William Nickols
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 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 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| 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: 2025-11-11 11:16:32 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 11:33:39 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 1026.5 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 65.196 0.494 65.867
maaslin_plot_results 64.695 0.352 65.217
maaslin_contrast_test 29.689 0.403 30.174
maaslin3 29.437 0.451 29.967
maaslin_write_results_lefse_format 24.938 0.131 25.133
maaslin_write_results 22.880 0.187 23.140
maaslin_fit 21.315 0.120 21.495
* 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")
2025-11-11 11:25:07.933251 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:25:08.07339 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:25:08.248248 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:25:08.290122 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:25:08.34955 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:25:08.479003 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:25:08.487831 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:25:08.507747 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:25:08.679271 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:25:08.68792 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:25:08.770024 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:25:08.837527 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:25:08.856999 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:25:08.937706 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:25:09.049061 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:25:32.797999 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:25:32.923168 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:25:33.068593 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:25:33.105143 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:25:33.163315 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:25:33.290349 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:25:33.298788 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:25:33.318094 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:25:33.480203 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:25:33.488852 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:25:33.573524 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:25:33.644375 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:25:33.664562 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:25:33.735178 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:25:33.859027 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:26:06.703673 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:26:06.83972 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:26:06.970731 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:26:07.009164 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:26:07.068887 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:26:07.201018 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:26:07.210036 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:26:07.230334 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:26:07.414102 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:26:07.425208 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:26:07.522238 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:26:07.598027 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:26:07.6201 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:26:07.698961 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:26:07.836674 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:26:28.368993 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:26:28.525142 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:26:28.654045 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:26:28.690822 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:26:28.74739 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:26:28.879162 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:26:28.887831 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:26:28.907538 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:26:29.071003 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:26:29.080187 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:26:29.170891 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:26:29.242198 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:26:29.263346 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:26:29.345881 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:26:29.470314 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:26:29.767447 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_linear.rds
2025-11-11 11:26:29.835492 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_linear.rds
2025-11-11 11:26:29.905111 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_logistic.rds
2025-11-11 11:26:30.246073 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_logistic.rds
2025-11-11 11:26:59.546858 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:26:59.678197 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:26:59.803174 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:26:59.838739 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:26:59.895899 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:27:00.020115 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:27:00.02844 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:27:00.047371 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:27:00.201071 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:27:00.209552 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:27:00.290641 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:27:00.357666 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:27:00.465109 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:27:00.54136 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:27:00.663815 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:27:21.405355 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:27:21.541196 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:27:21.675313 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:27:21.713674 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:27:21.773382 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:27:21.906347 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:27:21.915082 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:27:21.936153 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:27:22.112246 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:27:22.121755 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:27:22.213577 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:27:22.289404 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:27:22.31054 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:27:22.37827 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:27:22.496124 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:27:22.799619 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_linear.rds
2025-11-11 11:27:22.868672 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_linear.rds
2025-11-11 11:27:22.939004 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_logistic.rds
2025-11-11 11:27:23.287992 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_logistic.rds
2025-11-11 11:27:52.781053 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:27:52.90868 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:27:53.038543 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:27:53.076068 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:27:53.137032 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:27:53.268057 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:27:53.276648 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:27:53.296921 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:27:53.466569 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:27:53.475881 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:27:53.596449 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:27:53.673872 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:27:53.696265 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:27:53.770637 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:27:53.892003 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:28:12.470995 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:28:12.596699 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:28:12.723615 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:28:12.760337 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:28:12.815916 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:28:12.944057 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:28:12.952561 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:28:12.971499 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:28:13.128869 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:28:13.137799 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:28:13.219754 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:28:13.284086 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:28:13.302676 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:28:13.368577 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:28:13.494161 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:28:13.835113 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_linear.rds
2025-11-11 11:28:13.901093 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_linear.rds
2025-11-11 11:28:13.968967 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/residuals_logistic.rds
2025-11-11 11:28:14.303673 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb7134fc45/fits/fitted_logistic.rds
2025-11-11 11:28:43.207482 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:28:43.340512 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:28:43.469986 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:28:43.507588 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:28:43.566967 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:28:43.70214 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:28:43.710925 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:28:43.73099 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:28:43.900826 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:28:43.910263 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:28:44.000417 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:28:44.068374 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:28:44.08845 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:28:44.156096 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:28:44.273523 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:29:03.794041 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:29:03.93436 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:29:04.070056 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:29:04.106738 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:29:04.164618 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:29:04.292351 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:29:04.300927 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:29:04.320818 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:29:04.520569 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:29:04.541987 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:29:04.646714 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:29:04.714635 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:29:04.734821 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:29:04.800971 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:29:04.917253 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:29:37.169967 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:29:51.174088 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:30:26.52773 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:30:39.738717 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:30:40.724771 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_linear.rds
2025-11-11 11:30:40.786071 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_linear.rds
2025-11-11 11:30:40.825838 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_logistic.rds
2025-11-11 11:30:40.896928 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_logistic.rds
2025-11-11 11:31:11.669326 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:31:21.881209 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:31:22.411748 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_linear.rds
2025-11-11 11:31:22.480583 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_linear.rds
2025-11-11 11:31:22.52381 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_logistic.rds
2025-11-11 11:31:22.601182 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_logistic.rds
2025-11-11 11:31:48.750805 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:31:58.247211 WARNING::Fitting problem for feature 124 returning NA
2025-11-11 11:31:58.860628 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_linear.rds
2025-11-11 11:31:58.92396 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_linear.rds
2025-11-11 11:31:58.965553 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_logistic.rds
2025-11-11 11:31:59.041007 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_logistic.rds
2025-11-11 11:32:24.368508 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:32:24.548498 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:32:24.691255 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:32:24.734353 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:32:24.805022 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:32:24.939991 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:32:24.949147 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:32:24.969916 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:32:25.138537 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:32:25.147873 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:32:25.238485 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:32:25.313323 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:32:25.33476 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:32:25.406315 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:32:25.538904 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:32:45.51195 WARNING::Fitting problem for feature 50 returning NA
2025-11-11 11:32:45.633701 WARNING::Fitting problem for feature 62 returning NA
2025-11-11 11:32:45.755381 WARNING::Fitting problem for feature 74 returning NA
2025-11-11 11:32:45.790476 WARNING::Fitting problem for feature 78 returning NA
2025-11-11 11:32:45.847506 WARNING::Fitting problem for feature 84 returning NA
2025-11-11 11:32:45.972725 WARNING::Fitting problem for feature 96 returning NA
2025-11-11 11:32:45.981488 WARNING::Fitting problem for feature 97 returning NA
2025-11-11 11:32:46.000716 WARNING::Fitting problem for feature 99 returning NA
2025-11-11 11:32:46.160059 WARNING::Fitting problem for feature 114 returning NA
2025-11-11 11:32:46.168901 WARNING::Fitting problem for feature 115 returning NA
2025-11-11 11:32:46.251638 WARNING::Fitting problem for feature 123 returning NA
2025-11-11 11:32:46.3167 WARNING::Fitting problem for feature 130 returning NA
2025-11-11 11:32:46.335439 WARNING::Fitting problem for feature 132 returning NA
2025-11-11 11:32:46.399713 WARNING::Fitting problem for feature 139 returning NA
2025-11-11 11:32:46.508217 WARNING::Fitting problem for feature 150 returning NA
2025-11-11 11:32:46.912951 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_linear.rds
2025-11-11 11:32:46.973698 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_linear.rds
2025-11-11 11:32:47.036122 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/residuals_logistic.rds
2025-11-11 11:32:47.332733 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb464f4b77/fits/fitted_logistic.rds
2025-11-11 11:33:14.96538 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-11 11:33:14.993618 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-11 11:33:15.013614 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-11 11:33:15.098999 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-11 11:33:15.125953 ERROR::Effect name not found in metadata: d
2025-11-11 11:33:15.144041 ERROR::No user formula provided
2025-11-11 11:33:15.190823 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-11 11:33:15.209262 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-11 11:33:19.999177 INFO::Writing function arguments to log file
2025-11-11 11:33:20.020525 INFO::Verifying options selected are valid
2025-11-11 11:33:23.387163 INFO::Writing function arguments to log file
2025-11-11 11:33:23.408366 INFO::Verifying options selected are valid
2025-11-11 11:33:23.410144 INFO::Determining format of input files
2025-11-11 11:33:23.411824 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 11:33:23.415897 INFO::Running selected normalization method: TSS
2025-11-11 11:33:23.418501 INFO::Creating output feature tables folder
2025-11-11 11:33:23.420391 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/features/data_norm.tsv
2025-11-11 11:33:23.422959 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-11 11:33:23.424651 INFO::Total samples in data: 16
2025-11-11 11:33:23.426272 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-11 11:33:23.42785 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-11 11:33:23.431401 INFO::Total filtered features: 0
2025-11-11 11:33:23.433475 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-11 11:33:23.435796 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-11 11:33:23.437674 INFO::Filtered feature names from variance filtering:
2025-11-11 11:33:23.439212 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/features/filtered_data.tsv
2025-11-11 11:33:23.441643 INFO::Running selected transform method: LOG
2025-11-11 11:33:23.443598 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/features/data_transformed.tsv
2025-11-11 11:33:23.446191 INFO::Applying z-score to standardize continuous metadata
2025-11-11 11:33:23.453843 INFO::Running the linear model component
2025-11-11 11:33:23.497293 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:23.505134 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:23.512555 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:23.52496 INFO::Counting total values for each feature
2025-11-11 11:33:23.527984 INFO::Running the logistic model component
2025-11-11 11:33:23.550266 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:23.560677 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:23.571045 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:23.58587 INFO::Counting total values for each feature
2025-11-11 11:33:23.589502 INFO::Re-running abundances for warn_prevalence
2025-11-11 11:33:23.591066 INFO::Running selected normalization method: TSS
2025-11-11 11:33:23.593526 INFO::Running selected transform method: LOG
2025-11-11 11:33:23.616395 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:23.624174 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:23.631937 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:23.766788 INFO::Creating fits folder
2025-11-11 11:33:23.768518 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/fits/residuals_linear.rds
2025-11-11 11:33:23.770128 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/fits/fitted_linear.rds
2025-11-11 11:33:23.771838 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/fits/residuals_logistic.rds
2025-11-11 11:33:23.773536 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/fits/fitted_logistic.rds
2025-11-11 11:33:23.777438 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/all_results.tsv
2025-11-11 11:33:23.78011 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/Rtmp2pnA2v/file2df6bb62a974d8/significant_results.tsv
2025-11-11 11:33:23.782258 INFO::Creating output figures folder
2025-11-11 11:33:23.784524 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/figures/summary_plot.pdf
2025-11-11 11:33:26.046642 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/figures
2025-11-11 11:33:26.049288 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 11:33:26.05666 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 11:33:26.769187 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/figures/summary_plot.pdf
2025-11-11 11:33:29.09366 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb62a974d8/figures
2025-11-11 11:33:29.095841 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 11:33:29.103089 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 11:33:29.845804 INFO::Running the linear model component
2025-11-11 11:33:29.860048 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:29.866607 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:29.87313 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:29.883667 INFO::Counting total values for each feature
2025-11-11 11:33:29.886262 INFO::Running the logistic model component
2025-11-11 11:33:29.899402 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:29.908433 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:29.917704 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:29.930821 INFO::Counting total values for each feature
2025-11-11 11:33:29.933867 INFO::Re-running abundances for warn_prevalence
2025-11-11 11:33:29.935056 INFO::Running selected normalization method: TSS
2025-11-11 11:33:29.937264 INFO::Running selected transform method: LOG
2025-11-11 11:33:29.950991 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:29.957636 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:29.964186 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:30.099569 INFO::Creating output folder
2025-11-11 11:33:30.100995 INFO::Creating output figures folder
2025-11-11 11:33:30.102831 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb774fc39b/figures/summary_plot.pdf
2025-11-11 11:33:32.345357 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb774fc39b/figures
2025-11-11 11:33:32.347574 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-11 11:33:32.355 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-11 11:33:33.866043 INFO::Applying z-score to standardize continuous metadata
2025-11-11 11:33:33.877105 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-11 11:33:33.878398 INFO::Bypass z-score application to metadata
2025-11-11 11:33:33.882343 INFO::Bypass z-score application to metadata
2025-11-11 11:33:33.908315 INFO::Determining format of input files
2025-11-11 11:33:33.909731 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 11:33:33.910998 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-11 11:33:33.921674 INFO::Determining format of input files
2025-11-11 11:33:33.923281 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-11 11:33:33.925288 INFO::Input format is feature_specific_covariate samples as columns
2025-11-11 11:33:33.937066 INFO::Determining format of input files
2025-11-11 11:33:33.938575 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-11 11:33:33.940184 INFO::Input format is feature_specific_covariate samples as columns
2025-11-11 11:33:33.942736 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-11 11:33:33.943987 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-11 11:33:33.959768 INFO::Running selected transform method: LOG
2025-11-11 11:33:33.961415 INFO::Creating output feature tables folder
2025-11-11 11:33:33.962689 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb4ca26d7c/features/data_transformed.tsv
2025-11-11 11:33:33.968434 INFO::Running selected transform method: LOG
2025-11-11 11:33:33.970141 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb4ca26d7c/features/data_transformed.tsv
2025-11-11 11:33:33.975613 INFO::Running selected transform method: PLOG
2025-11-11 11:33:33.978078 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb4ca26d7c/features/data_transformed.tsv
2025-11-11 11:33:33.982255 INFO::Running selected transform method: NONE
2025-11-11 11:33:33.983535 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb4ca26d7c/features/data_transformed.tsv
2025-11-11 11:33:33.993675 INFO::Running the linear model component
2025-11-11 11:33:34.007629 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:34.014167 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:34.02063 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:34.031372 INFO::Counting total values for each feature
2025-11-11 11:33:34.034011 INFO::Running the logistic model component
2025-11-11 11:33:34.047974 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:34.057127 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:34.06608 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:34.079058 INFO::Counting total values for each feature
2025-11-11 11:33:34.082137 INFO::Re-running abundances for warn_prevalence
2025-11-11 11:33:34.083303 INFO::Running selected normalization method: TSS
2025-11-11 11:33:34.085444 INFO::Running selected transform method: LOG
2025-11-11 11:33:34.099473 INFO::Fitting model to feature number 1, a
2025-11-11 11:33:34.105793 INFO::Fitting model to feature number 2, b
2025-11-11 11:33:34.111945 INFO::Fitting model to feature number 3, c
2025-11-11 11:33:34.241521 INFO::Creating output folder
2025-11-11 11:33:34.243089 INFO::Creating fits folder
2025-11-11 11:33:34.244526 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb44b25e9d/fits/residuals_linear.rds
2025-11-11 11:33:34.246119 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb44b25e9d/fits/fitted_linear.rds
2025-11-11 11:33:34.247776 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb44b25e9d/fits/residuals_logistic.rds
2025-11-11 11:33:34.249461 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb44b25e9d/fits/fitted_logistic.rds
2025-11-11 11:33:34.253317 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp2pnA2v/file2df6bb44b25e9d/all_results.tsv
2025-11-11 11:33:34.255756 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/Rtmp2pnA2v/file2df6bb44b25e9d/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
513.523 5.401 520.356
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 29.437 | 0.451 | 29.967 | |
| maaslin_check_arguments | 0.217 | 0.000 | 0.217 | |
| maaslin_check_formula | 0.213 | 0.000 | 0.214 | |
| maaslin_compute_formula | 0.235 | 0.004 | 0.240 | |
| maaslin_contrast_test | 29.689 | 0.403 | 30.174 | |
| maaslin_filter | 0.622 | 0.004 | 0.628 | |
| maaslin_fit | 21.315 | 0.120 | 21.495 | |
| maaslin_log_arguments | 0.187 | 0.008 | 0.196 | |
| maaslin_normalize | 0.366 | 0.006 | 0.374 | |
| maaslin_plot_results | 64.695 | 0.352 | 65.217 | |
| maaslin_plot_results_from_output | 65.196 | 0.494 | 65.867 | |
| maaslin_process_metadata | 0.679 | 0.009 | 0.689 | |
| maaslin_read_data | 0.199 | 0.000 | 0.200 | |
| maaslin_reorder_data | 0.199 | 0.012 | 0.212 | |
| maaslin_transform | 0.819 | 0.000 | 0.822 | |
| maaslin_write_results | 22.880 | 0.187 | 23.140 | |
| maaslin_write_results_lefse_format | 24.938 | 0.131 | 25.133 | |
| preprocess_dna_mtx | 0.005 | 0.001 | 0.005 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.006 | |