William Nickols
| Snapshot Date: 2025-11-27 13:45 -0500 (Thu, 27 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-01 12:01 -0500 (Mon, 01 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4610 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | 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: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-11-28 08:19:17 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 08:52:10 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 1973.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 102.796 1.601 127.059
maaslin_plot_results 102.299 1.454 126.570
maaslin_contrast_test 43.093 1.840 55.928
maaslin3 41.490 1.585 54.214
maaslin_write_results_lefse_format 37.723 0.792 47.025
maaslin_write_results 32.800 0.894 41.075
maaslin_fit 32.270 1.266 41.208
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-28 08:35:46.743362 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:35:47.859089 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:35:48.136428 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:35:48.211393 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:35:48.329106 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:35:48.606943 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:35:48.624113 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:35:48.661788 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:35:48.97693 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:35:48.993042 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:35:49.169159 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:35:49.311909 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:35:49.362402 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:35:49.493633 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:35:49.733581 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:36:31.129063 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:36:31.383557 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:36:31.661774 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:36:31.738521 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:36:31.858778 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:36:32.128566 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:36:32.145076 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:36:32.181191 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:36:32.553944 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:36:32.570846 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:36:32.728602 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:36:32.854287 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:36:32.895303 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:36:33.03035 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:36:33.265549 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:36:44.716 R[76402:64363594] XType: com.apple.fonts is not accessible.
2025-11-28 08:36:44.716 R[76402:64363594] XType: XTFontStaticRegistry is enabled.
2025-11-28 08:37:40.800239 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:37:41.04371 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:37:41.287548 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:37:41.358052 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:37:41.472666 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:37:41.73505 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:37:41.752707 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:37:41.791383 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:37:43.414582 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:37:43.433794 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:37:43.648299 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:37:43.829389 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:37:43.871388 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:37:44.026082 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:37:44.27588 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:38:19.26844 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:38:19.504439 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:38:19.728879 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:38:19.796254 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:38:19.899807 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:38:20.125959 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:38:20.140867 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:38:20.175388 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:38:20.467245 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:38:20.486376 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:38:20.637376 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:38:20.761558 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:38:20.799875 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:38:20.926294 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:38:21.139338 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:38:21.749855 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_linear.rds
2025-11-28 08:38:21.870062 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_linear.rds
2025-11-28 08:38:21.99731 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_logistic.rds
2025-11-28 08:38:22.678701 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_logistic.rds
2025-11-28 08:39:19.299011 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:39:19.531228 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:39:19.75596 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:39:19.830084 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:39:19.936803 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:39:20.200946 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:39:20.218888 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:39:20.25613 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:39:20.569618 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:39:20.586963 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:39:20.751003 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:39:20.884999 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:39:20.92776 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:39:21.072026 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:39:21.312987 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:39:55.787553 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:39:56.01953 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:39:56.248218 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:39:56.312204 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:39:56.413349 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:39:56.647441 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:39:56.665858 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:39:56.701831 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:39:57.006713 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:39:57.026184 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:39:57.18048 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:39:57.34977 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:39:57.386004 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:39:57.510867 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:39:57.726843 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:39:58.324481 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_linear.rds
2025-11-28 08:39:58.484956 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_linear.rds
2025-11-28 08:39:58.593692 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_logistic.rds
2025-11-28 08:39:59.241952 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_logistic.rds
2025-11-28 08:40:55.090812 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:40:55.317147 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:40:55.544719 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:40:55.613407 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:40:55.727448 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:40:55.970153 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:40:55.989467 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:40:56.028347 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:40:56.326005 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:40:56.342382 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:40:56.500749 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:40:56.63031 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:40:56.667006 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:40:56.796268 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:40:57.027332 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:41:29.716064 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:41:29.950598 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:41:30.184907 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:41:30.254671 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:41:30.358972 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:41:30.611218 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:41:30.626758 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:41:30.668245 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:41:30.982546 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:41:31.012155 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:41:31.176715 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:41:31.304089 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:41:31.340583 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:41:31.466912 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:41:31.680008 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:41:32.271292 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_linear.rds
2025-11-28 08:41:32.386774 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_linear.rds
2025-11-28 08:41:32.513318 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/residuals_logistic.rds
2025-11-28 08:41:33.151025 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72f6c7f86/fits/fitted_logistic.rds
2025-11-28 08:42:29.365534 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:42:29.598878 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:42:29.824236 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:42:29.894433 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:42:30.001425 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:42:30.237524 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:42:30.257206 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:42:30.293164 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:42:30.570199 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:42:30.585344 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:42:30.730275 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:42:30.849537 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:42:30.887611 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:42:31.011936 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:42:31.221936 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:43:03.610351 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:43:03.860254 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:43:04.217313 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:43:04.281675 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:43:04.387762 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:43:04.665056 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:43:04.680773 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:43:04.718183 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:43:05.038563 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:43:05.055955 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:43:05.201976 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:43:05.331066 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:43:05.372062 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:43:05.501162 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:43:05.716965 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:44:14.891986 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:44:40.261125 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:45:46.855172 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:46:10.871166 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:46:12.650803 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_linear.rds
2025-11-28 08:46:12.766702 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_linear.rds
2025-11-28 08:46:12.836317 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_logistic.rds
2025-11-28 08:46:12.980906 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_logistic.rds
2025-11-28 08:47:13.497042 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:47:26.59156 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:47:27.583158 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_linear.rds
2025-11-28 08:47:27.701143 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_linear.rds
2025-11-28 08:47:27.778737 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_logistic.rds
2025-11-28 08:47:27.944716 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_logistic.rds
2025-11-28 08:48:19.015152 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:48:33.751933 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 08:48:34.708461 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_linear.rds
2025-11-28 08:48:34.838686 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_linear.rds
2025-11-28 08:48:34.920379 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_logistic.rds
2025-11-28 08:48:35.086497 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_logistic.rds
2025-11-28 08:49:25.835829 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:49:26.070449 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:49:26.313897 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:49:26.38598 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:49:26.503167 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:49:26.74697 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:49:26.766602 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:49:26.803567 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:49:27.164367 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:49:27.183267 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:49:27.349761 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:49:27.49209 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:49:27.535255 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:49:27.694581 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:49:27.947795 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:50:02.724527 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 08:50:02.970806 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 08:50:03.214888 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 08:50:03.323525 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 08:50:03.436981 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 08:50:03.676887 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 08:50:03.694318 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 08:50:03.734678 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 08:50:04.067955 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 08:50:04.08478 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 08:50:04.259934 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 08:50:04.409707 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 08:50:04.452129 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 08:50:04.590987 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 08:50:04.82903 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 08:50:05.653237 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_linear.rds
2025-11-28 08:50:05.806929 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_linear.rds
2025-11-28 08:50:05.945337 WARNING::Deleting existing residuals file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/residuals_logistic.rds
2025-11-28 08:50:06.670607 WARNING::Deleting existing fitted file: /tmp/RtmpuYLEib/file12a72549fae7d/fits/fitted_logistic.rds
2025-11-28 08:51:05.33362 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-28 08:51:05.389936 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-28 08:51:05.427442 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-28 08:51:05.607153 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-28 08:51:05.657802 ERROR::Effect name not found in metadata: d
2025-11-28 08:51:05.693906 ERROR::No user formula provided
2025-11-28 08:51:05.789107 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-28 08:51:05.824089 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-28 08:51:16.928367 INFO::Writing function arguments to log file
2025-11-28 08:51:16.987048 INFO::Verifying options selected are valid
2025-11-28 08:51:24.028461 INFO::Writing function arguments to log file
2025-11-28 08:51:24.063469 INFO::Verifying options selected are valid
2025-11-28 08:51:24.066095 INFO::Determining format of input files
2025-11-28 08:51:24.069794 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 08:51:24.075943 INFO::Running selected normalization method: TSS
2025-11-28 08:51:24.082515 INFO::Creating output feature tables folder
2025-11-28 08:51:24.085552 INFO::Writing normalized data to file /tmp/RtmpuYLEib/file12a724ef6ad57/features/data_norm.tsv
2025-11-28 08:51:24.090877 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-28 08:51:24.095636 INFO::Total samples in data: 16
2025-11-28 08:51:24.098424 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-28 08:51:24.101254 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-28 08:51:24.106568 INFO::Total filtered features: 0
2025-11-28 08:51:24.113257 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-28 08:51:24.116584 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-28 08:51:24.119398 INFO::Filtered feature names from variance filtering:
2025-11-28 08:51:24.12735 INFO::Writing filtered data to file /tmp/RtmpuYLEib/file12a724ef6ad57/features/filtered_data.tsv
2025-11-28 08:51:24.132275 INFO::Running selected transform method: LOG
2025-11-28 08:51:24.135403 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuYLEib/file12a724ef6ad57/features/data_transformed.tsv
2025-11-28 08:51:24.139511 INFO::Applying z-score to standardize continuous metadata
2025-11-28 08:51:24.150886 INFO::Running the linear model component
2025-11-28 08:51:24.207756 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:24.225079 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:24.239994 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:24.264142 INFO::Counting total values for each feature
2025-11-28 08:51:24.308869 INFO::Running the logistic model component
2025-11-28 08:51:24.50742 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:24.52325 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:24.538213 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:24.563244 INFO::Counting total values for each feature
2025-11-28 08:51:24.569174 INFO::Re-running abundances for warn_prevalence
2025-11-28 08:51:24.57179 INFO::Running selected normalization method: TSS
2025-11-28 08:51:24.576246 INFO::Running selected transform method: LOG
2025-11-28 08:51:24.629523 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:24.639927 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:24.650536 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:24.911881 INFO::Creating fits folder
2025-11-28 08:51:24.915203 INFO::Writing residuals to file /tmp/RtmpuYLEib/file12a724ef6ad57/fits/residuals_linear.rds
2025-11-28 08:51:24.918592 INFO::Writing fitted values to file /tmp/RtmpuYLEib/file12a724ef6ad57/fits/fitted_linear.rds
2025-11-28 08:51:24.924295 INFO::Writing residuals to file /tmp/RtmpuYLEib/file12a724ef6ad57/fits/residuals_logistic.rds
2025-11-28 08:51:24.927486 INFO::Writing fitted values to file /tmp/RtmpuYLEib/file12a724ef6ad57/fits/fitted_logistic.rds
2025-11-28 08:51:24.936563 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpuYLEib/file12a724ef6ad57/all_results.tsv
2025-11-28 08:51:24.945304 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/RtmpuYLEib/file12a724ef6ad57/significant_results.tsv
2025-11-28 08:51:24.949515 INFO::Creating output figures folder
2025-11-28 08:51:24.958126 INFO::Writing summary plot of significant
results to file: /tmp/RtmpuYLEib/file12a724ef6ad57/figures/summary_plot.pdf
2025-11-28 08:51:30.30732 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuYLEib/file12a724ef6ad57/figures
2025-11-28 08:51:30.322373 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 08:51:30.342841 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 08:51:32.086353 INFO::Writing summary plot of
significant results to file: /tmp/RtmpuYLEib/file12a724ef6ad57/figures/summary_plot.pdf
2025-11-28 08:51:39.947356 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuYLEib/file12a724ef6ad57/figures
2025-11-28 08:51:39.951036 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 08:51:39.964363 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 08:51:41.735842 INFO::Running the linear model component
2025-11-28 08:51:41.762094 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:41.775487 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:41.791915 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:41.818781 INFO::Counting total values for each feature
2025-11-28 08:51:41.825334 INFO::Running the logistic model component
2025-11-28 08:51:41.85292 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:41.870406 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:41.891824 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:41.9187 INFO::Counting total values for each feature
2025-11-28 08:51:41.927588 INFO::Re-running abundances for warn_prevalence
2025-11-28 08:51:41.929792 INFO::Running selected normalization method: TSS
2025-11-28 08:51:41.933276 INFO::Running selected transform method: LOG
2025-11-28 08:51:41.963596 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:41.976585 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:41.988792 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:42.247937 INFO::Creating output folder
2025-11-28 08:51:42.250337 INFO::Creating output figures folder
2025-11-28 08:51:42.255492 INFO::Writing summary plot of significant
results to file: /tmp/RtmpuYLEib/file12a72706ab40d/figures/summary_plot.pdf
2025-11-28 08:51:47.036993 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuYLEib/file12a72706ab40d/figures
2025-11-28 08:51:47.04063 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 08:51:47.059891 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 08:51:50.57322 INFO::Applying z-score to standardize continuous metadata
2025-11-28 08:51:50.596851 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-28 08:51:50.598823 INFO::Bypass z-score application to metadata
2025-11-28 08:51:50.610558 INFO::Bypass z-score application to metadata
2025-11-28 08:51:50.705759 INFO::Determining format of input files
2025-11-28 08:51:50.707856 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 08:51:50.713658 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-28 08:51:50.738351 INFO::Determining format of input files
2025-11-28 08:51:50.74444 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-28 08:51:50.747753 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 08:51:50.770919 INFO::Determining format of input files
2025-11-28 08:51:50.773225 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 08:51:50.780149 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 08:51:50.784685 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-28 08:51:50.78648 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-28 08:51:50.82706 INFO::Running selected transform method: LOG
2025-11-28 08:51:50.829431 INFO::Creating output feature tables folder
2025-11-28 08:51:50.835364 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuYLEib/file12a7265a7b26a/features/data_transformed.tsv
2025-11-28 08:51:50.850853 INFO::Running selected transform method: LOG
2025-11-28 08:51:50.853383 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuYLEib/file12a7265a7b26a/features/data_transformed.tsv
2025-11-28 08:51:50.867902 INFO::Running selected transform method: PLOG
2025-11-28 08:51:50.871395 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuYLEib/file12a7265a7b26a/features/data_transformed.tsv
2025-11-28 08:51:50.882097 INFO::Running selected transform method: NONE
2025-11-28 08:51:50.884097 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuYLEib/file12a7265a7b26a/features/data_transformed.tsv
2025-11-28 08:51:50.914987 INFO::Running the linear model component
2025-11-28 08:51:50.944194 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:50.9593 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:50.973039 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:50.999095 INFO::Counting total values for each feature
2025-11-28 08:51:51.006506 INFO::Running the logistic model component
2025-11-28 08:51:51.037708 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:51.056415 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:51.078132 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:51.107018 INFO::Counting total values for each feature
2025-11-28 08:51:51.11175 INFO::Re-running abundances for warn_prevalence
2025-11-28 08:51:51.113589 INFO::Running selected normalization method: TSS
2025-11-28 08:51:51.12227 INFO::Running selected transform method: LOG
2025-11-28 08:51:51.15214 INFO::Fitting model to feature number 1, a
2025-11-28 08:51:51.166486 INFO::Fitting model to feature number 2, b
2025-11-28 08:51:51.181985 INFO::Fitting model to feature number 3, c
2025-11-28 08:51:51.483817 INFO::Creating output folder
2025-11-28 08:51:51.490976 INFO::Creating fits folder
2025-11-28 08:51:51.493281 INFO::Writing residuals to file /tmp/RtmpuYLEib/file12a7264b28149/fits/residuals_linear.rds
2025-11-28 08:51:51.495703 INFO::Writing fitted values to file /tmp/RtmpuYLEib/file12a7264b28149/fits/fitted_linear.rds
2025-11-28 08:51:51.499051 INFO::Writing residuals to file /tmp/RtmpuYLEib/file12a7264b28149/fits/residuals_logistic.rds
2025-11-28 08:51:51.504207 INFO::Writing fitted values to file /tmp/RtmpuYLEib/file12a7264b28149/fits/fitted_logistic.rds
2025-11-28 08:51:51.510497 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpuYLEib/file12a7264b28149/all_results.tsv
2025-11-28 08:51:51.521286 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/RtmpuYLEib/file12a7264b28149/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
818.971 14.190 992.486
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 41.490 | 1.585 | 54.214 | |
| maaslin_check_arguments | 0.279 | 0.007 | 0.336 | |
| maaslin_check_formula | 0.299 | 0.015 | 0.384 | |
| maaslin_compute_formula | 0.305 | 0.016 | 0.410 | |
| maaslin_contrast_test | 43.093 | 1.840 | 55.928 | |
| maaslin_filter | 1.210 | 0.090 | 1.624 | |
| maaslin_fit | 32.270 | 1.266 | 41.208 | |
| maaslin_log_arguments | 0.291 | 0.015 | 0.411 | |
| maaslin_normalize | 0.680 | 0.049 | 0.878 | |
| maaslin_plot_results | 102.299 | 1.454 | 126.570 | |
| maaslin_plot_results_from_output | 102.796 | 1.601 | 127.059 | |
| maaslin_process_metadata | 1.204 | 0.076 | 1.641 | |
| maaslin_read_data | 0.280 | 0.015 | 0.400 | |
| maaslin_reorder_data | 0.306 | 0.016 | 0.412 | |
| maaslin_transform | 1.512 | 0.119 | 2.119 | |
| maaslin_write_results | 32.800 | 0.894 | 41.075 | |
| maaslin_write_results_lefse_format | 37.723 | 0.792 | 47.025 | |
| preprocess_dna_mtx | 0.009 | 0.001 | 0.012 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.014 | |