William Nickols
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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 2025-09-01 11:43 -0400 (Mon, 01 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 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 | | ||||||||
| kunpeng2 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.0.0.tar.gz |
| StartedAt: 2025-08-29 11:15:03 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 11:31:06 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 962.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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 53.146 0.313 53.583
maaslin_plot_results_from_output 52.811 0.215 53.155
maaslin3 31.208 0.738 32.033
maaslin_contrast_test 30.808 0.383 31.282
maaslin_write_results_lefse_format 24.794 0.124 24.975
maaslin_write_results 24.168 0.168 24.393
maaslin_fit 22.308 0.108 22.477
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-08-29 11:23:37.139244 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:23:37.266454 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:23:37.405641 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:23:37.441619 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:23:37.51198 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:23:37.638795 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:23:37.647319 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:23:37.666824 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:23:37.837144 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:23:37.845872 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:23:37.928056 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:23:37.99397 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:23:38.01334 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:23:38.079546 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:23:38.20472 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:24:03.171727 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:24:03.298995 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:24:03.425539 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:24:03.461737 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:24:03.519611 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:24:03.65636 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:24:03.665338 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:24:03.686231 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:24:03.863087 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:24:03.872648 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:24:03.984014 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:24:04.05246 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:24:04.072251 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:24:04.141958 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:24:04.259915 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:24:27.956286 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:24:28.124867 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:24:28.249079 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:24:28.284955 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:24:28.341544 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:24:28.464905 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:24:28.473423 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:24:28.492587 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:24:28.64942 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:24:28.658103 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:24:28.738471 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:24:29.87929 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:24:29.898496 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:24:29.963873 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:24:30.0785 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:24:51.693091 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:24:51.825667 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:24:51.959508 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:24:51.998654 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:24:52.061612 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:24:52.206557 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:24:52.215943 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:24:52.236305 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:24:52.392751 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:24:52.401839 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:24:52.487944 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:24:52.557699 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:24:52.579619 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:24:52.657449 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:24:52.818276 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:24:53.150728 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_linear.rds
2025-08-29 11:24:53.220198 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_linear.rds
2025-08-29 11:24:53.29165 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_logistic.rds
2025-08-29 11:24:53.639874 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_logistic.rds
2025-08-29 11:25:15.67866 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:25:15.807698 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:25:15.93203 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:25:15.967786 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:25:16.024688 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:25:16.150943 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:25:16.159658 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:25:16.178967 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:25:16.336003 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:25:16.34497 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:25:16.429196 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:25:16.494746 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:25:16.515173 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:25:16.58618 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:25:16.699318 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:25:37.701111 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:25:37.839434 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:25:39.20592 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:25:39.245481 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:25:39.307154 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:25:39.443423 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:25:39.452566 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:25:39.473314 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:25:39.640939 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:25:39.650486 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:25:39.742786 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:25:39.81566 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:25:39.837022 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:25:39.912049 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:25:40.032961 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:25:40.350599 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_linear.rds
2025-08-29 11:25:40.417172 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_linear.rds
2025-08-29 11:25:40.485258 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_logistic.rds
2025-08-29 11:25:40.821015 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_logistic.rds
2025-08-29 11:26:02.390764 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:26:02.527017 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:26:02.658123 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:26:02.697486 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:26:02.761756 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:26:02.89917 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:26:02.908415 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:26:02.929646 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:26:03.104664 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:26:03.113432 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:26:03.198993 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:26:03.267174 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:26:03.287593 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:26:03.357321 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:26:03.472591 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:26:24.661335 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:26:24.790133 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:26:24.915819 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:26:24.952255 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:26:25.00924 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:26:25.135077 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:26:25.143603 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:26:25.162974 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:26:25.321078 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:26:25.330498 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:26:25.41351 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:26:25.481314 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:26:25.499932 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:26:25.564262 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:26:25.679821 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:26:25.977764 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_linear.rds
2025-08-29 11:26:26.045047 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_linear.rds
2025-08-29 11:26:26.117529 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/residuals_logistic.rds
2025-08-29 11:26:26.41258 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e642472768/fits/fitted_logistic.rds
2025-08-29 11:26:47.996057 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:26:48.130989 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:26:48.26099 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:26:48.299381 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:26:48.358472 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:26:48.49141 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:26:48.500257 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:26:48.520278 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:26:48.690924 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:26:48.700008 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:26:48.785746 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:26:48.857042 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:26:48.878316 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:26:48.951751 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:26:49.077373 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:27:10.154291 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:27:10.30297 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:27:10.437472 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:27:10.482909 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:27:10.543391 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:27:10.675997 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:27:10.691404 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:27:10.712181 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:27:10.877726 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:27:10.886733 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:27:10.969882 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:27:11.038094 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:27:11.058545 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:27:11.133702 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:27:11.257329 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:27:37.443171 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:27:53.247441 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:28:20.067839 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:28:35.340211 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:28:36.285867 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_linear.rds
2025-08-29 11:28:36.355304 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_linear.rds
2025-08-29 11:28:36.399845 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_logistic.rds
2025-08-29 11:28:36.484271 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_logistic.rds
2025-08-29 11:29:00.733057 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:29:09.310719 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:29:09.939164 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_linear.rds
2025-08-29 11:29:10.009348 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_linear.rds
2025-08-29 11:29:10.054969 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_logistic.rds
2025-08-29 11:29:10.13864 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_logistic.rds
2025-08-29 11:29:30.980179 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:29:39.325307 WARNING::Fitting problem for feature 124 returning NA
2025-08-29 11:29:39.80025 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_linear.rds
2025-08-29 11:29:39.870362 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_linear.rds
2025-08-29 11:29:39.915451 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_logistic.rds
2025-08-29 11:29:39.998961 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_logistic.rds
2025-08-29 11:30:00.203567 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:30:00.335924 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:30:00.462235 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:30:00.499272 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:30:00.557161 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:30:00.686854 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:30:00.695636 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:30:00.715435 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:30:00.882023 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:30:00.890767 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:30:00.974347 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:30:01.042894 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:30:01.063176 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:30:01.132095 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:30:01.250604 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:30:20.95357 WARNING::Fitting problem for feature 50 returning NA
2025-08-29 11:30:21.078967 WARNING::Fitting problem for feature 62 returning NA
2025-08-29 11:30:21.20157 WARNING::Fitting problem for feature 74 returning NA
2025-08-29 11:30:21.237707 WARNING::Fitting problem for feature 78 returning NA
2025-08-29 11:30:21.294424 WARNING::Fitting problem for feature 84 returning NA
2025-08-29 11:30:21.421113 WARNING::Fitting problem for feature 96 returning NA
2025-08-29 11:30:21.429909 WARNING::Fitting problem for feature 97 returning NA
2025-08-29 11:30:21.450156 WARNING::Fitting problem for feature 99 returning NA
2025-08-29 11:30:21.614125 WARNING::Fitting problem for feature 114 returning NA
2025-08-29 11:30:21.623268 WARNING::Fitting problem for feature 115 returning NA
2025-08-29 11:30:21.703733 WARNING::Fitting problem for feature 123 returning NA
2025-08-29 11:30:21.774168 WARNING::Fitting problem for feature 130 returning NA
2025-08-29 11:30:21.795166 WARNING::Fitting problem for feature 132 returning NA
2025-08-29 11:30:21.86278 WARNING::Fitting problem for feature 139 returning NA
2025-08-29 11:30:21.973521 WARNING::Fitting problem for feature 150 returning NA
2025-08-29 11:30:23.726264 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_linear.rds
2025-08-29 11:30:23.788151 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_linear.rds
2025-08-29 11:30:23.851679 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/residuals_logistic.rds
2025-08-29 11:30:24.149201 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e6b2003ef/fits/fitted_logistic.rds
2025-08-29 11:30:44.714545 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-29 11:30:44.740572 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-29 11:30:44.758995 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-29 11:30:44.84148 ERROR::No fixed, group, or
ordered effects included in formula.
2025-08-29 11:30:44.867507 ERROR::Effect name not found in metadata: d
2025-08-29 11:30:44.88501 ERROR::No user formula provided
2025-08-29 11:30:44.928902 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-29 11:30:44.947 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-08-29 11:30:49.817413 INFO::Writing function arguments to log file
2025-08-29 11:30:49.838392 INFO::Verifying options selected are valid
2025-08-29 11:30:52.317644 INFO::Writing function arguments to log file
2025-08-29 11:30:52.334538 INFO::Verifying options selected are valid
2025-08-29 11:30:52.335992 INFO::Determining format of input files
2025-08-29 11:30:52.337337 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-29 11:30:52.340516 INFO::Running selected normalization method: TSS
2025-08-29 11:30:52.342519 INFO::Creating output feature tables folder
2025-08-29 11:30:52.343886 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/features/data_norm.tsv
2025-08-29 11:30:52.345889 INFO::Filter data based on min abundance and min prevalence
2025-08-29 11:30:52.347182 INFO::Total samples in data: 16
2025-08-29 11:30:52.348452 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-29 11:30:52.351288 INFO::Total filtered features: 0
2025-08-29 11:30:52.3529 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-29 11:30:52.354633 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-29 11:30:52.356052 INFO::Filtered feature names from variance filtering:
2025-08-29 11:30:52.357391 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/features/filtered_data.tsv
2025-08-29 11:30:52.35953 INFO::Running selected transform method: LOG
2025-08-29 11:30:52.361264 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/features/data_transformed.tsv
2025-08-29 11:30:52.363621 INFO::Applying z-score to standardize continuous metadata
2025-08-29 11:30:52.371115 INFO::Running the linear model component
2025-08-29 11:30:52.391393 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:52.397782 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:52.403953 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:52.414533 INFO::Counting total values for each feature
2025-08-29 11:30:52.417506 INFO::Running the logistic model component
2025-08-29 11:30:52.437658 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:52.446994 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:52.456388 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:52.469877 INFO::Counting total values for each feature
2025-08-29 11:30:52.473115 INFO::Re-running abundances for warn_prevalence
2025-08-29 11:30:52.474416 INFO::Running selected normalization method: TSS
2025-08-29 11:30:52.476552 INFO::Running selected transform method: LOG
2025-08-29 11:30:52.496568 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:52.503019 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:52.509314 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:52.644586 INFO::Creating fits folder
2025-08-29 11:30:52.646257 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/fits/residuals_linear.rds
2025-08-29 11:30:52.647799 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/fits/fitted_linear.rds
2025-08-29 11:30:52.649335 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/fits/residuals_logistic.rds
2025-08-29 11:30:52.650838 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/fits/fitted_logistic.rds
2025-08-29 11:30:52.654554 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/all_results.tsv
2025-08-29 11:30:52.65695 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): /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/significant_results.tsv
2025-08-29 11:30:52.658798 INFO::Creating output figures folder
2025-08-29 11:30:52.660823 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/figures/summary_plot.pdf
2025-08-29 11:30:54.381725 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/figures
2025-08-29 11:30:54.384277 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-29 11:30:54.391593 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-29 11:30:54.905371 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/figures/summary_plot.pdf
2025-08-29 11:30:56.645457 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66381a576/figures
2025-08-29 11:30:56.647596 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-29 11:30:56.654605 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-29 11:30:57.157245 INFO::Running the linear model component
2025-08-29 11:30:57.170652 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:57.176828 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:57.182874 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:57.193502 INFO::Counting total values for each feature
2025-08-29 11:30:57.196047 INFO::Running the logistic model component
2025-08-29 11:30:57.209134 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:57.218055 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:57.226739 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:57.239504 INFO::Counting total values for each feature
2025-08-29 11:30:57.242502 INFO::Re-running abundances for warn_prevalence
2025-08-29 11:30:57.243595 INFO::Running selected normalization method: TSS
2025-08-29 11:30:57.245513 INFO::Running selected transform method: LOG
2025-08-29 11:30:57.258874 INFO::Fitting model to feature number 1, a
2025-08-29 11:30:57.264992 INFO::Fitting model to feature number 2, b
2025-08-29 11:30:57.270859 INFO::Fitting model to feature number 3, c
2025-08-29 11:30:57.401497 INFO::Creating output folder
2025-08-29 11:30:57.402843 INFO::Creating output figures folder
2025-08-29 11:30:57.404664 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66d58e3b9/figures/summary_plot.pdf
2025-08-29 11:30:59.109864 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66d58e3b9/figures
2025-08-29 11:30:59.112245 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-29 11:30:59.119423 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-29 11:31:00.321308 INFO::Applying z-score to standardize continuous metadata
2025-08-29 11:31:00.332367 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-29 11:31:00.333597 INFO::Bypass z-score application to metadata
2025-08-29 11:31:00.337313 INFO::Bypass z-score application to metadata
2025-08-29 11:31:00.363229 INFO::Determining format of input files
2025-08-29 11:31:00.364645 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-29 11:31:00.365865 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-29 11:31:00.376622 INFO::Determining format of input files
2025-08-29 11:31:00.378204 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-29 11:31:00.380102 INFO::Input format is feature_specific_covariate samples as columns
2025-08-29 11:31:00.391705 INFO::Determining format of input files
2025-08-29 11:31:00.393168 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-29 11:31:00.39466 INFO::Input format is feature_specific_covariate samples as columns
2025-08-29 11:31:00.39708 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-29 11:31:00.398176 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-29 11:31:00.413696 INFO::Running selected transform method: LOG
2025-08-29 11:31:00.415259 INFO::Creating output feature tables folder
2025-08-29 11:31:00.416478 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e67fd8613e/features/data_transformed.tsv
2025-08-29 11:31:00.42218 INFO::Running selected transform method: LOG
2025-08-29 11:31:00.423804 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e67fd8613e/features/data_transformed.tsv
2025-08-29 11:31:00.42938 INFO::Running selected transform method: PLOG
2025-08-29 11:31:00.431832 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e67fd8613e/features/data_transformed.tsv
2025-08-29 11:31:00.43604 INFO::Running selected transform method: NONE
2025-08-29 11:31:00.437274 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e67fd8613e/features/data_transformed.tsv
2025-08-29 11:31:00.447587 INFO::Running the linear model component
2025-08-29 11:31:00.460894 INFO::Fitting model to feature number 1, a
2025-08-29 11:31:00.4671 INFO::Fitting model to feature number 2, b
2025-08-29 11:31:00.473256 INFO::Fitting model to feature number 3, c
2025-08-29 11:31:00.483807 INFO::Counting total values for each feature
2025-08-29 11:31:00.48638 INFO::Running the logistic model component
2025-08-29 11:31:00.499553 INFO::Fitting model to feature number 1, a
2025-08-29 11:31:00.509312 INFO::Fitting model to feature number 2, b
2025-08-29 11:31:00.519034 INFO::Fitting model to feature number 3, c
2025-08-29 11:31:00.532458 INFO::Counting total values for each feature
2025-08-29 11:31:00.535576 INFO::Re-running abundances for warn_prevalence
2025-08-29 11:31:00.536783 INFO::Running selected normalization method: TSS
2025-08-29 11:31:00.538779 INFO::Running selected transform method: LOG
2025-08-29 11:31:00.552149 INFO::Fitting model to feature number 1, a
2025-08-29 11:31:00.558419 INFO::Fitting model to feature number 2, b
2025-08-29 11:31:00.564685 INFO::Fitting model to feature number 3, c
2025-08-29 11:31:00.696394 INFO::Creating output folder
2025-08-29 11:31:00.697768 INFO::Creating fits folder
2025-08-29 11:31:00.698909 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/fits/residuals_linear.rds
2025-08-29 11:31:00.700189 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/fits/fitted_linear.rds
2025-08-29 11:31:00.701524 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/fits/residuals_logistic.rds
2025-08-29 11:31:00.702794 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/fits/fitted_logistic.rds
2025-08-29 11:31:00.706269 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/all_results.tsv
2025-08-29 11:31:00.708457 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): /home/biocbuild/tmp/Rtmppg4bxY/file1da3e66af2994c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
451.649 6.200 458.979
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 31.208 | 0.738 | 32.033 | |
| maaslin_check_arguments | 0.206 | 0.000 | 0.208 | |
| maaslin_check_formula | 0.206 | 0.004 | 0.210 | |
| maaslin_compute_formula | 0.239 | 0.004 | 0.243 | |
| maaslin_contrast_test | 30.808 | 0.383 | 31.282 | |
| maaslin_filter | 0.633 | 0.020 | 0.655 | |
| maaslin_fit | 22.308 | 0.108 | 22.477 | |
| maaslin_log_arguments | 0.207 | 0.000 | 0.207 | |
| maaslin_normalize | 0.413 | 0.000 | 0.414 | |
| maaslin_plot_results | 53.146 | 0.313 | 53.583 | |
| maaslin_plot_results_from_output | 52.811 | 0.215 | 53.155 | |
| maaslin_process_metadata | 0.660 | 0.032 | 0.694 | |
| maaslin_read_data | 0.215 | 0.000 | 0.216 | |
| maaslin_reorder_data | 0.220 | 0.004 | 0.225 | |
| maaslin_transform | 0.859 | 0.016 | 0.877 | |
| maaslin_write_results | 24.168 | 0.168 | 24.393 | |
| maaslin_write_results_lefse_format | 24.794 | 0.124 | 24.975 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.006 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |