William Nickols
| Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-11 12:06 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4532 |
| 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 1147/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.0.tar.gz |
| StartedAt: 2025-08-10 23:44:16 -0400 (Sun, 10 Aug 2025) |
| EndedAt: 2025-08-11 00:03:42 -0400 (Mon, 11 Aug 2025) |
| EllapsedTime: 1165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* 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 35.563 0.224 35.757
maaslin_plot_results_from_output 35.433 0.266 35.704
maaslin3 18.975 0.472 19.449
maaslin_contrast_test 17.889 0.323 18.213
maaslin_write_results_lefse_format 13.946 0.037 13.984
maaslin_write_results 13.565 0.196 13.764
maaslin_fit 12.839 0.079 12.920
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.0’ ** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-08-10 23:50:07.450199 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:50:07.523995 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:50:07.607457 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:50:07.628402 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:50:07.669165 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:50:07.742589 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:50:07.747721 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:50:07.758991 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:50:07.856904 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:50:07.862071 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:50:07.910526 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:50:07.949651 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:50:07.961265 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:50:08.000914 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:50:08.074358 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:50:23.072439 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:50:23.151321 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:50:23.231514 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:50:23.256448 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:50:23.295462 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:50:23.395181 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:50:23.400778 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:50:23.413038 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:50:23.510233 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:50:23.51545 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:50:23.564049 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:50:23.604947 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:50:23.617283 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:50:23.660341 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:50:23.731261 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:50:42.072932 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:50:42.171332 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:50:42.246684 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:50:42.269422 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:50:42.30383 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:50:42.377997 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:50:42.383393 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:50:42.395036 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:50:42.490455 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:50:42.496292 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:50:42.57971 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:50:42.622666 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:50:42.634674 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:50:42.675313 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:50:42.742248 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:50:55.778033 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:50:55.874568 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:50:55.951909 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:50:55.973624 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:50:56.007098 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:50:56.08058 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:50:56.085685 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:50:56.097244 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:50:56.190432 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:50:56.195759 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:50:56.245366 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:50:56.286311 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:50:56.298733 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:50:56.340344 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:50:56.412007 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:50:56.617315 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_linear.rds
2025-08-10 23:50:56.678246 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_linear.rds
2025-08-10 23:50:56.740781 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_logistic.rds
2025-08-10 23:50:57.04005 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_logistic.rds
2025-08-10 23:51:13.80488 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:51:13.906308 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:51:13.983907 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:51:14.006733 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:51:14.043551 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:51:14.121944 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:51:14.127732 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:51:14.140308 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:51:14.24195 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:51:14.248026 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:51:14.299691 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:51:14.342456 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:51:14.35465 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:51:14.396718 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:51:14.468495 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:51:26.900775 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:51:26.974387 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:51:27.049997 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:51:27.071947 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:51:27.106593 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:51:27.184211 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:51:27.18991 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:51:27.202295 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:51:27.304993 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:51:27.31124 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:51:27.364175 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:51:27.405667 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:51:27.418303 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:51:27.459815 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:51:27.531583 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:51:27.78098 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_linear.rds
2025-08-10 23:51:27.843799 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_linear.rds
2025-08-10 23:51:27.907559 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_logistic.rds
2025-08-10 23:51:28.208564 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_logistic.rds
2025-08-10 23:51:44.971792 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:51:45.058226 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:51:45.144937 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:51:45.170084 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:51:45.210628 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:51:45.297906 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:51:45.304198 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:51:45.317312 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:51:45.415517 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:51:45.420946 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:51:45.470758 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:51:45.533985 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:51:45.550953 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:51:45.591269 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:51:45.659027 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:51:57.539605 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:51:57.613936 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:51:57.688507 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:51:57.710065 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:51:57.744488 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:51:57.818993 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:51:57.824261 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:51:57.835911 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:51:57.933077 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:51:57.938546 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:51:57.988847 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:51:58.029665 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:51:58.04167 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:51:58.084146 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:51:58.156618 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:51:58.403069 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_linear.rds
2025-08-10 23:51:58.464488 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_linear.rds
2025-08-10 23:51:58.527508 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/residuals_logistic.rds
2025-08-10 23:51:58.827365 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb635411b78f/fits/fitted_logistic.rds
2025-08-10 23:52:15.49164 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:52:15.569501 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:52:15.645864 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:52:15.667943 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:52:15.703354 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:52:15.782656 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:52:15.788399 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:52:15.801001 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:52:15.927554 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:52:15.933255 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:52:15.983835 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:52:16.0249 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:52:16.036927 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:52:16.077885 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:52:16.148104 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:52:29.11611 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:52:29.196693 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:52:29.274909 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:52:29.298418 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:52:29.337682 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:52:29.423899 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:52:29.429607 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:52:29.441722 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:52:29.539631 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:52:29.545362 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:52:29.596748 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:52:29.637136 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:52:29.648977 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:52:29.689411 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:52:29.759361 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:52:48.854808 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:52:57.631954 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:53:18.072825 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:53:27.970949 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:53:28.697876 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_linear.rds
2025-08-10 23:53:28.759687 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_linear.rds
2025-08-10 23:53:28.79834 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_logistic.rds
2025-08-10 23:53:28.867259 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_logistic.rds
2025-08-10 23:53:47.1368 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:53:52.444336 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:53:52.800461 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_linear.rds
2025-08-10 23:53:52.862489 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_linear.rds
2025-08-10 23:53:52.901122 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_logistic.rds
2025-08-10 23:53:52.970349 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_logistic.rds
2025-08-10 23:54:08.328822 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:54:14.128432 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 23:54:14.471673 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_linear.rds
2025-08-10 23:54:14.533713 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_linear.rds
2025-08-10 23:54:14.572496 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_logistic.rds
2025-08-10 23:54:14.640898 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_logistic.rds
2025-08-10 23:54:31.116817 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:54:31.202935 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:54:31.311384 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:54:31.335402 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:54:31.373361 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:54:31.458135 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:54:31.463977 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:54:31.476665 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:54:31.57924 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:54:31.584973 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:54:31.640677 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:54:31.684614 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:54:31.697413 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:54:31.739194 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:54:31.809826 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:54:43.158346 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 23:54:43.243212 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 23:54:43.328208 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 23:54:43.353303 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 23:54:43.398235 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 23:54:43.489022 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 23:54:43.494927 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 23:54:43.508035 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 23:54:43.610937 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 23:54:43.616888 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 23:54:43.669399 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 23:54:43.711874 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 23:54:43.723818 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 23:54:43.765538 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 23:54:43.839243 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 23:54:45.251797 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_linear.rds
2025-08-10 23:54:45.313124 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_linear.rds
2025-08-10 23:54:45.376813 WARNING::Deleting existing residuals file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/residuals_logistic.rds
2025-08-10 23:54:45.676782 WARNING::Deleting existing fitted file: /tmp/Rtmp1KukDt/file1fdb633b1beebb/fits/fitted_logistic.rds
2025-08-10 23:55:01.720681 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-10 23:55:01.74485 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-10 23:55:01.761784 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-10 23:55:01.844625 ERROR::No fixed, group, or
ordered effects included in formula.
2025-08-10 23:55:01.862262 ERROR::Effect name not found in metadata: d
2025-08-10 23:55:01.874329 ERROR::No user formula provided
2025-08-10 23:55:01.906533 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-10 23:55:01.918525 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-08-10 23:55:04.940295 INFO::Writing function arguments to log file
2025-08-10 23:55:04.95399 INFO::Verifying options selected are valid
2025-08-10 23:55:06.873805 INFO::Writing function arguments to log file
2025-08-10 23:55:06.886283 INFO::Verifying options selected are valid
2025-08-10 23:55:06.88746 INFO::Determining format of input files
2025-08-10 23:55:06.888441 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 23:55:06.890761 INFO::Running selected normalization method: TSS
2025-08-10 23:55:06.892289 INFO::Creating output feature tables folder
2025-08-10 23:55:06.893241 INFO::Writing normalized data to file /tmp/Rtmp1KukDt/file1fdb6343849f25/features/data_norm.tsv
2025-08-10 23:55:06.894706 INFO::Filter data based on min abundance and min prevalence
2025-08-10 23:55:06.895589 INFO::Total samples in data: 16
2025-08-10 23:55:06.896463 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-10 23:55:06.89837 INFO::Total filtered features: 0
2025-08-10 23:55:06.899333 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-10 23:55:06.900482 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-10 23:55:06.901407 INFO::Filtered feature names from variance filtering:
2025-08-10 23:55:06.902275 INFO::Writing filtered data to file /tmp/Rtmp1KukDt/file1fdb6343849f25/features/filtered_data.tsv
2025-08-10 23:55:06.903759 INFO::Running selected transform method: LOG
2025-08-10 23:55:06.904939 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp1KukDt/file1fdb6343849f25/features/data_transformed.tsv
2025-08-10 23:55:06.90658 INFO::Applying z-score to standardize continuous metadata
2025-08-10 23:55:06.912183 INFO::Running the linear model component
2025-08-10 23:55:06.926244 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:06.930928 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:06.93529 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:06.94288 INFO::Counting total values for each feature
2025-08-10 23:55:06.944816 INFO::Running the logistic model component
2025-08-10 23:55:06.95897 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:06.965835 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:06.972484 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:06.982364 INFO::Counting total values for each feature
2025-08-10 23:55:06.984802 INFO::Re-running abundances for warn_prevalence
2025-08-10 23:55:06.985826 INFO::Running selected normalization method: TSS
2025-08-10 23:55:06.987449 INFO::Running selected transform method: LOG
2025-08-10 23:55:07.002101 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:07.007001 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:07.011718 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:07.100894 INFO::Creating fits folder
2025-08-10 23:55:07.102097 INFO::Writing residuals to file /tmp/Rtmp1KukDt/file1fdb6343849f25/fits/residuals_linear.rds
2025-08-10 23:55:07.103271 INFO::Writing fitted values to file /tmp/Rtmp1KukDt/file1fdb6343849f25/fits/fitted_linear.rds
2025-08-10 23:55:07.10443 INFO::Writing residuals to file /tmp/Rtmp1KukDt/file1fdb6343849f25/fits/residuals_logistic.rds
2025-08-10 23:55:07.105579 INFO::Writing fitted values to file /tmp/Rtmp1KukDt/file1fdb6343849f25/fits/fitted_logistic.rds
2025-08-10 23:55:07.108166 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp1KukDt/file1fdb6343849f25/all_results.tsv
2025-08-10 23:55:07.109895 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/Rtmp1KukDt/file1fdb6343849f25/significant_results.tsv
2025-08-10 23:55:07.111276 INFO::Creating output figures folder
2025-08-10 23:55:07.112647 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp1KukDt/file1fdb6343849f25/figures/summary_plot.pdf
2025-08-10 23:55:08.399431 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp1KukDt/file1fdb6343849f25/figures
2025-08-10 23:55:08.401371 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 23:55:08.406575 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 23:55:08.80452 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp1KukDt/file1fdb6343849f25/figures/summary_plot.pdf
2025-08-10 23:55:10.10198 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp1KukDt/file1fdb6343849f25/figures
2025-08-10 23:55:10.10351 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 23:55:10.108437 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 23:55:10.511979 INFO::Running the linear model component
2025-08-10 23:55:10.521113 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:10.525451 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:10.529527 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:10.536745 INFO::Counting total values for each feature
2025-08-10 23:55:10.538582 INFO::Running the logistic model component
2025-08-10 23:55:10.547614 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:10.554144 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:10.560276 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:10.570055 INFO::Counting total values for each feature
2025-08-10 23:55:10.572271 INFO::Re-running abundances for warn_prevalence
2025-08-10 23:55:10.573103 INFO::Running selected normalization method: TSS
2025-08-10 23:55:10.574521 INFO::Running selected transform method: LOG
2025-08-10 23:55:10.583763 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:10.588307 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:10.592935 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:10.683599 INFO::Creating output folder
2025-08-10 23:55:10.684588 INFO::Creating output figures folder
2025-08-10 23:55:10.685855 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp1KukDt/file1fdb635bf4cfab/figures/summary_plot.pdf
2025-08-10 23:55:11.982321 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp1KukDt/file1fdb635bf4cfab/figures
2025-08-10 23:55:11.98413 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 23:55:11.989375 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 23:55:12.850479 INFO::Applying z-score to standardize continuous metadata
2025-08-10 23:55:12.859468 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-10 23:55:12.860408 INFO::Bypass z-score application to metadata
2025-08-10 23:55:12.863053 INFO::Bypass z-score application to metadata
2025-08-10 23:55:12.882004 INFO::Determining format of input files
2025-08-10 23:55:12.882995 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 23:55:12.883879 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-10 23:55:12.891217 INFO::Determining format of input files
2025-08-10 23:55:12.892264 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-10 23:55:12.893607 INFO::Input format is feature_specific_covariate samples as columns
2025-08-10 23:55:12.901465 INFO::Determining format of input files
2025-08-10 23:55:12.902344 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 23:55:12.903317 INFO::Input format is feature_specific_covariate samples as columns
2025-08-10 23:55:12.904941 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-10 23:55:12.90571 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-10 23:55:12.916464 INFO::Running selected transform method: LOG
2025-08-10 23:55:12.917589 INFO::Creating output feature tables folder
2025-08-10 23:55:12.918479 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp1KukDt/file1fdb63470f2501/features/data_transformed.tsv
2025-08-10 23:55:12.922453 INFO::Running selected transform method: LOG
2025-08-10 23:55:12.923491 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp1KukDt/file1fdb63470f2501/features/data_transformed.tsv
2025-08-10 23:55:12.927352 INFO::Running selected transform method: PLOG
2025-08-10 23:55:12.928937 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp1KukDt/file1fdb63470f2501/features/data_transformed.tsv
2025-08-10 23:55:12.931796 INFO::Running selected transform method: NONE
2025-08-10 23:55:12.932625 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp1KukDt/file1fdb63470f2501/features/data_transformed.tsv
2025-08-10 23:55:12.940737 INFO::Running the linear model component
2025-08-10 23:55:12.949822 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:12.954245 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:12.958174 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:12.965282 INFO::Counting total values for each feature
2025-08-10 23:55:12.966902 INFO::Running the logistic model component
2025-08-10 23:55:12.975519 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:12.982009 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:12.987958 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:12.997034 INFO::Counting total values for each feature
2025-08-10 23:55:12.999145 INFO::Re-running abundances for warn_prevalence
2025-08-10 23:55:12.999931 INFO::Running selected normalization method: TSS
2025-08-10 23:55:13.00137 INFO::Running selected transform method: LOG
2025-08-10 23:55:13.010484 INFO::Fitting model to feature number 1, a
2025-08-10 23:55:13.014946 INFO::Fitting model to feature number 2, b
2025-08-10 23:55:13.019198 INFO::Fitting model to feature number 3, c
2025-08-10 23:55:13.111861 INFO::Creating output folder
2025-08-10 23:55:13.112948 INFO::Creating fits folder
2025-08-10 23:55:13.113924 INFO::Writing residuals to file /tmp/Rtmp1KukDt/file1fdb63209f856d/fits/residuals_linear.rds
2025-08-10 23:55:13.115046 INFO::Writing fitted values to file /tmp/Rtmp1KukDt/file1fdb63209f856d/fits/fitted_linear.rds
2025-08-10 23:55:13.116211 INFO::Writing residuals to file /tmp/Rtmp1KukDt/file1fdb63209f856d/fits/residuals_logistic.rds
2025-08-10 23:55:13.117339 INFO::Writing fitted values to file /tmp/Rtmp1KukDt/file1fdb63209f856d/fits/fitted_logistic.rds
2025-08-10 23:55:13.120051 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp1KukDt/file1fdb63209f856d/all_results.tsv
2025-08-10 23:55:13.121722 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/Rtmp1KukDt/file1fdb63209f856d/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
312.504 4.304 316.828
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 18.975 | 0.472 | 19.449 | |
| maaslin_check_arguments | 0.146 | 0.002 | 0.148 | |
| maaslin_check_formula | 0.134 | 0.003 | 0.137 | |
| maaslin_compute_formula | 0.139 | 0.000 | 0.140 | |
| maaslin_contrast_test | 17.889 | 0.323 | 18.213 | |
| maaslin_filter | 0.436 | 0.009 | 0.446 | |
| maaslin_fit | 12.839 | 0.079 | 12.920 | |
| maaslin_log_arguments | 0.128 | 0.002 | 0.130 | |
| maaslin_normalize | 0.261 | 0.003 | 0.264 | |
| maaslin_plot_results | 35.563 | 0.224 | 35.757 | |
| maaslin_plot_results_from_output | 35.433 | 0.266 | 35.704 | |
| maaslin_process_metadata | 0.431 | 0.005 | 0.437 | |
| maaslin_read_data | 0.125 | 0.002 | 0.127 | |
| maaslin_reorder_data | 0.130 | 0.002 | 0.133 | |
| maaslin_transform | 0.565 | 0.005 | 0.570 | |
| maaslin_write_results | 13.565 | 0.196 | 13.764 | |
| maaslin_write_results_lefse_format | 13.946 | 0.037 | 13.984 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |