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 12:02 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-11-28 11:20:57 -0000 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 11:38:36 -0000 (Fri, 28 Nov 2025) |
| EllapsedTime: 1059.4 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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_from_output 67.179 0.443 67.812
maaslin_plot_results 66.176 0.327 66.684
maaslin_contrast_test 30.720 0.415 31.215
maaslin3 28.680 1.241 30.001
maaslin_write_results_lefse_format 24.530 0.052 24.646
maaslin_write_results 21.725 0.115 21.900
maaslin_fit 21.360 0.122 21.541
* 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-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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")
2025-11-28 11:29:50.293841 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:29:50.432982 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:29:50.613258 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:29:50.651215 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:29:50.713177 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:29:50.842011 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:29:50.850707 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:29:50.870256 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:29:51.043693 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:29:51.052532 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:29:51.136776 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:29:51.205028 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:29:51.224867 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:29:51.307647 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:29:51.427512 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:30:16.111205 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:30:16.234501 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:30:16.383883 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:30:16.420404 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:30:16.478866 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:30:16.603648 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:30:16.612208 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:30:16.631593 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:30:16.788074 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:30:16.796486 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:30:16.877082 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:30:16.943153 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:30:16.962191 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:30:17.027736 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:30:17.138103 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:30:50.32231 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:30:50.466668 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:30:50.612238 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:30:50.657825 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:30:50.751253 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:30:50.891826 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:30:50.901697 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:30:50.924609 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:30:51.108855 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:30:51.119278 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:30:51.21242 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:30:51.282476 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:30:51.3029 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:30:51.374814 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:30:51.499703 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:31:12.91217 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:31:13.043844 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:31:13.205599 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:31:13.243952 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:31:13.305713 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:31:13.447753 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:31:13.45821 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:31:13.482479 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:31:13.677601 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:31:13.68783 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:31:13.785449 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:31:13.863857 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:31:13.888756 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:31:13.974473 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:31:14.117438 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:31:14.463051 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_linear.rds
2025-11-28 11:31:14.530861 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_linear.rds
2025-11-28 11:31:14.602938 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_logistic.rds
2025-11-28 11:31:14.954244 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_logistic.rds
2025-11-28 11:31:45.593707 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:31:45.741181 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:31:45.886899 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:31:45.929487 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:31:45.995823 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:31:46.144125 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:31:46.154233 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:31:46.176793 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:31:46.363431 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:31:46.373428 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:31:46.471283 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:31:46.550889 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:31:46.746953 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:31:46.830364 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:31:46.97601 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:32:07.73221 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:32:07.864914 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:32:07.997425 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:32:08.039471 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:32:08.096241 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:32:08.2202 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:32:08.228876 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:32:08.287214 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:32:08.45133 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:32:08.46009 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:32:08.546444 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:32:08.616273 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:32:08.637141 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:32:08.707165 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:32:08.834833 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:32:09.138264 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_linear.rds
2025-11-28 11:32:09.207378 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_linear.rds
2025-11-28 11:32:09.278479 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_logistic.rds
2025-11-28 11:32:09.634255 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_logistic.rds
2025-11-28 11:32:39.69479 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:32:39.828101 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:32:39.968334 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:32:40.045853 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:32:40.11096 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:32:40.246444 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:32:40.255539 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:32:40.277053 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:32:40.445856 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:32:40.455201 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:32:40.540603 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:32:40.613181 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:32:40.635341 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:32:40.7142 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:32:40.84672 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:32:59.86984 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:33:00.009327 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:33:00.14821 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:33:00.189582 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:33:00.251454 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:33:00.384901 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:33:00.394021 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:33:00.415254 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:33:00.629053 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:33:00.638644 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:33:00.728023 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:33:00.799628 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:33:00.819844 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:33:00.891185 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:33:01.023981 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:33:01.338802 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_linear.rds
2025-11-28 11:33:01.408526 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_linear.rds
2025-11-28 11:33:01.480155 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/residuals_logistic.rds
2025-11-28 11:33:01.829447 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a303bad0097/fits/fitted_logistic.rds
2025-11-28 11:33:31.524096 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:33:31.666505 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:33:31.808091 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:33:31.849927 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:33:31.913726 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:33:32.053259 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:33:32.063308 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:33:32.087216 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:33:32.253523 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:33:32.262397 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:33:32.347562 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:33:32.417638 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:33:32.437078 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:33:32.508236 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:33:32.636019 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:33:52.768081 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:33:52.919267 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:33:53.062007 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:33:53.105226 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:33:53.169583 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:33:53.314614 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:33:53.323665 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:33:53.344811 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:33:53.514151 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:33:53.523347 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:33:53.613572 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:33:53.683249 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:33:53.703488 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:33:53.777423 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:33:53.906328 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:34:26.788784 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:34:40.717202 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:35:17.982496 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:35:32.410438 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:35:33.479395 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_linear.rds
2025-11-28 11:35:33.552786 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_linear.rds
2025-11-28 11:35:33.596776 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_logistic.rds
2025-11-28 11:35:33.675213 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_logistic.rds
2025-11-28 11:36:06.018014 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:36:15.726185 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:36:16.268725 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_linear.rds
2025-11-28 11:36:16.340219 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_linear.rds
2025-11-28 11:36:16.385306 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_logistic.rds
2025-11-28 11:36:16.466798 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_logistic.rds
2025-11-28 11:36:43.267952 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:36:52.806374 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 11:36:53.297937 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_linear.rds
2025-11-28 11:36:53.366847 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_linear.rds
2025-11-28 11:36:53.410753 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_logistic.rds
2025-11-28 11:36:53.492344 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_logistic.rds
2025-11-28 11:37:20.680111 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:37:20.816271 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:37:20.949476 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:37:20.988726 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:37:21.051892 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:37:21.233334 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:37:21.242916 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:37:21.264793 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:37:21.447437 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:37:21.456684 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:37:21.545495 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:37:21.616733 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:37:21.637571 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:37:21.708584 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:37:21.830426 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:37:41.431186 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 11:37:41.57669 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 11:37:41.721863 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 11:37:41.763485 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 11:37:41.831722 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 11:37:41.982739 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 11:37:41.992921 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 11:37:42.015795 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 11:37:42.212626 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 11:37:42.224117 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 11:37:42.322767 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 11:37:42.396594 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 11:37:42.418074 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 11:37:42.489991 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 11:37:42.618207 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 11:37:43.050082 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_linear.rds
2025-11-28 11:37:43.117718 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_linear.rds
2025-11-28 11:37:43.187304 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/residuals_logistic.rds
2025-11-28 11:37:43.521454 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpoYf8Az/file164a30332cf782/fits/fitted_logistic.rds
2025-11-28 11:38:11.96175 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-28 11:38:11.988656 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-28 11:38:12.007482 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-28 11:38:12.092729 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-28 11:38:12.120317 ERROR::Effect name not found in metadata: d
2025-11-28 11:38:12.138545 ERROR::No user formula provided
2025-11-28 11:38:12.186678 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-28 11:38:12.205032 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-28 11:38:17.173055 INFO::Writing function arguments to log file
2025-11-28 11:38:17.195711 INFO::Verifying options selected are valid
2025-11-28 11:38:20.573164 INFO::Writing function arguments to log file
2025-11-28 11:38:20.592057 INFO::Verifying options selected are valid
2025-11-28 11:38:20.593674 INFO::Determining format of input files
2025-11-28 11:38:20.595082 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 11:38:20.598469 INFO::Running selected normalization method: TSS
2025-11-28 11:38:20.600593 INFO::Creating output feature tables folder
2025-11-28 11:38:20.602153 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/features/data_norm.tsv
2025-11-28 11:38:20.604213 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-28 11:38:20.605624 INFO::Total samples in data: 16
2025-11-28 11:38:20.606906 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-28 11:38:20.608178 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-28 11:38:20.611153 INFO::Total filtered features: 0
2025-11-28 11:38:20.612693 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-28 11:38:20.614507 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-28 11:38:20.615915 INFO::Filtered feature names from variance filtering:
2025-11-28 11:38:20.61731 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/features/filtered_data.tsv
2025-11-28 11:38:20.619434 INFO::Running selected transform method: LOG
2025-11-28 11:38:20.621279 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/features/data_transformed.tsv
2025-11-28 11:38:20.623751 INFO::Applying z-score to standardize continuous metadata
2025-11-28 11:38:20.631165 INFO::Running the linear model component
2025-11-28 11:38:20.653303 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:20.660182 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:20.66724 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:20.678257 INFO::Counting total values for each feature
2025-11-28 11:38:20.681074 INFO::Running the logistic model component
2025-11-28 11:38:20.702297 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:20.711873 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:20.721436 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:20.734899 INFO::Counting total values for each feature
2025-11-28 11:38:20.738307 INFO::Re-running abundances for warn_prevalence
2025-11-28 11:38:20.739796 INFO::Running selected normalization method: TSS
2025-11-28 11:38:20.742168 INFO::Running selected transform method: LOG
2025-11-28 11:38:20.76354 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:20.770203 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:20.776942 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:20.917267 INFO::Creating fits folder
2025-11-28 11:38:20.919084 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/fits/residuals_linear.rds
2025-11-28 11:38:20.920789 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/fits/fitted_linear.rds
2025-11-28 11:38:20.922685 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/fits/residuals_logistic.rds
2025-11-28 11:38:20.924442 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/fits/fitted_logistic.rds
2025-11-28 11:38:20.928619 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/all_results.tsv
2025-11-28 11:38:20.93136 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/RtmpoYf8Az/file164a307dc9bf5b/significant_results.tsv
2025-11-28 11:38:20.933542 INFO::Creating output figures folder
2025-11-28 11:38:20.935747 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/figures/summary_plot.pdf
2025-11-28 11:38:23.288402 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/figures
2025-11-28 11:38:23.291317 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 11:38:23.299217 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 11:38:24.038692 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/figures/summary_plot.pdf
2025-11-28 11:38:26.337252 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpoYf8Az/file164a307dc9bf5b/figures
2025-11-28 11:38:26.339403 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 11:38:26.346469 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 11:38:27.099285 INFO::Running the linear model component
2025-11-28 11:38:27.112952 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:27.11938 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:27.125924 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:27.136559 INFO::Counting total values for each feature
2025-11-28 11:38:27.139175 INFO::Running the logistic model component
2025-11-28 11:38:27.152582 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:27.162225 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:27.17157 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:27.184886 INFO::Counting total values for each feature
2025-11-28 11:38:27.187957 INFO::Re-running abundances for warn_prevalence
2025-11-28 11:38:27.189285 INFO::Running selected normalization method: TSS
2025-11-28 11:38:27.191329 INFO::Running selected transform method: LOG
2025-11-28 11:38:27.2053 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:27.211812 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:27.218297 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:27.356764 INFO::Creating output folder
2025-11-28 11:38:27.35823 INFO::Creating output figures folder
2025-11-28 11:38:27.360111 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpoYf8Az/file164a3076764061/figures/summary_plot.pdf
2025-11-28 11:38:29.702775 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpoYf8Az/file164a3076764061/figures
2025-11-28 11:38:29.705242 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 11:38:29.712425 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 11:38:31.122665 INFO::Applying z-score to standardize continuous metadata
2025-11-28 11:38:31.133819 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-28 11:38:31.135073 INFO::Bypass z-score application to metadata
2025-11-28 11:38:31.138951 INFO::Bypass z-score application to metadata
2025-11-28 11:38:31.165836 INFO::Determining format of input files
2025-11-28 11:38:31.167198 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 11:38:31.168433 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-28 11:38:31.17926 INFO::Determining format of input files
2025-11-28 11:38:31.180875 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-28 11:38:31.182804 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 11:38:31.194548 INFO::Determining format of input files
2025-11-28 11:38:31.196031 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 11:38:31.197612 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 11:38:31.200065 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 11:38:31.201313 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 11:38:31.216964 INFO::Running selected transform method: LOG
2025-11-28 11:38:31.218591 INFO::Creating output feature tables folder
2025-11-28 11:38:31.219832 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a3026b8fa8e/features/data_transformed.tsv
2025-11-28 11:38:31.225611 INFO::Running selected transform method: LOG
2025-11-28 11:38:31.227227 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a3026b8fa8e/features/data_transformed.tsv
2025-11-28 11:38:31.232697 INFO::Running selected transform method: PLOG
2025-11-28 11:38:31.235212 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a3026b8fa8e/features/data_transformed.tsv
2025-11-28 11:38:31.23941 INFO::Running selected transform method: NONE
2025-11-28 11:38:31.24065 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpoYf8Az/file164a3026b8fa8e/features/data_transformed.tsv
2025-11-28 11:38:31.250797 INFO::Running the linear model component
2025-11-28 11:38:31.264575 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:31.27108 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:31.277437 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:31.287858 INFO::Counting total values for each feature
2025-11-28 11:38:31.290484 INFO::Running the logistic model component
2025-11-28 11:38:31.304345 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:31.313936 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:31.323273 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:31.337275 INFO::Counting total values for each feature
2025-11-28 11:38:31.340348 INFO::Re-running abundances for warn_prevalence
2025-11-28 11:38:31.341603 INFO::Running selected normalization method: TSS
2025-11-28 11:38:31.343635 INFO::Running selected transform method: LOG
2025-11-28 11:38:31.357517 INFO::Fitting model to feature number 1, a
2025-11-28 11:38:31.364002 INFO::Fitting model to feature number 2, b
2025-11-28 11:38:31.370674 INFO::Fitting model to feature number 3, c
2025-11-28 11:38:31.512252 INFO::Creating output folder
2025-11-28 11:38:31.513961 INFO::Creating fits folder
2025-11-28 11:38:31.515602 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpoYf8Az/file164a30777f26a4/fits/residuals_linear.rds
2025-11-28 11:38:31.517506 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpoYf8Az/file164a30777f26a4/fits/fitted_linear.rds
2025-11-28 11:38:31.51952 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpoYf8Az/file164a30777f26a4/fits/residuals_logistic.rds
2025-11-28 11:38:31.521616 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpoYf8Az/file164a30777f26a4/fits/fitted_logistic.rds
2025-11-28 11:38:31.526035 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpoYf8Az/file164a30777f26a4/all_results.tsv
2025-11-28 11:38:31.528803 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/RtmpoYf8Az/file164a30777f26a4/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
526.666 8.191 536.295
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.680 | 1.241 | 30.001 | |
| maaslin_check_arguments | 0.217 | 0.000 | 0.218 | |
| maaslin_check_formula | 0.211 | 0.000 | 0.212 | |
| maaslin_compute_formula | 0.251 | 0.000 | 0.252 | |
| maaslin_contrast_test | 30.720 | 0.415 | 31.215 | |
| maaslin_filter | 0.666 | 0.024 | 0.692 | |
| maaslin_fit | 21.360 | 0.122 | 21.541 | |
| maaslin_log_arguments | 0.190 | 0.000 | 0.191 | |
| maaslin_normalize | 0.361 | 0.008 | 0.369 | |
| maaslin_plot_results | 66.176 | 0.327 | 66.684 | |
| maaslin_plot_results_from_output | 67.179 | 0.443 | 67.812 | |
| maaslin_process_metadata | 0.651 | 0.008 | 0.661 | |
| maaslin_read_data | 0.183 | 0.008 | 0.192 | |
| maaslin_reorder_data | 0.206 | 0.000 | 0.206 | |
| maaslin_transform | 0.752 | 0.032 | 0.786 | |
| maaslin_write_results | 21.725 | 0.115 | 21.900 | |
| maaslin_write_results_lefse_format | 24.530 | 0.052 | 24.646 | |
| preprocess_dna_mtx | 0.006 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |