William Nickols
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_21 |
| git_last_commit: d86be18 |
| git_last_commit_date: 2025-10-12 11:15:12 -0400 (Sun, 12 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 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" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1.0.2 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.0.2 |
| 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_1.0.2.tar.gz |
| StartedAt: 2025-10-14 10:44:39 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 11:02:46 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 1086.7 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_1.0.2.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 ‘1.0.2’
* 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 67.074 0.268 67.513
maaslin_plot_results_from_output 65.728 0.327 66.222
maaslin3 31.800 0.450 32.333
maaslin_contrast_test 31.073 0.188 31.336
maaslin_write_results_lefse_format 25.608 0.074 25.753
maaslin_write_results 24.463 0.180 24.706
maaslin_fit 21.784 0.103 21.946
* 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 ‘1.0.2’ ** 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")
2025-10-14 10:53:47.958343 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:53:48.087991 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:53:48.235356 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:53:48.283671 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:53:48.34031 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:53:48.465691 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:53:48.474163 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:53:48.493092 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:53:48.659715 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:53:48.668051 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:53:48.747943 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:53:48.815512 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:53:48.834932 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:53:48.916044 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:53:49.031339 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:54:15.17998 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:54:15.313061 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:54:15.445134 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:54:15.505333 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:54:15.57009 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:54:15.710956 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:54:15.720131 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:54:15.740964 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:54:15.911957 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:54:15.921381 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:54:16.012897 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:54:16.086533 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:54:16.107868 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:54:16.181553 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:54:16.310295 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:54:49.580394 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:54:49.716161 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:54:49.84849 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:54:49.887568 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:54:49.947632 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:54:50.082713 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:54:50.091592 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:54:50.111934 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:54:50.280509 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:54:50.289689 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:54:50.381822 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:54:50.45469 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:54:50.475887 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:54:50.549924 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:54:50.67277 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:55:12.95848 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:55:13.093531 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:55:13.231303 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:55:13.272321 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:55:13.336935 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:55:13.476919 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:55:13.48669 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:55:13.509754 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:55:13.721564 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:55:13.730447 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:55:13.815093 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:55:13.884752 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:55:13.904265 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:55:13.971043 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:55:14.085938 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:55:14.405986 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_linear.rds
2025-10-14 10:55:14.474975 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_linear.rds
2025-10-14 10:55:14.545759 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_logistic.rds
2025-10-14 10:55:14.892849 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_logistic.rds
2025-10-14 10:55:45.418619 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:55:45.564857 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:55:45.734561 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:55:45.776068 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:55:45.836054 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:55:45.962763 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:55:45.971301 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:55:45.990401 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:55:46.148422 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:55:46.157336 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:55:46.239341 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:55:46.305928 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:55:46.325321 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:55:46.391008 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:55:46.507965 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:56:07.596253 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:56:07.73713 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:56:07.881173 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:56:07.920374 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:56:07.979891 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:56:08.113477 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:56:08.122305 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:56:08.142657 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:56:08.312857 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:56:08.322227 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:56:08.410512 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:56:08.481434 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:56:08.502582 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:56:08.579153 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:56:08.710286 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:56:09.005952 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_linear.rds
2025-10-14 10:56:09.068826 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_linear.rds
2025-10-14 10:56:09.140149 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_logistic.rds
2025-10-14 10:56:09.448653 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_logistic.rds
2025-10-14 10:56:39.406404 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:56:39.541376 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:56:39.669118 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:56:39.705189 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:56:39.762541 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:56:39.889526 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:56:39.898145 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:56:39.917435 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:56:40.074884 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:56:40.083548 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:56:40.172693 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:56:40.27843 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:56:40.298565 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:56:40.367916 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:56:40.485039 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:57:01.833047 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:57:01.96533 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:57:02.096157 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:57:02.133263 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:57:02.192969 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:57:02.325631 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:57:02.334697 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:57:02.355543 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:57:02.527225 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:57:02.536838 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:57:02.636323 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:57:02.7074 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:57:02.727969 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:57:02.799295 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:57:02.924764 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:57:03.261448 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_linear.rds
2025-10-14 10:57:03.324302 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_linear.rds
2025-10-14 10:57:03.38923 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/residuals_logistic.rds
2025-10-14 10:57:03.698498 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b70ffac4d/fits/fitted_logistic.rds
2025-10-14 10:57:34.859266 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:57:34.998378 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:57:35.165525 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:57:35.205041 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:57:35.267125 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:57:35.402586 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:57:35.411513 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:57:35.431474 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:57:35.596844 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:57:35.610673 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:57:35.699486 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:57:35.77008 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:57:35.790495 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:57:35.860808 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:57:35.983708 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:57:55.882556 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:57:56.017998 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:57:56.150803 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:57:56.191001 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:57:56.255879 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:57:56.388552 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:57:56.397545 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:57:56.417749 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:57:56.581055 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:57:56.589894 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:57:56.673762 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:57:56.74112 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:57:56.760877 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:57:56.830242 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:57:56.993984 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:58:31.092514 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:58:47.295382 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:59:22.199288 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:59:37.030262 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:59:38.01283 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_linear.rds
2025-10-14 10:59:38.084126 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_linear.rds
2025-10-14 10:59:38.129755 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_logistic.rds
2025-10-14 10:59:38.213378 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_logistic.rds
2025-10-14 11:00:10.501654 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 11:00:21.251238 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 11:00:21.758401 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_linear.rds
2025-10-14 11:00:21.828039 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_linear.rds
2025-10-14 11:00:21.872844 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_logistic.rds
2025-10-14 11:00:21.955871 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_logistic.rds
2025-10-14 11:00:48.854175 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 11:00:59.799927 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 11:01:00.344458 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_linear.rds
2025-10-14 11:01:00.415772 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_linear.rds
2025-10-14 11:01:00.460772 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_logistic.rds
2025-10-14 11:01:00.542928 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_logistic.rds
2025-10-14 11:01:26.536126 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 11:01:26.679179 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 11:01:26.812825 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 11:01:26.85015 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 11:01:26.910547 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 11:01:27.044942 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 11:01:27.05365 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 11:01:27.074278 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 11:01:27.236099 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 11:01:27.24489 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 11:01:27.326695 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 11:01:27.392515 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 11:01:27.411952 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 11:01:27.521406 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 11:01:27.638084 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 11:01:49.348975 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 11:01:49.479287 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 11:01:49.612367 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 11:01:49.649869 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 11:01:49.70898 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 11:01:49.839418 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 11:01:49.848332 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 11:01:49.868308 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 11:01:50.034243 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 11:01:50.043986 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 11:01:50.13619 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 11:01:50.210935 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 11:01:50.232049 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 11:01:50.30381 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 11:01:50.423959 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 11:01:50.794647 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_linear.rds
2025-10-14 11:01:50.865353 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_linear.rds
2025-10-14 11:01:50.93577 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/residuals_logistic.rds
2025-10-14 11:01:51.278146 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b476dbdd5/fits/fitted_logistic.rds
2025-10-14 11:02:19.930101 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-14 11:02:19.957152 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-14 11:02:19.976211 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-14 11:02:20.060372 ERROR::No fixed, group, or
ordered effects included in formula.
2025-10-14 11:02:20.087741 ERROR::Effect name not found in metadata: d
2025-10-14 11:02:20.106228 ERROR::No user formula provided
2025-10-14 11:02:20.154265 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-14 11:02:20.172652 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-10-14 11:02:26.614931 INFO::Writing function arguments to log file
2025-10-14 11:02:26.63755 INFO::Verifying options selected are valid
2025-10-14 11:02:30.077453 INFO::Writing function arguments to log file
2025-10-14 11:02:30.095856 INFO::Verifying options selected are valid
2025-10-14 11:02:30.097425 INFO::Determining format of input files
2025-10-14 11:02:30.098803 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 11:02:30.102285 INFO::Running selected normalization method: TSS
2025-10-14 11:02:30.104522 INFO::Creating output feature tables folder
2025-10-14 11:02:30.106035 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/features/data_norm.tsv
2025-10-14 11:02:30.108106 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-14 11:02:30.109487 INFO::Total samples in data: 16
2025-10-14 11:02:30.110769 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-14 11:02:30.11205 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-14 11:02:30.11498 INFO::Total filtered features: 0
2025-10-14 11:02:30.116597 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-14 11:02:30.118461 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-14 11:02:30.11992 INFO::Filtered feature names from variance filtering:
2025-10-14 11:02:30.121311 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/features/filtered_data.tsv
2025-10-14 11:02:30.12347 INFO::Running selected transform method: LOG
2025-10-14 11:02:30.125255 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/features/data_transformed.tsv
2025-10-14 11:02:30.127555 INFO::Applying z-score to standardize continuous metadata
2025-10-14 11:02:30.135022 INFO::Running the linear model component
2025-10-14 11:02:30.156706 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:30.163253 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:30.169833 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:30.180993 INFO::Counting total values for each feature
2025-10-14 11:02:30.183853 INFO::Running the logistic model component
2025-10-14 11:02:30.205635 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:30.215158 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:30.224918 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:30.238973 INFO::Counting total values for each feature
2025-10-14 11:02:30.242339 INFO::Re-running abundances for warn_prevalence
2025-10-14 11:02:30.243735 INFO::Running selected normalization method: TSS
2025-10-14 11:02:30.246045 INFO::Running selected transform method: LOG
2025-10-14 11:02:30.2676 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:30.274135 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:30.280989 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:30.415547 INFO::Creating fits folder
2025-10-14 11:02:30.417308 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/fits/residuals_linear.rds
2025-10-14 11:02:30.418877 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/fits/fitted_linear.rds
2025-10-14 11:02:30.420752 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/fits/residuals_logistic.rds
2025-10-14 11:02:30.422739 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/fits/fitted_logistic.rds
2025-10-14 11:02:30.427122 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/all_results.tsv
2025-10-14 11:02:30.429667 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/RtmpcLRMws/file18f04b6be159a1/significant_results.tsv
2025-10-14 11:02:30.431574 INFO::Creating output figures folder
2025-10-14 11:02:30.433649 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/figures/summary_plot.pdf
2025-10-14 11:02:32.731667 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/figures
2025-10-14 11:02:32.734602 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 11:02:32.742181 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 11:02:33.465168 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/figures/summary_plot.pdf
2025-10-14 11:02:35.761698 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpcLRMws/file18f04b6be159a1/figures
2025-10-14 11:02:35.763841 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 11:02:35.770885 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 11:02:36.486646 INFO::Running the linear model component
2025-10-14 11:02:36.500801 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:36.507521 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:36.514085 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:36.52469 INFO::Counting total values for each feature
2025-10-14 11:02:36.527318 INFO::Running the logistic model component
2025-10-14 11:02:36.540582 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:36.549755 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:36.558699 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:36.571849 INFO::Counting total values for each feature
2025-10-14 11:02:36.575021 INFO::Re-running abundances for warn_prevalence
2025-10-14 11:02:36.576161 INFO::Running selected normalization method: TSS
2025-10-14 11:02:36.578187 INFO::Running selected transform method: LOG
2025-10-14 11:02:36.591581 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:36.59787 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:36.603944 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:36.755486 INFO::Creating output folder
2025-10-14 11:02:36.756976 INFO::Creating output figures folder
2025-10-14 11:02:36.7589 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpcLRMws/file18f04b156d69d4/figures/summary_plot.pdf
2025-10-14 11:02:39.058546 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpcLRMws/file18f04b156d69d4/figures
2025-10-14 11:02:39.061263 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 11:02:39.068478 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 11:02:40.479513 INFO::Applying z-score to standardize continuous metadata
2025-10-14 11:02:40.490592 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-14 11:02:40.491854 INFO::Bypass z-score application to metadata
2025-10-14 11:02:40.495619 INFO::Bypass z-score application to metadata
2025-10-14 11:02:40.52229 INFO::Determining format of input files
2025-10-14 11:02:40.52368 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 11:02:40.524989 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-14 11:02:40.53576 INFO::Determining format of input files
2025-10-14 11:02:40.537438 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-14 11:02:40.539375 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 11:02:40.551043 INFO::Determining format of input files
2025-10-14 11:02:40.552556 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 11:02:40.554145 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 11:02:40.55672 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-14 11:02:40.557954 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-14 11:02:40.573914 INFO::Running selected transform method: LOG
2025-10-14 11:02:40.575544 INFO::Creating output feature tables folder
2025-10-14 11:02:40.57687 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b317e1b88/features/data_transformed.tsv
2025-10-14 11:02:40.582529 INFO::Running selected transform method: LOG
2025-10-14 11:02:40.584269 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b317e1b88/features/data_transformed.tsv
2025-10-14 11:02:40.590086 INFO::Running selected transform method: PLOG
2025-10-14 11:02:40.592685 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b317e1b88/features/data_transformed.tsv
2025-10-14 11:02:40.596991 INFO::Running selected transform method: NONE
2025-10-14 11:02:40.598266 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b317e1b88/features/data_transformed.tsv
2025-10-14 11:02:40.608258 INFO::Running the linear model component
2025-10-14 11:02:40.62204 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:40.628968 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:40.636213 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:40.647631 INFO::Counting total values for each feature
2025-10-14 11:02:40.650348 INFO::Running the logistic model component
2025-10-14 11:02:40.664354 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:40.674276 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:40.684248 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:40.698626 INFO::Counting total values for each feature
2025-10-14 11:02:40.701893 INFO::Re-running abundances for warn_prevalence
2025-10-14 11:02:40.703223 INFO::Running selected normalization method: TSS
2025-10-14 11:02:40.705461 INFO::Running selected transform method: LOG
2025-10-14 11:02:40.719688 INFO::Fitting model to feature number 1, a
2025-10-14 11:02:40.726502 INFO::Fitting model to feature number 2, b
2025-10-14 11:02:40.733388 INFO::Fitting model to feature number 3, c
2025-10-14 11:02:40.875304 INFO::Creating output folder
2025-10-14 11:02:40.876826 INFO::Creating fits folder
2025-10-14 11:02:40.878201 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b696e5c37/fits/residuals_linear.rds
2025-10-14 11:02:40.879622 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b696e5c37/fits/fitted_linear.rds
2025-10-14 11:02:40.881456 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b696e5c37/fits/residuals_logistic.rds
2025-10-14 11:02:40.883229 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpcLRMws/file18f04b696e5c37/fits/fitted_logistic.rds
2025-10-14 11:02:40.887643 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpcLRMws/file18f04b696e5c37/all_results.tsv
2025-10-14 11:02:40.890294 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/RtmpcLRMws/file18f04b696e5c37/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
542.250 5.479 548.980
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 31.800 | 0.450 | 32.333 | |
| maaslin_check_arguments | 0.214 | 0.000 | 0.219 | |
| maaslin_check_formula | 0.218 | 0.000 | 0.217 | |
| maaslin_compute_formula | 0.218 | 0.004 | 0.223 | |
| maaslin_contrast_test | 31.073 | 0.188 | 31.336 | |
| maaslin_filter | 0.660 | 0.008 | 0.669 | |
| maaslin_fit | 21.784 | 0.103 | 21.946 | |
| maaslin_log_arguments | 0.21 | 0.00 | 0.21 | |
| maaslin_normalize | 0.405 | 0.014 | 0.420 | |
| maaslin_plot_results | 67.074 | 0.268 | 67.513 | |
| maaslin_plot_results_from_output | 65.728 | 0.327 | 66.222 | |
| maaslin_process_metadata | 0.698 | 0.012 | 0.711 | |
| maaslin_read_data | 0.206 | 0.004 | 0.210 | |
| maaslin_reorder_data | 0.218 | 0.000 | 0.220 | |
| maaslin_transform | 0.796 | 0.024 | 0.822 | |
| maaslin_write_results | 24.463 | 0.180 | 24.706 | |
| maaslin_write_results_lefse_format | 25.608 | 0.074 | 25.753 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.006 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |