William Nickols
| Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: 705d8bd |
| git_last_commit_date: 2025-03-10 09:56:10 -0400 (Mon, 10 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
| 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 1140/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.11 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 0.99.11 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.11.tar.gz |
| StartedAt: 2025-03-13 23:23:35 -0400 (Thu, 13 Mar 2025) |
| EndedAt: 2025-03-13 23:42:58 -0400 (Thu, 13 Mar 2025) |
| EllapsedTime: 1162.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘0.99.11’
* 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 36.043 0.335 36.351
maaslin_plot_results_from_output 35.376 0.285 35.670
maaslin3 19.440 0.510 19.964
maaslin_contrast_test 18.379 0.405 18.785
maaslin_write_results 14.119 0.185 14.304
maaslin_write_results_lefse_format 14.250 0.048 14.298
maaslin_fit 13.216 0.141 13.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘0.99.11’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-03-13 23:29:31.536107 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:29:31.630868 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:29:31.717112 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:29:31.73854 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:29:31.783749 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:29:31.858004 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:29:31.863272 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:29:31.87487 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:29:31.975692 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:29:31.981078 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:29:32.030974 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:29:32.070807 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:29:32.082646 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:29:32.122351 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:29:32.196492 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:29:47.82367 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:29:47.899203 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:29:47.995029 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:29:48.018851 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:29:48.054739 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:29:48.132246 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:29:48.137703 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:29:48.149703 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:29:48.246979 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:29:48.252471 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:29:48.302246 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:29:48.344158 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:29:48.35653 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:29:48.400358 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:29:48.472572 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:30:06.892761 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:30:06.978895 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:30:07.077489 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:30:07.100013 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:30:07.135173 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:30:07.212234 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:30:07.217651 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:30:07.229561 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:30:07.326581 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:30:07.332298 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:30:07.382358 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:30:07.425411 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:30:07.43747 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:30:07.478351 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:30:07.590883 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:30:20.866467 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:30:20.941915 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:30:21.016297 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:30:21.038388 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:30:21.073937 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:30:21.149271 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:30:21.154717 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:30:21.166889 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:30:21.263708 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:30:21.269512 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:30:21.321687 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:30:21.36375 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:30:21.37592 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:30:21.418483 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:30:21.503637 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:30:21.744904 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_linear.rds
2025-03-13 23:30:21.805549 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_linear.rds
2025-03-13 23:30:21.868391 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_logistic.rds
2025-03-13 23:30:22.170501 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_logistic.rds
2025-03-13 23:30:38.759558 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:30:38.838758 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:30:38.913765 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:30:38.935874 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:30:38.970756 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:30:39.046485 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:30:39.051971 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:30:39.064008 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:30:39.160813 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:30:39.166483 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:30:39.218081 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:30:39.259702 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:30:39.271749 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:30:39.313965 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:30:39.390087 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:30:52.293816 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:30:52.369109 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:30:52.443194 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:30:52.464978 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:30:52.499233 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:30:52.576736 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:30:52.582073 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:30:52.593936 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:30:52.690364 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:30:52.695807 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:30:52.746755 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:30:52.790226 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:30:52.803153 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:30:52.847358 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:30:52.92284 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:30:53.13267 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_linear.rds
2025-03-13 23:30:53.193187 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_linear.rds
2025-03-13 23:30:53.255872 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_logistic.rds
2025-03-13 23:30:53.554012 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_logistic.rds
2025-03-13 23:31:10.089425 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:31:10.170069 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:31:10.248913 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:31:10.271513 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:31:10.306268 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:31:10.390044 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:31:10.396633 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:31:10.410096 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:31:10.516512 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:31:10.522599 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:31:10.580297 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:31:10.627525 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:31:10.641727 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:31:10.689301 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:31:10.772592 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:31:22.583402 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:31:22.662366 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:31:22.741221 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:31:22.763912 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:31:22.799412 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:31:22.875459 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:31:22.880763 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:31:22.89239 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:31:22.986062 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:31:22.991383 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:31:23.042821 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:31:23.085013 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:31:23.097314 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:31:23.138831 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:31:23.20907 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:31:23.425703 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_linear.rds
2025-03-13 23:31:23.487049 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_linear.rds
2025-03-13 23:31:23.550927 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/residuals_logistic.rds
2025-03-13 23:31:23.8519 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b714deec57/fits/fitted_logistic.rds
2025-03-13 23:31:40.403335 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:31:40.480479 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:31:40.557939 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:31:40.580878 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:31:40.616383 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:31:40.693729 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:31:40.699194 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:31:40.711133 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:31:40.807675 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:31:40.813433 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:31:40.865451 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:31:40.906528 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:31:40.918547 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:31:40.959706 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:31:41.030565 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:31:53.016638 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:31:53.091784 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:31:53.20714 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:31:53.231127 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:31:53.267748 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:31:53.345152 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:31:53.350448 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:31:53.362091 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:31:53.456795 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:31:53.462297 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:31:53.512126 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:31:53.55225 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:31:53.563998 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:31:53.604382 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:31:53.674689 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:32:12.523602 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:32:22.427142 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:32:42.067727 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:32:52.186093 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:32:52.838964 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_linear.rds
2025-03-13 23:32:52.900264 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_linear.rds
2025-03-13 23:32:52.939096 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_logistic.rds
2025-03-13 23:32:53.007944 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_logistic.rds
2025-03-13 23:33:11.074704 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:33:16.296364 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:33:16.693365 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_linear.rds
2025-03-13 23:33:16.755815 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_linear.rds
2025-03-13 23:33:16.794462 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_logistic.rds
2025-03-13 23:33:16.867685 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_logistic.rds
2025-03-13 23:33:32.418649 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:33:37.640804 WARNING::Fitting problem for feature 124 returning NA
2025-03-13 23:33:37.973672 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_linear.rds
2025-03-13 23:33:38.035319 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_linear.rds
2025-03-13 23:33:38.073487 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_logistic.rds
2025-03-13 23:33:38.144044 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_logistic.rds
2025-03-13 23:33:53.234287 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:33:53.315379 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:33:53.393214 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:33:53.415719 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:33:53.45157 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:33:53.53363 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:33:53.539459 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:33:53.552005 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:33:53.653151 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:33:53.658994 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:33:53.711131 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:33:53.78363 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:33:53.796559 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:33:53.838866 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:33:53.909947 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:34:04.938006 WARNING::Fitting problem for feature 50 returning NA
2025-03-13 23:34:05.016093 WARNING::Fitting problem for feature 62 returning NA
2025-03-13 23:34:05.090615 WARNING::Fitting problem for feature 74 returning NA
2025-03-13 23:34:05.111805 WARNING::Fitting problem for feature 78 returning NA
2025-03-13 23:34:05.146209 WARNING::Fitting problem for feature 84 returning NA
2025-03-13 23:34:05.222844 WARNING::Fitting problem for feature 96 returning NA
2025-03-13 23:34:05.228447 WARNING::Fitting problem for feature 97 returning NA
2025-03-13 23:34:05.241206 WARNING::Fitting problem for feature 99 returning NA
2025-03-13 23:34:05.341154 WARNING::Fitting problem for feature 114 returning NA
2025-03-13 23:34:05.346886 WARNING::Fitting problem for feature 115 returning NA
2025-03-13 23:34:06.396157 WARNING::Fitting problem for feature 123 returning NA
2025-03-13 23:34:06.436968 WARNING::Fitting problem for feature 130 returning NA
2025-03-13 23:34:06.449423 WARNING::Fitting problem for feature 132 returning NA
2025-03-13 23:34:06.491035 WARNING::Fitting problem for feature 139 returning NA
2025-03-13 23:34:06.559866 WARNING::Fitting problem for feature 150 returning NA
2025-03-13 23:34:06.806073 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_linear.rds
2025-03-13 23:34:06.866759 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_linear.rds
2025-03-13 23:34:06.929856 WARNING::Deleting existing residuals file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/residuals_logistic.rds
2025-03-13 23:34:07.228086 WARNING::Deleting existing fitted file: /tmp/RtmpPf0dlG/file1559b7323cb897/fits/fitted_logistic.rds
2025-03-13 23:34:23.058725 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-03-13 23:34:23.071153 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-03-13 23:34:23.077558 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-03-13 23:34:23.123737 ERROR::No fixed, group, or
ordered effects included in formula.
2025-03-13 23:34:23.134965 ERROR::Effect name not found in metadata: d
2025-03-13 23:34:23.140873 ERROR::No user formula provided
2025-03-13 23:34:23.165721 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-03-13 23:34:23.171911 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-03-13 23:34:26.041743 INFO::Writing function arguments to log file
2025-03-13 23:34:26.055027 INFO::Verifying options selected are valid
2025-03-13 23:34:27.880623 INFO::Writing function arguments to log file
2025-03-13 23:34:27.892242 INFO::Verifying options selected are valid
2025-03-13 23:34:27.893347 INFO::Determining format of input files
2025-03-13 23:34:27.8944 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-13 23:34:27.896679 INFO::Running selected normalization method: TSS
2025-03-13 23:34:27.898147 INFO::Creating output feature tables folder
2025-03-13 23:34:27.89913 INFO::Writing normalized data to file /tmp/RtmpPf0dlG/file1559b7372515ce/features/data_norm.tsv
2025-03-13 23:34:27.900604 INFO::Filter data based on min abundance and min prevalence
2025-03-13 23:34:27.901485 INFO::Total samples in data: 16
2025-03-13 23:34:27.902344 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-03-13 23:34:27.904213 INFO::Total filtered features: 0
2025-03-13 23:34:27.905141 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-13 23:34:27.906346 INFO::Total features filtered by non-zero variance filtering: 0
2025-03-13 23:34:27.907318 INFO::Filtered feature names from variance filtering:
2025-03-13 23:34:27.90822 INFO::Writing filtered data to file /tmp/RtmpPf0dlG/file1559b7372515ce/features/filtered_data.tsv
2025-03-13 23:34:27.909751 INFO::Running selected transform method: LOG
2025-03-13 23:34:27.910964 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPf0dlG/file1559b7372515ce/features/data_transformed.tsv
2025-03-13 23:34:27.912719 INFO::Applying z-score to standardize continuous metadata
2025-03-13 23:34:27.918104 INFO::Running the linear model component
2025-03-13 23:34:27.935505 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:27.940136 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:27.944414 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:27.951614 INFO::Counting total values for each feature
2025-03-13 23:34:27.953456 INFO::Running the logistic model component
2025-03-13 23:34:27.971086 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:27.977745 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:27.984207 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:27.993659 INFO::Counting total values for each feature
2025-03-13 23:34:27.995969 INFO::Re-running abundances for warn_prevalence
2025-03-13 23:34:27.996941 INFO::Running selected normalization method: TSS
2025-03-13 23:34:27.998465 INFO::Running selected transform method: LOG
2025-03-13 23:34:28.01614 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:28.028831 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:28.033962 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:28.129243 INFO::Creating fits folder
2025-03-13 23:34:28.130666 INFO::Writing residuals to file /tmp/RtmpPf0dlG/file1559b7372515ce/fits/residuals_linear.rds
2025-03-13 23:34:28.131973 INFO::Writing fitted values to file /tmp/RtmpPf0dlG/file1559b7372515ce/fits/fitted_linear.rds
2025-03-13 23:34:28.13331 INFO::Writing residuals to file /tmp/RtmpPf0dlG/file1559b7372515ce/fits/residuals_logistic.rds
2025-03-13 23:34:28.134642 INFO::Writing fitted values to file /tmp/RtmpPf0dlG/file1559b7372515ce/fits/fitted_logistic.rds
2025-03-13 23:34:28.137551 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpPf0dlG/file1559b7372515ce/all_results.tsv
2025-03-13 23:34:28.139275 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/RtmpPf0dlG/file1559b7372515ce/significant_results.tsv
2025-03-13 23:34:28.140686 INFO::Creating output figures folder
2025-03-13 23:34:28.142102 INFO::Writing summary plot of significant
results to file: /tmp/RtmpPf0dlG/file1559b7372515ce/figures/summary_plot.pdf
2025-03-13 23:34:29.416501 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPf0dlG/file1559b7372515ce/figures
2025-03-13 23:34:29.418532 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-13 23:34:29.423688 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-13 23:34:29.814113 INFO::Writing summary plot of
significant results to file: /tmp/RtmpPf0dlG/file1559b7372515ce/figures/summary_plot.pdf
2025-03-13 23:34:31.041822 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPf0dlG/file1559b7372515ce/figures
2025-03-13 23:34:31.04331 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-13 23:34:31.048071 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-13 23:34:31.437564 INFO::Running the linear model component
2025-03-13 23:34:31.44961 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:31.45415 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:31.458074 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:31.464813 INFO::Counting total values for each feature
2025-03-13 23:34:31.466457 INFO::Running the logistic model component
2025-03-13 23:34:31.477871 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:31.484117 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:31.489718 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:31.498092 INFO::Counting total values for each feature
2025-03-13 23:34:31.500054 INFO::Re-running abundances for warn_prevalence
2025-03-13 23:34:31.500825 INFO::Running selected normalization method: TSS
2025-03-13 23:34:31.502177 INFO::Running selected transform method: LOG
2025-03-13 23:34:31.513777 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:31.518212 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:31.52232 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:31.610836 INFO::Creating output folder
2025-03-13 23:34:31.611867 INFO::Creating output figures folder
2025-03-13 23:34:31.613172 INFO::Writing summary plot of significant
results to file: /tmp/RtmpPf0dlG/file1559b7305fe4d5/figures/summary_plot.pdf
2025-03-13 23:34:32.836136 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPf0dlG/file1559b7305fe4d5/figures
2025-03-13 23:34:32.838017 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-13 23:34:32.843068 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-13 23:34:33.67649 INFO::Applying z-score to standardize continuous metadata
2025-03-13 23:34:33.68459 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-03-13 23:34:33.685527 INFO::Bypass z-score application to metadata
2025-03-13 23:34:33.688097 INFO::Bypass z-score application to metadata
2025-03-13 23:34:33.712466 INFO::Determining format of input files
2025-03-13 23:34:33.713515 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-13 23:34:33.714374 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-03-13 23:34:33.721744 INFO::Determining format of input files
2025-03-13 23:34:33.722875 INFO::Input format is data samples as columns and metadata samples as rows
2025-03-13 23:34:33.72421 INFO::Input format is feature_specific_covariate samples as columns
2025-03-13 23:34:33.732176 INFO::Determining format of input files
2025-03-13 23:34:33.733146 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-13 23:34:33.734157 INFO::Input format is feature_specific_covariate samples as columns
2025-03-13 23:34:33.735821 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-03-13 23:34:33.736588 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-03-13 23:34:33.747605 INFO::Running selected transform method: LOG
2025-03-13 23:34:33.748779 INFO::Creating output feature tables folder
2025-03-13 23:34:33.74966 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPf0dlG/file1559b74c5ce437/features/data_transformed.tsv
2025-03-13 23:34:33.753876 INFO::Running selected transform method: LOG
2025-03-13 23:34:33.754935 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPf0dlG/file1559b74c5ce437/features/data_transformed.tsv
2025-03-13 23:34:33.75874 INFO::Running selected transform method: PLOG
2025-03-13 23:34:33.760307 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPf0dlG/file1559b74c5ce437/features/data_transformed.tsv
2025-03-13 23:34:33.763246 INFO::Running selected transform method: NONE
2025-03-13 23:34:33.764021 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPf0dlG/file1559b74c5ce437/features/data_transformed.tsv
2025-03-13 23:34:33.771909 INFO::Running the linear model component
2025-03-13 23:34:33.784791 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:33.790029 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:33.79431 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:33.801881 INFO::Counting total values for each feature
2025-03-13 23:34:33.80371 INFO::Running the logistic model component
2025-03-13 23:34:33.816271 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:33.823705 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:33.830263 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:33.840114 INFO::Counting total values for each feature
2025-03-13 23:34:33.842561 INFO::Re-running abundances for warn_prevalence
2025-03-13 23:34:33.843529 INFO::Running selected normalization method: TSS
2025-03-13 23:34:33.844995 INFO::Running selected transform method: LOG
2025-03-13 23:34:33.85764 INFO::Fitting model to feature number 1, a
2025-03-13 23:34:33.862539 INFO::Fitting model to feature number 2, b
2025-03-13 23:34:33.866721 INFO::Fitting model to feature number 3, c
2025-03-13 23:34:33.956851 INFO::Creating output folder
2025-03-13 23:34:33.95792 INFO::Creating fits folder
2025-03-13 23:34:33.958822 INFO::Writing residuals to file /tmp/RtmpPf0dlG/file1559b7477ea6ab/fits/residuals_linear.rds
2025-03-13 23:34:33.959818 INFO::Writing fitted values to file /tmp/RtmpPf0dlG/file1559b7477ea6ab/fits/fitted_linear.rds
2025-03-13 23:34:33.9609 INFO::Writing residuals to file /tmp/RtmpPf0dlG/file1559b7477ea6ab/fits/residuals_logistic.rds
2025-03-13 23:34:33.961948 INFO::Writing fitted values to file /tmp/RtmpPf0dlG/file1559b7477ea6ab/fits/fitted_logistic.rds
2025-03-13 23:34:33.964607 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpPf0dlG/file1559b7477ea6ab/all_results.tsv
2025-03-13 23:34:33.96619 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/RtmpPf0dlG/file1559b7477ea6ab/significant_results.tsv
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 94 ]
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 94 ]
>
>
> proc.time()
user system elapsed
308.984 4.562 313.552
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.440 | 0.510 | 19.964 | |
| maaslin_check_arguments | 0.138 | 0.001 | 0.139 | |
| maaslin_check_formula | 0.136 | 0.004 | 0.140 | |
| maaslin_compute_formula | 0.142 | 0.005 | 0.147 | |
| maaslin_contrast_test | 18.379 | 0.405 | 18.785 | |
| maaslin_filter | 0.431 | 0.018 | 0.450 | |
| maaslin_fit | 13.216 | 0.141 | 13.358 | |
| maaslin_log_arguments | 0.134 | 0.003 | 0.137 | |
| maaslin_normalize | 0.270 | 0.002 | 0.272 | |
| maaslin_plot_results | 36.043 | 0.335 | 36.351 | |
| maaslin_plot_results_from_output | 35.376 | 0.285 | 35.670 | |
| maaslin_process_metadata | 0.460 | 0.014 | 0.475 | |
| maaslin_read_data | 0.147 | 0.002 | 0.149 | |
| maaslin_reorder_data | 0.141 | 0.004 | 0.146 | |
| maaslin_transform | 0.555 | 0.048 | 0.603 | |
| maaslin_write_results | 14.119 | 0.185 | 14.304 | |
| maaslin_write_results_lefse_format | 14.250 | 0.048 | 14.298 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.004 | |