William Nickols
| Snapshot Date: 2025-09-08 13:40 -0400 (Mon, 08 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7584c46 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-11 11:40 -0400 (Thu, 11 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| 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 1155/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.0.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2025-09-10 01:15:35 -0400 (Wed, 10 Sep 2025) |
| EndedAt: 2025-09-10 01:29:03 -0400 (Wed, 10 Sep 2025) |
| EllapsedTime: 808.0 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.0’
* 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 43.652 2.019 45.849
maaslin_plot_results_from_output 42.899 1.441 44.625
maaslin3 24.045 1.270 25.483
maaslin_contrast_test 23.193 1.637 24.902
maaslin_write_results_lefse_format 19.050 1.157 20.264
maaslin_write_results 17.331 1.271 18.737
maaslin_fit 15.336 1.130 16.605
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.0.0’ ** 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 (2025-06-14 r88325) -- "Great Square Root"
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")
2025-09-10 01:22:33.826147 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:22:33.923072 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:22:34.0111 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:22:34.047248 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:22:34.083692 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:22:34.165473 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:22:34.171656 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:22:34.184648 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:22:34.299172 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:22:34.30547 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:22:34.35923 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:22:34.427706 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:22:34.441354 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:22:34.485158 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:22:34.557353 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:22:54.086846 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:22:54.17457 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:22:54.256874 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:22:54.282095 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:22:54.323428 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:22:54.42739 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:22:54.434411 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:22:54.44845 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:22:54.553317 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:22:54.5596 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:22:54.614153 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:22:54.658712 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:22:54.672496 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:22:54.71713 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:22:54.797954 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:22:58.123 R[74987:362466658] XType: Using static font registry.
2025-09-10 01:23:18.381456 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:23:18.466303 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:23:18.549245 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:23:18.575222 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:23:18.618158 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:23:18.703267 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:23:18.709568 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:23:18.722176 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:23:18.829706 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:23:18.836291 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:23:18.891307 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:23:18.936652 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:23:18.950662 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:23:18.995754 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:23:19.077742 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:23:34.666765 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:23:34.752089 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:23:34.837215 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:23:34.86338 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:23:34.94159 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:23:35.036197 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:23:35.044432 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:23:35.062223 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:23:35.176895 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:23:35.183838 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:23:35.242216 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:23:35.289493 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:23:35.303864 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:23:35.351508 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:23:35.433372 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:23:35.676775 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_linear.rds
2025-09-10 01:23:35.776619 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_linear.rds
2025-09-10 01:23:35.880154 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_logistic.rds
2025-09-10 01:23:36.393359 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_logistic.rds
2025-09-10 01:23:56.960852 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:23:57.044684 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:23:57.126699 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:23:57.153963 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:23:57.195801 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:23:57.285083 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:23:57.292147 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:23:57.306392 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:23:57.42309 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:23:57.430288 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:23:57.488397 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:23:57.53501 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:23:57.549634 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:23:57.69912 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:23:57.781432 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:24:13.486379 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:24:13.574554 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:24:13.664618 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:24:13.693482 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:24:13.734295 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:24:13.831836 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:24:13.838344 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:24:13.851448 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:24:13.971357 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:24:13.978622 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:24:14.040428 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:24:14.087641 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:24:14.102484 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:24:14.156156 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:24:14.249949 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:24:14.524009 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_linear.rds
2025-09-10 01:24:14.624674 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_linear.rds
2025-09-10 01:24:14.729569 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_logistic.rds
2025-09-10 01:24:15.237471 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_logistic.rds
2025-09-10 01:24:36.01103 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:24:36.100853 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:24:36.188414 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:24:36.21543 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:24:36.255389 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:24:36.349474 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:24:36.356417 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:24:36.370736 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:24:36.522695 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:24:36.529404 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:24:36.586077 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:24:36.632176 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:24:36.646617 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:24:36.692785 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:24:36.771207 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:24:51.953396 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:24:52.045021 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:24:52.136016 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:24:52.163816 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:24:52.206819 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:24:52.298541 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:24:52.30528 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:24:52.319829 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:24:52.442817 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:24:52.450697 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:24:52.520796 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:24:52.569846 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:24:52.585088 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:24:52.634693 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:24:52.723891 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:24:52.944033 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_linear.rds
2025-09-10 01:24:53.042206 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_linear.rds
2025-09-10 01:24:53.14531 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/residuals_logistic.rds
2025-09-10 01:24:53.655783 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb573e734e/fits/fitted_logistic.rds
2025-09-10 01:25:14.148674 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:25:14.194768 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:25:14.259744 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:25:14.279834 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:25:14.319418 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:25:14.44004 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:25:14.447336 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:25:14.461722 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:25:14.579535 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:25:14.587001 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:25:14.648985 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:25:14.69854 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:25:14.713782 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:25:14.764273 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:25:14.843523 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:25:29.949204 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:25:30.040207 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:25:30.122607 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:25:30.147242 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:25:30.185824 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:25:30.272104 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:25:30.27894 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:25:30.293103 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:25:30.410145 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:25:30.417576 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:25:30.479888 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:25:30.532424 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:25:30.604979 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:25:30.649803 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:25:30.727511 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:25:54.232358 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:26:06.007947 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:26:30.109259 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:26:41.699707 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:26:42.535326 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_linear.rds
2025-09-10 01:26:42.636038 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_linear.rds
2025-09-10 01:26:42.703886 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_logistic.rds
2025-09-10 01:26:42.822042 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_logistic.rds
2025-09-10 01:27:05.515859 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:27:13.511521 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:27:13.879972 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_linear.rds
2025-09-10 01:27:13.981302 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_linear.rds
2025-09-10 01:27:14.048948 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_logistic.rds
2025-09-10 01:27:14.170133 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_logistic.rds
2025-09-10 01:27:32.544912 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:27:40.648487 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 01:27:41.016907 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_linear.rds
2025-09-10 01:27:41.116701 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_linear.rds
2025-09-10 01:27:41.183268 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_logistic.rds
2025-09-10 01:27:41.308562 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_logistic.rds
2025-09-10 01:27:58.925533 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:27:59.016802 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:27:59.113095 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:27:59.14768 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:27:59.188077 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:27:59.285867 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:27:59.292938 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:27:59.308118 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:27:59.428266 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:27:59.435895 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:27:59.499547 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:27:59.548734 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:27:59.56297 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:27:59.610194 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:27:59.691234 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:28:14.783541 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 01:28:14.879483 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 01:28:14.974295 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 01:28:15.00071 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 01:28:15.042695 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 01:28:15.138384 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 01:28:15.145527 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 01:28:15.162889 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 01:28:15.290521 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 01:28:15.299138 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 01:28:15.365095 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 01:28:15.416575 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 01:28:15.432055 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 01:28:15.484286 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 01:28:15.578197 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 01:28:15.945864 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_linear.rds
2025-09-10 01:28:16.04669 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_linear.rds
2025-09-10 01:28:16.145526 WARNING::Deleting existing residuals file: /tmp/RtmprwVeoQ/file124eb59474504/fits/residuals_logistic.rds
2025-09-10 01:28:16.660338 WARNING::Deleting existing fitted file: /tmp/RtmprwVeoQ/file124eb59474504/fits/fitted_logistic.rds
2025-09-10 01:28:36.032094 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-10 01:28:36.051421 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-10 01:28:36.06481 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-10 01:28:36.124141 ERROR::No fixed, group, or
ordered effects included in formula.
2025-09-10 01:28:36.143279 ERROR::Effect name not found in metadata: d
2025-09-10 01:28:36.156673 ERROR::No user formula provided
2025-09-10 01:28:36.189911 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-10 01:28:36.204421 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-09-10 01:28:39.36465 INFO::Writing function arguments to log file
2025-09-10 01:28:39.380946 INFO::Verifying options selected are valid
2025-09-10 01:28:41.607832 INFO::Writing function arguments to log file
2025-09-10 01:28:41.620953 INFO::Verifying options selected are valid
2025-09-10 01:28:41.622238 INFO::Determining format of input files
2025-09-10 01:28:41.623232 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 01:28:41.625649 INFO::Running selected normalization method: TSS
2025-09-10 01:28:41.627285 INFO::Creating output feature tables folder
2025-09-10 01:28:41.628467 INFO::Writing normalized data to file /tmp/RtmprwVeoQ/file124ebac44caf/features/data_norm.tsv
2025-09-10 01:28:41.630265 INFO::Filter data based on min abundance and min prevalence
2025-09-10 01:28:41.631186 INFO::Total samples in data: 16
2025-09-10 01:28:41.632011 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-10 01:28:41.633857 INFO::Total filtered features: 0
2025-09-10 01:28:41.634998 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 01:28:41.636165 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-10 01:28:41.637105 INFO::Filtered feature names from variance filtering:
2025-09-10 01:28:41.637975 INFO::Writing filtered data to file /tmp/RtmprwVeoQ/file124ebac44caf/features/filtered_data.tsv
2025-09-10 01:28:41.639762 INFO::Running selected transform method: LOG
2025-09-10 01:28:41.641169 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmprwVeoQ/file124ebac44caf/features/data_transformed.tsv
2025-09-10 01:28:41.643272 INFO::Applying z-score to standardize continuous metadata
2025-09-10 01:28:41.651112 INFO::Running the linear model component
2025-09-10 01:28:41.667249 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:41.674707 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:41.679696 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:41.687722 INFO::Counting total values for each feature
2025-09-10 01:28:41.690013 INFO::Running the logistic model component
2025-09-10 01:28:41.705421 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:41.71254 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:41.720523 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:41.733304 INFO::Counting total values for each feature
2025-09-10 01:28:41.736724 INFO::Re-running abundances for warn_prevalence
2025-09-10 01:28:41.737992 INFO::Running selected normalization method: TSS
2025-09-10 01:28:41.739699 INFO::Running selected transform method: LOG
2025-09-10 01:28:41.755657 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:41.760669 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:41.765112 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:41.869878 INFO::Creating fits folder
2025-09-10 01:28:41.871726 INFO::Writing residuals to file /tmp/RtmprwVeoQ/file124ebac44caf/fits/residuals_linear.rds
2025-09-10 01:28:41.873225 INFO::Writing fitted values to file /tmp/RtmprwVeoQ/file124ebac44caf/fits/fitted_linear.rds
2025-09-10 01:28:41.874666 INFO::Writing residuals to file /tmp/RtmprwVeoQ/file124ebac44caf/fits/residuals_logistic.rds
2025-09-10 01:28:41.876317 INFO::Writing fitted values to file /tmp/RtmprwVeoQ/file124ebac44caf/fits/fitted_logistic.rds
2025-09-10 01:28:41.879543 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmprwVeoQ/file124ebac44caf/all_results.tsv
2025-09-10 01:28:41.88205 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/RtmprwVeoQ/file124ebac44caf/significant_results.tsv
2025-09-10 01:28:41.883896 INFO::Creating output figures folder
2025-09-10 01:28:41.885567 INFO::Writing summary plot of significant
results to file: /tmp/RtmprwVeoQ/file124ebac44caf/figures/summary_plot.pdf
2025-09-10 01:28:43.464166 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmprwVeoQ/file124ebac44caf/figures
2025-09-10 01:28:43.466655 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 01:28:43.473545 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 01:28:43.971873 INFO::Writing summary plot of
significant results to file: /tmp/RtmprwVeoQ/file124ebac44caf/figures/summary_plot.pdf
2025-09-10 01:28:45.474664 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmprwVeoQ/file124ebac44caf/figures
2025-09-10 01:28:45.477022 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 01:28:45.482853 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 01:28:45.955474 INFO::Running the linear model component
2025-09-10 01:28:45.963852 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:45.968411 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:45.972449 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:45.979871 INFO::Counting total values for each feature
2025-09-10 01:28:45.981751 INFO::Running the logistic model component
2025-09-10 01:28:45.989743 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:45.996316 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:46.002181 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:46.011573 INFO::Counting total values for each feature
2025-09-10 01:28:46.013894 INFO::Re-running abundances for warn_prevalence
2025-09-10 01:28:46.014715 INFO::Running selected normalization method: TSS
2025-09-10 01:28:46.01609 INFO::Running selected transform method: LOG
2025-09-10 01:28:46.024386 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:46.029064 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:46.033269 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:46.124519 INFO::Creating output folder
2025-09-10 01:28:46.125882 INFO::Creating output figures folder
2025-09-10 01:28:46.127161 INFO::Writing summary plot of significant
results to file: /tmp/RtmprwVeoQ/file124eb7d264109/figures/summary_plot.pdf
2025-09-10 01:28:47.639752 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmprwVeoQ/file124eb7d264109/figures
2025-09-10 01:28:47.641583 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 01:28:47.647189 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 01:28:48.749009 INFO::Applying z-score to standardize continuous metadata
2025-09-10 01:28:48.75825 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-10 01:28:48.759303 INFO::Bypass z-score application to metadata
2025-09-10 01:28:48.761967 INFO::Bypass z-score application to metadata
2025-09-10 01:28:48.783537 INFO::Determining format of input files
2025-09-10 01:28:48.784615 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 01:28:48.78537 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-10 01:28:48.792689 INFO::Determining format of input files
2025-09-10 01:28:48.793922 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-10 01:28:48.795171 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 01:28:48.803019 INFO::Determining format of input files
2025-09-10 01:28:48.803986 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 01:28:48.804972 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 01:28:48.806589 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-10 01:28:48.807317 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-10 01:28:48.819148 INFO::Running selected transform method: LOG
2025-09-10 01:28:48.82042 INFO::Creating output feature tables folder
2025-09-10 01:28:48.821507 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmprwVeoQ/file124eb51e7319/features/data_transformed.tsv
2025-09-10 01:28:48.825829 INFO::Running selected transform method: LOG
2025-09-10 01:28:48.826919 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmprwVeoQ/file124eb51e7319/features/data_transformed.tsv
2025-09-10 01:28:48.830787 INFO::Running selected transform method: PLOG
2025-09-10 01:28:48.832459 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmprwVeoQ/file124eb51e7319/features/data_transformed.tsv
2025-09-10 01:28:48.83547 INFO::Running selected transform method: NONE
2025-09-10 01:28:48.836237 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmprwVeoQ/file124eb51e7319/features/data_transformed.tsv
2025-09-10 01:28:48.845353 INFO::Running the linear model component
2025-09-10 01:28:48.854726 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:48.859377 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:48.863228 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:48.870558 INFO::Counting total values for each feature
2025-09-10 01:28:48.872388 INFO::Running the logistic model component
2025-09-10 01:28:48.880276 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:48.887084 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:48.892856 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:48.901971 INFO::Counting total values for each feature
2025-09-10 01:28:48.904165 INFO::Re-running abundances for warn_prevalence
2025-09-10 01:28:48.904911 INFO::Running selected normalization method: TSS
2025-09-10 01:28:48.906198 INFO::Running selected transform method: LOG
2025-09-10 01:28:48.914233 INFO::Fitting model to feature number 1, a
2025-09-10 01:28:48.9186 INFO::Fitting model to feature number 2, b
2025-09-10 01:28:48.922452 INFO::Fitting model to feature number 3, c
2025-09-10 01:28:49.013907 INFO::Creating output folder
2025-09-10 01:28:49.015147 INFO::Creating fits folder
2025-09-10 01:28:49.016035 INFO::Writing residuals to file /tmp/RtmprwVeoQ/file124eb121670ef/fits/residuals_linear.rds
2025-09-10 01:28:49.017347 INFO::Writing fitted values to file /tmp/RtmprwVeoQ/file124eb121670ef/fits/fitted_linear.rds
2025-09-10 01:28:49.01841 INFO::Writing residuals to file /tmp/RtmprwVeoQ/file124eb121670ef/fits/residuals_logistic.rds
2025-09-10 01:28:49.019505 INFO::Writing fitted values to file /tmp/RtmprwVeoQ/file124eb121670ef/fits/fitted_logistic.rds
2025-09-10 01:28:49.022287 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmprwVeoQ/file124eb121670ef/all_results.tsv
2025-09-10 01:28:49.024266 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/RtmprwVeoQ/file124eb121670ef/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
374.087 13.215 388.630
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 24.045 | 1.270 | 25.483 | |
| maaslin_check_arguments | 0.224 | 0.004 | 0.229 | |
| maaslin_check_formula | 0.187 | 0.007 | 0.194 | |
| maaslin_compute_formula | 0.196 | 0.009 | 0.205 | |
| maaslin_contrast_test | 23.193 | 1.637 | 24.902 | |
| maaslin_filter | 0.701 | 0.052 | 0.757 | |
| maaslin_fit | 15.336 | 1.130 | 16.605 | |
| maaslin_log_arguments | 0.191 | 0.007 | 0.198 | |
| maaslin_normalize | 0.400 | 0.026 | 0.428 | |
| maaslin_plot_results | 43.652 | 2.019 | 45.849 | |
| maaslin_plot_results_from_output | 42.899 | 1.441 | 44.625 | |
| maaslin_process_metadata | 0.628 | 0.045 | 0.680 | |
| maaslin_read_data | 0.184 | 0.006 | 0.193 | |
| maaslin_reorder_data | 0.196 | 0.008 | 0.204 | |
| maaslin_transform | 0.904 | 0.057 | 0.976 | |
| maaslin_write_results | 17.331 | 1.271 | 18.737 | |
| maaslin_write_results_lefse_format | 19.050 | 1.157 | 20.264 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.004 | |