William Nickols
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 1152/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-12 19:19:01 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 19:24:22 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 321.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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 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 17.137 0.732 18.495
maaslin_plot_results 16.945 0.739 18.590
maaslin3 8.987 0.511 9.995
maaslin_contrast_test 6.735 0.577 7.598
maaslin_write_results_lefse_format 6.001 0.569 6.849
maaslin_write_results 5.603 0.472 6.559
maaslin_fit 5.098 0.605 5.927
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2025-11-12 19:21:44.544673 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:21:44.925996 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:21:44.967882 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:21:44.977429 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:21:44.9931 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:21:45.025945 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:21:45.028239 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:21:45.03763 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:21:45.071871 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:21:45.073895 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:21:45.092241 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:21:45.110261 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:21:45.115944 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:21:45.144037 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:21:45.168914 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:21:52.348341 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:21:52.375521 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:21:52.408609 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:21:52.416819 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:21:52.429209 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:21:52.460071 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:21:52.462142 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:21:52.466706 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:21:52.525874 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:21:52.527935 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:21:52.544282 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:21:52.558709 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:21:52.562918 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:21:52.576036 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:21:52.611275 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:21:54.250 R[66003:7030644] XType: Using static font registry.
2025-11-12 19:22:03.16644 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:03.193812 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:03.21936 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:03.227373 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:03.239471 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:03.270175 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:03.272504 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:03.277538 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:03.31148 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:03.313606 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:03.330971 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:03.348331 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:03.353812 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:03.370646 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:03.39741 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:09.201843 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:09.228507 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:09.26534 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:09.274546 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:09.287575 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:09.315636 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:09.318145 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:09.323085 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:09.357409 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:09.359383 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:09.377825 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:09.394874 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:09.399805 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:09.416192 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:09.446395 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:09.545972 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_linear.rds
2025-11-12 19:22:09.581106 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_linear.rds
2025-11-12 19:22:09.639434 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_logistic.rds
2025-11-12 19:22:09.824094 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_logistic.rds
2025-11-12 19:22:19.07436 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:19.102516 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:19.129644 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:19.138542 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:19.151279 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:19.177858 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:19.180086 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:19.18467 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:19.219988 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:19.222608 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:19.250777 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:19.265172 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:19.269476 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:19.283797 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:19.308459 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:25.197686 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:25.252808 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:25.285574 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:25.293971 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:25.306263 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:25.334973 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:25.336943 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:25.340879 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:25.379123 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:25.381351 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:25.400857 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:25.41826 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:25.430321 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:25.450255 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:25.48187 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:25.563603 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_linear.rds
2025-11-12 19:22:25.601159 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_linear.rds
2025-11-12 19:22:25.635977 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_logistic.rds
2025-11-12 19:22:25.833918 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_logistic.rds
2025-11-12 19:22:34.840753 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:34.878809 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:34.910152 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:34.918891 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:34.932923 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:34.95988 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:34.961988 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:34.966116 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:35.001034 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:35.003619 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:35.022244 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:35.03821 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:35.042865 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:35.057685 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:35.087102 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:40.344478 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:40.372825 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:40.399962 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:40.408721 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:40.423703 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:40.452391 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:40.454536 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:40.458849 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:40.49612 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:40.498605 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:40.517504 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:40.531301 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:40.535711 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:40.556586 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:40.583817 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:40.728914 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_linear.rds
2025-11-12 19:22:40.762737 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_linear.rds
2025-11-12 19:22:40.807326 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/residuals_logistic.rds
2025-11-12 19:22:40.995067 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33410860d/fits/fitted_logistic.rds
2025-11-12 19:22:49.952564 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:49.979633 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:50.009815 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:50.017639 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:50.029715 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:50.058537 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:50.060976 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:50.065826 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:50.102851 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:50.105105 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:50.123723 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:50.143986 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:50.148362 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:50.172461 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:50.200557 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:22:55.384062 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:22:55.410994 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:22:55.454058 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:22:55.463466 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:22:55.476239 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:22:55.502931 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:22:55.505021 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:22:55.509217 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:22:55.546057 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:22:55.54842 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:22:55.566238 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:22:55.57992 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:22:55.584503 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:22:55.598182 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:22:55.622865 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:23:05.345041 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:09.405143 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:19.855276 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:23.950367 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:24.155894 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_linear.rds
2025-11-12 19:23:24.189922 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_linear.rds
2025-11-12 19:23:24.217571 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_logistic.rds
2025-11-12 19:23:24.258947 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_logistic.rds
2025-11-12 19:23:34.131027 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:37.037978 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:37.160075 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_linear.rds
2025-11-12 19:23:37.195787 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_linear.rds
2025-11-12 19:23:37.224539 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_logistic.rds
2025-11-12 19:23:37.267878 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_logistic.rds
2025-11-12 19:23:45.335187 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:48.18641 WARNING::Fitting problem for feature 124 returning NA
2025-11-12 19:23:48.286303 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_linear.rds
2025-11-12 19:23:48.322391 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_linear.rds
2025-11-12 19:23:48.34713 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_logistic.rds
2025-11-12 19:23:48.387578 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_logistic.rds
2025-11-12 19:23:56.420262 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:23:56.452812 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:23:56.482816 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:23:56.490742 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:23:56.503688 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:23:56.530964 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:23:56.533047 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:23:56.537149 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:23:56.57989 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:23:56.582149 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:23:56.601033 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:23:56.615548 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:23:56.620256 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:23:56.639894 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:23:56.672631 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:24:02.110093 WARNING::Fitting problem for feature 50 returning NA
2025-11-12 19:24:02.138109 WARNING::Fitting problem for feature 62 returning NA
2025-11-12 19:24:02.167294 WARNING::Fitting problem for feature 74 returning NA
2025-11-12 19:24:02.178159 WARNING::Fitting problem for feature 78 returning NA
2025-11-12 19:24:02.190656 WARNING::Fitting problem for feature 84 returning NA
2025-11-12 19:24:02.216775 WARNING::Fitting problem for feature 96 returning NA
2025-11-12 19:24:02.218843 WARNING::Fitting problem for feature 97 returning NA
2025-11-12 19:24:02.223314 WARNING::Fitting problem for feature 99 returning NA
2025-11-12 19:24:02.265135 WARNING::Fitting problem for feature 114 returning NA
2025-11-12 19:24:02.267301 WARNING::Fitting problem for feature 115 returning NA
2025-11-12 19:24:02.292632 WARNING::Fitting problem for feature 123 returning NA
2025-11-12 19:24:02.308856 WARNING::Fitting problem for feature 130 returning NA
2025-11-12 19:24:02.31335 WARNING::Fitting problem for feature 132 returning NA
2025-11-12 19:24:02.329482 WARNING::Fitting problem for feature 139 returning NA
2025-11-12 19:24:02.365303 WARNING::Fitting problem for feature 150 returning NA
2025-11-12 19:24:02.467988 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_linear.rds
2025-11-12 19:24:02.508828 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_linear.rds
2025-11-12 19:24:02.547211 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/residuals_logistic.rds
2025-11-12 19:24:02.736417 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d37005a00/fits/fitted_logistic.rds
2025-11-12 19:24:12.004642 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-12 19:24:12.010702 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-12 19:24:12.016995 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-12 19:24:12.03637 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-12 19:24:12.043931 ERROR::Effect name not found in metadata: d
2025-11-12 19:24:12.048879 ERROR::No user formula provided
2025-11-12 19:24:12.059388 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-12 19:24:12.063449 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-12 19:24:13.141548 INFO::Writing function arguments to log file
2025-11-12 19:24:13.147049 INFO::Verifying options selected are valid
2025-11-12 19:24:14.082483 INFO::Writing function arguments to log file
2025-11-12 19:24:14.091723 INFO::Verifying options selected are valid
2025-11-12 19:24:14.092136 INFO::Determining format of input files
2025-11-12 19:24:14.092458 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 19:24:14.093294 INFO::Running selected normalization method: TSS
2025-11-12 19:24:14.093837 INFO::Creating output feature tables folder
2025-11-12 19:24:14.094235 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/features/data_norm.tsv
2025-11-12 19:24:14.094841 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-12 19:24:14.095146 INFO::Total samples in data: 16
2025-11-12 19:24:14.095432 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-12 19:24:14.095709 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-12 19:24:14.096354 INFO::Total filtered features: 0
2025-11-12 19:24:14.096692 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-12 19:24:14.09708 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-12 19:24:14.097385 INFO::Filtered feature names from variance filtering:
2025-11-12 19:24:14.097683 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/features/filtered_data.tsv
2025-11-12 19:24:14.09825 INFO::Running selected transform method: LOG
2025-11-12 19:24:14.098655 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/features/data_transformed.tsv
2025-11-12 19:24:14.099286 INFO::Applying z-score to standardize continuous metadata
2025-11-12 19:24:14.101467 INFO::Running the linear model component
2025-11-12 19:24:14.106759 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:14.108437 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:14.109818 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:14.11243 INFO::Counting total values for each feature
2025-11-12 19:24:14.113117 INFO::Running the logistic model component
2025-11-12 19:24:14.118173 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:14.12258 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:14.125091 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:14.128436 INFO::Counting total values for each feature
2025-11-12 19:24:14.129299 INFO::Re-running abundances for warn_prevalence
2025-11-12 19:24:14.129701 INFO::Running selected normalization method: TSS
2025-11-12 19:24:14.130255 INFO::Running selected transform method: LOG
2025-11-12 19:24:14.135349 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:14.136959 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:14.138336 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:14.170801 INFO::Creating fits folder
2025-11-12 19:24:14.171381 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/fits/residuals_linear.rds
2025-11-12 19:24:14.17189 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/fits/fitted_linear.rds
2025-11-12 19:24:14.172342 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/fits/residuals_logistic.rds
2025-11-12 19:24:14.172806 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/fits/fitted_logistic.rds
2025-11-12 19:24:14.173811 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/all_results.tsv
2025-11-12 19:24:14.17452 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/significant_results.tsv
2025-11-12 19:24:14.175084 INFO::Creating output figures folder
2025-11-12 19:24:14.175594 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/figures/summary_plot.pdf
2025-11-12 19:24:14.807277 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/figures
2025-11-12 19:24:14.808075 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 19:24:14.810133 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 19:24:15.020325 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/figures/summary_plot.pdf
2025-11-12 19:24:15.667976 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d3585f17b8/figures
2025-11-12 19:24:15.668778 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 19:24:15.670986 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 19:24:15.892167 INFO::Running the linear model component
2025-11-12 19:24:15.90145 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:15.902947 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:15.904143 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:15.907105 INFO::Counting total values for each feature
2025-11-12 19:24:15.907671 INFO::Running the logistic model component
2025-11-12 19:24:15.910177 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:15.91202 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:15.91369 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:15.91635 INFO::Counting total values for each feature
2025-11-12 19:24:15.917006 INFO::Re-running abundances for warn_prevalence
2025-11-12 19:24:15.917236 INFO::Running selected normalization method: TSS
2025-11-12 19:24:15.917656 INFO::Running selected transform method: LOG
2025-11-12 19:24:15.92046 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:15.921697 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:15.922832 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:15.949979 INFO::Creating output folder
2025-11-12 19:24:15.950442 INFO::Creating output figures folder
2025-11-12 19:24:15.9509 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33d8dc0c/figures/summary_plot.pdf
2025-11-12 19:24:16.59401 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d33d8dc0c/figures
2025-11-12 19:24:16.594689 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-12 19:24:16.596699 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-12 19:24:17.026436 INFO::Applying z-score to standardize continuous metadata
2025-11-12 19:24:17.029351 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-12 19:24:17.029656 INFO::Bypass z-score application to metadata
2025-11-12 19:24:17.030459 INFO::Bypass z-score application to metadata
2025-11-12 19:24:17.039 INFO::Determining format of input files
2025-11-12 19:24:17.039388 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 19:24:17.03971 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-12 19:24:17.041891 INFO::Determining format of input files
2025-11-12 19:24:17.042216 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-12 19:24:17.042594 INFO::Input format is feature_specific_covariate samples as columns
2025-11-12 19:24:17.044978 INFO::Determining format of input files
2025-11-12 19:24:17.045263 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-12 19:24:17.045561 INFO::Input format is feature_specific_covariate samples as columns
2025-11-12 19:24:17.046015 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-12 19:24:17.046281 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-12 19:24:17.050177 INFO::Running selected transform method: LOG
2025-11-12 19:24:17.050537 INFO::Creating output feature tables folder
2025-11-12 19:24:17.050943 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d34626c071/features/data_transformed.tsv
2025-11-12 19:24:17.052459 INFO::Running selected transform method: LOG
2025-11-12 19:24:17.05283 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d34626c071/features/data_transformed.tsv
2025-11-12 19:24:17.054112 INFO::Running selected transform method: PLOG
2025-11-12 19:24:17.05468 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d34626c071/features/data_transformed.tsv
2025-11-12 19:24:17.055583 INFO::Running selected transform method: NONE
2025-11-12 19:24:17.055815 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d34626c071/features/data_transformed.tsv
2025-11-12 19:24:17.058755 INFO::Running the linear model component
2025-11-12 19:24:17.061495 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:17.063023 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:17.064204 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:17.066742 INFO::Counting total values for each feature
2025-11-12 19:24:17.067321 INFO::Running the logistic model component
2025-11-12 19:24:17.070089 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:17.07213 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:17.073978 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:17.076802 INFO::Counting total values for each feature
2025-11-12 19:24:17.077465 INFO::Re-running abundances for warn_prevalence
2025-11-12 19:24:17.077697 INFO::Running selected normalization method: TSS
2025-11-12 19:24:17.078113 INFO::Running selected transform method: LOG
2025-11-12 19:24:17.080708 INFO::Fitting model to feature number 1, a
2025-11-12 19:24:17.081991 INFO::Fitting model to feature number 2, b
2025-11-12 19:24:17.083942 INFO::Fitting model to feature number 3, c
2025-11-12 19:24:17.117196 INFO::Creating output folder
2025-11-12 19:24:17.117763 INFO::Creating fits folder
2025-11-12 19:24:17.118122 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/fits/residuals_linear.rds
2025-11-12 19:24:17.118626 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/fits/fitted_linear.rds
2025-11-12 19:24:17.119054 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/fits/residuals_logistic.rds
2025-11-12 19:24:17.119462 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/fits/fitted_logistic.rds
2025-11-12 19:24:17.120497 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/all_results.tsv
2025-11-12 19:24:17.12121 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp4oHV78/file101d31a245eb2/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.089 4.142 157.481
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.987 | 0.511 | 9.995 | |
| maaslin_check_arguments | 0.077 | 0.004 | 0.084 | |
| maaslin_check_formula | 0.061 | 0.003 | 0.067 | |
| maaslin_compute_formula | 0.063 | 0.004 | 0.071 | |
| maaslin_contrast_test | 6.735 | 0.577 | 7.598 | |
| maaslin_filter | 0.234 | 0.018 | 0.268 | |
| maaslin_fit | 5.098 | 0.605 | 5.927 | |
| maaslin_log_arguments | 0.062 | 0.004 | 0.067 | |
| maaslin_normalize | 0.151 | 0.016 | 0.176 | |
| maaslin_plot_results | 16.945 | 0.739 | 18.590 | |
| maaslin_plot_results_from_output | 17.137 | 0.732 | 18.495 | |
| maaslin_process_metadata | 0.246 | 0.025 | 0.284 | |
| maaslin_read_data | 0.055 | 0.003 | 0.059 | |
| maaslin_reorder_data | 0.060 | 0.004 | 0.068 | |
| maaslin_transform | 0.288 | 0.026 | 0.330 | |
| maaslin_write_results | 5.603 | 0.472 | 6.559 | |
| maaslin_write_results_lefse_format | 6.001 | 0.569 | 6.849 | |
| preprocess_dna_mtx | 0.001 | 0.001 | 0.001 | |
| preprocess_taxa_mtx | 0.002 | 0.000 | 0.001 | |