41a364d0/fits/fitted_linear.rds
2025-11-14 01:20:36.576292 INFO::Writing residuals to file /tmp/RtmpZWmh1n/file247bdc41a364d0/fits/residuals_logistic.rds
2025-11-14 01:20:36.577299 INFO::Writing fitted values to file /tmp/RtmpZWmh1n/file247bdc41a364d0/fits/fitted_logistic.rds
2025-11-14 01:20:36.57978 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpZWmh1n/file247bdc41a364d0/all_results.tsv
2025-11-14 01:20:36.581284 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/RtmpZWmh1n/file247bdc41a364d0/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.632 4.811 367.444
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.979 | 0.446 | 20.427 | |
| maaslin_check_arguments | 0.139 | 0.001 | 0.140 | |
| maaslin_check_formula | 0.133 | 0.002 | 0.135 | |
| maaslin_compute_formula | 0.158 | 0.003 | 0.160 | |
| maaslin_contrast_test | 18.194 | 0.338 | 18.533 | |
| maaslin_filter | 0.45 | 0.02 | 0.47 | |
| maaslin_fit | 12.818 | 0.155 | 12.974 | |
| maaslin_log_arguments | 0.133 | 0.001 | 0.134 | |
| maaslin_normalize | 0.261 | 0.004 | 0.265 | |
| maaslin_plot_results | 43.894 | 0.295 | 44.164 | |
| maaslin_plot_results_from_output | 43.974 | 0.340 | 44.320 | |
| maaslin_process_metadata | 0.480 | 0.028 | 0.508 | |
| maaslin_read_data | 0.126 | 0.008 | 0.134 | |
| maaslin_reorder_data | 0.129 | 0.008 | 0.136 | |
| maaslin_transform | 0.533 | 0.050 | 0.582 | |
| maaslin_write_results | 13.804 | 0.809 | 14.614 | |
| maaslin_write_results_lefse_format | 15.048 | 0.661 | 15.710 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |