Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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 1143/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: ed6ae28
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on taishan

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.

raw results


Summary

Package: maaslin3
Version: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2025-06-17 08:59:13 -0000 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 09:14:26 -0000 (Tue, 17 Jun 2025)
EllapsedTime: 913.2 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.1.0.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 ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results               52.437  0.251  52.823
maaslin_plot_results_from_output   51.073  0.287  51.459
maaslin_contrast_test              30.877  0.395  31.365
maaslin3                           29.065  0.697  29.855
maaslin_write_results_lefse_format 23.573  0.100  23.730
maaslin_write_results              22.348  0.216  22.609
maaslin_fit                        21.772  0.211  22.047
* 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

Installation output

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 ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

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")
2025-06-17 09:07:19.249409 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:07:19.37093 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:07:19.504797 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:07:19.539107 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:07:19.606472 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:07:19.728089 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:07:19.736085 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:07:19.754381 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:07:19.91954 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:07:19.927727 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:07:20.006731 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:07:20.069958 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:07:20.088763 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:07:20.155439 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:07:20.283924 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:07:44.117553 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:07:44.24325 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:07:44.363871 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:07:44.402976 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:07:44.465208 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:07:44.631276 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:07:44.640438 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:07:44.661364 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:07:44.835562 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:07:44.845287 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:07:44.935991 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:07:45.0009 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:07:45.01997 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:07:45.085202 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:07:45.193452 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:08:08.418906 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:08:08.561193 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:08:08.678862 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:08:08.712708 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:08:08.766079 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:08:08.884609 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:08:08.892636 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:08:08.910633 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:08:09.059019 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:08:09.067031 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:08:09.182901 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:08:09.250136 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:08:09.268768 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:08:09.332433 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:08:09.43978 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:08:30.10128 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:08:30.227657 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:08:30.348658 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:08:30.383353 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:08:30.437924 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:08:30.560513 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:08:30.568614 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:08:30.586865 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:08:30.737075 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:08:30.745123 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:08:30.82281 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:08:30.885302 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:08:30.903493 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:08:30.966964 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:08:31.090643 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:08:31.420781 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_linear.rds
2025-06-17 09:08:31.490004 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_linear.rds
2025-06-17 09:08:31.56052 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_logistic.rds
2025-06-17 09:08:31.901847 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_logistic.rds
2025-06-17 09:08:52.983402 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:08:53.126977 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:08:53.248029 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:08:53.283327 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:08:53.339553 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:08:53.460217 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:08:53.468357 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:08:53.486968 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:08:53.639932 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:08:53.648212 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:08:53.726418 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:08:53.789099 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:08:53.807284 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:08:53.869786 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:08:53.984301 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:09:13.672621 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:09:13.811233 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:09:13.934349 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:09:13.969923 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:09:14.029665 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:09:14.152325 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:09:14.16044 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:09:14.181145 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:09:14.354548 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:09:14.364763 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:09:14.455714 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:09:14.528054 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:09:14.549202 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:09:14.622586 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:09:14.748504 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:09:15.094445 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_linear.rds
2025-06-17 09:09:15.162398 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_linear.rds
2025-06-17 09:09:15.232881 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_logistic.rds
2025-06-17 09:09:15.575444 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_logistic.rds
2025-06-17 09:09:36.245679 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:09:36.371873 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:09:36.493902 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:09:36.528959 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:09:36.584604 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:09:36.710929 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:09:36.719268 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:09:36.738479 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:09:37.024886 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:09:37.034126 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:09:37.115454 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:09:37.180679 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:09:37.19966 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:09:37.265018 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:09:37.375028 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:09:56.603952 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:09:56.780935 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:09:56.91359 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:09:56.949871 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:09:57.012323 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:09:57.1517 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:09:57.16005 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:09:57.179007 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:09:57.335265 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:09:57.344032 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:09:57.425955 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:09:57.492553 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:09:57.511381 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:09:57.57724 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:09:57.691128 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:09:57.9835 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_linear.rds
2025-06-17 09:09:58.05266 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_linear.rds
2025-06-17 09:09:58.123489 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/residuals_logistic.rds
2025-06-17 09:09:58.466746 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c64a08eca/fits/fitted_logistic.rds
2025-06-17 09:10:19.379358 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:10:19.505465 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:10:19.63306 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:10:19.668175 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:10:19.724886 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:10:19.848217 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:10:19.856629 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:10:19.87529 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:10:20.029734 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:10:20.038894 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:10:20.127544 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:10:20.193288 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:10:20.212589 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:10:20.277489 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:10:20.398473 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:10:39.906124 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:10:40.03568 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:10:40.166049 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:10:40.204489 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:10:40.261351 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:10:40.390075 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:10:40.400777 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:10:40.423499 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:10:40.584252 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:10:40.593287 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:10:40.680346 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:10:40.749605 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:10:40.770036 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:10:40.836072 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:10:41.010353 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:11:05.782206 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:11:20.409922 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:11:46.514316 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:12:00.929864 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:12:01.895168 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_linear.rds
2025-06-17 09:12:01.958523 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_linear.rds
2025-06-17 09:12:01.999717 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_logistic.rds
2025-06-17 09:12:02.075406 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_logistic.rds
2025-06-17 09:12:25.479127 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:12:33.202351 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:12:33.805538 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_linear.rds
2025-06-17 09:12:33.87533 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_linear.rds
2025-06-17 09:12:33.919595 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_logistic.rds
2025-06-17 09:12:34.000262 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_logistic.rds
2025-06-17 09:12:54.063159 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:13:02.773914 WARNING::Fitting problem for feature 124 returning NA
2025-06-17 09:13:03.291836 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_linear.rds
2025-06-17 09:13:03.361762 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_linear.rds
2025-06-17 09:13:03.405334 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_logistic.rds
2025-06-17 09:13:03.484128 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_logistic.rds
2025-06-17 09:13:21.960671 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:13:22.106544 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:13:22.245471 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:13:22.286736 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:13:22.352847 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:13:22.489094 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:13:22.497757 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:13:22.517884 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:13:22.71859 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:13:22.733829 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:13:22.818552 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:13:22.884232 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:13:22.903559 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:13:22.974278 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:13:23.094995 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:13:41.6327 WARNING::Fitting problem for feature 50 returning NA
2025-06-17 09:13:41.756963 WARNING::Fitting problem for feature 62 returning NA
2025-06-17 09:13:41.882187 WARNING::Fitting problem for feature 74 returning NA
2025-06-17 09:13:41.919566 WARNING::Fitting problem for feature 78 returning NA
2025-06-17 09:13:41.978042 WARNING::Fitting problem for feature 84 returning NA
2025-06-17 09:13:42.108669 WARNING::Fitting problem for feature 96 returning NA
2025-06-17 09:13:42.117504 WARNING::Fitting problem for feature 97 returning NA
2025-06-17 09:13:42.147164 WARNING::Fitting problem for feature 99 returning NA
2025-06-17 09:13:42.306949 WARNING::Fitting problem for feature 114 returning NA
2025-06-17 09:13:42.315673 WARNING::Fitting problem for feature 115 returning NA
2025-06-17 09:13:42.39853 WARNING::Fitting problem for feature 123 returning NA
2025-06-17 09:13:42.468495 WARNING::Fitting problem for feature 130 returning NA
2025-06-17 09:13:42.489418 WARNING::Fitting problem for feature 132 returning NA
2025-06-17 09:13:42.558204 WARNING::Fitting problem for feature 139 returning NA
2025-06-17 09:13:42.67163 WARNING::Fitting problem for feature 150 returning NA
2025-06-17 09:13:43.047131 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_linear.rds
2025-06-17 09:13:43.117158 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_linear.rds
2025-06-17 09:13:43.189489 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/residuals_logistic.rds
2025-06-17 09:13:43.545678 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c330b4c56/fits/fitted_logistic.rds
2025-06-17 09:14:05.024354 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-06-17 09:14:05.050894 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-06-17 09:14:05.068727 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-06-17 09:14:05.148793 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-06-17 09:14:05.174603 ERROR::Effect name not found in metadata: d
2025-06-17 09:14:05.192358 ERROR::No user formula provided
2025-06-17 09:14:05.239088 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-06-17 09:14:05.258079 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-06-17 09:14:10.089041 INFO::Writing function arguments to log file
2025-06-17 09:14:10.111615 INFO::Verifying options selected are valid
2025-06-17 09:14:12.658199 INFO::Writing function arguments to log file
2025-06-17 09:14:12.677064 INFO::Verifying options selected are valid
2025-06-17 09:14:12.678733 INFO::Determining format of input files
2025-06-17 09:14:12.680265 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-17 09:14:12.683932 INFO::Running selected normalization method: TSS
2025-06-17 09:14:12.686121 INFO::Creating output feature tables folder
2025-06-17 09:14:12.687605 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/features/data_norm.tsv
2025-06-17 09:14:12.68982 INFO::Filter data based on min abundance and min prevalence
2025-06-17 09:14:12.691267 INFO::Total samples in data: 16
2025-06-17 09:14:12.692635 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-06-17 09:14:12.695564 INFO::Total filtered features: 0
2025-06-17 09:14:12.697281 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-17 09:14:12.699108 INFO::Total features filtered by non-zero variance filtering: 0
2025-06-17 09:14:12.70057 INFO::Filtered feature names from variance filtering:
2025-06-17 09:14:12.702048 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/features/filtered_data.tsv
2025-06-17 09:14:12.704255 INFO::Running selected transform method: LOG
2025-06-17 09:14:12.706175 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/features/data_transformed.tsv
2025-06-17 09:14:12.708622 INFO::Applying z-score to standardize continuous metadata
2025-06-17 09:14:12.716235 INFO::Running the linear model component
2025-06-17 09:14:12.739602 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:12.746664 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:12.753758 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:12.76466 INFO::Counting total values for each feature
2025-06-17 09:14:12.767493 INFO::Running the logistic model component
2025-06-17 09:14:12.790145 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:12.799968 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:12.809699 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:12.823416 INFO::Counting total values for each feature
2025-06-17 09:14:12.826802 INFO::Re-running abundances for warn_prevalence
2025-06-17 09:14:12.828351 INFO::Running selected normalization method: TSS
2025-06-17 09:14:12.830628 INFO::Running selected transform method: LOG
2025-06-17 09:14:12.853141 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:12.859842 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:12.866712 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:12.999877 INFO::Creating fits folder
2025-06-17 09:14:13.001657 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/fits/residuals_linear.rds
2025-06-17 09:14:13.003255 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/fits/fitted_linear.rds
2025-06-17 09:14:13.005069 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/fits/residuals_logistic.rds
2025-06-17 09:14:13.006796 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/fits/fitted_logistic.rds
2025-06-17 09:14:13.010737 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/all_results.tsv
2025-06-17 09:14:13.013355 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/RtmpRYvTvd/file30fb7c17af7764/significant_results.tsv
2025-06-17 09:14:13.015371 INFO::Creating output figures folder
2025-06-17 09:14:13.017536 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/figures/summary_plot.pdf
2025-06-17 09:14:14.748795 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/figures
2025-06-17 09:14:14.751511 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-17 09:14:14.758873 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-17 09:14:15.258734 INFO::Writing summary plot of
                        significant results to file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/figures/summary_plot.pdf
2025-06-17 09:14:17.043869 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c17af7764/figures
2025-06-17 09:14:17.046182 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-17 09:14:17.053815 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-17 09:14:17.576982 INFO::Running the linear model component
2025-06-17 09:14:17.591141 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:17.597644 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:17.60392 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:17.614637 INFO::Counting total values for each feature
2025-06-17 09:14:17.617323 INFO::Running the logistic model component
2025-06-17 09:14:17.631099 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:17.640709 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:17.650153 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:17.664513 INFO::Counting total values for each feature
2025-06-17 09:14:17.667754 INFO::Re-running abundances for warn_prevalence
2025-06-17 09:14:17.669075 INFO::Running selected normalization method: TSS
2025-06-17 09:14:17.671158 INFO::Running selected transform method: LOG
2025-06-17 09:14:17.68546 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:17.692082 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:17.698695 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:17.836535 INFO::Creating output folder
2025-06-17 09:14:17.837945 INFO::Creating output figures folder
2025-06-17 09:14:17.83971 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c650d5dab/figures/summary_plot.pdf
2025-06-17 09:14:19.567034 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c650d5dab/figures
2025-06-17 09:14:19.569478 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-17 09:14:19.576481 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-17 09:14:20.74978 INFO::Applying z-score to standardize continuous metadata
2025-06-17 09:14:20.760967 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-06-17 09:14:20.7623 INFO::Bypass z-score application to metadata
2025-06-17 09:14:20.766465 INFO::Bypass z-score application to metadata
2025-06-17 09:14:20.794215 INFO::Determining format of input files
2025-06-17 09:14:20.795645 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-17 09:14:20.797244 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-06-17 09:14:20.808561 INFO::Determining format of input files
2025-06-17 09:14:20.810277 INFO::Input format is data samples as columns and metadata samples as rows
2025-06-17 09:14:20.81244 INFO::Input format is feature_specific_covariate samples as columns
2025-06-17 09:14:20.825332 INFO::Determining format of input files
2025-06-17 09:14:20.826901 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-17 09:14:20.828598 INFO::Input format is feature_specific_covariate samples as columns
2025-06-17 09:14:20.831356 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-06-17 09:14:20.832641 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-06-17 09:14:20.849536 INFO::Running selected transform method: LOG
2025-06-17 09:14:20.851227 INFO::Creating output feature tables folder
2025-06-17 09:14:20.852578 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c6425c164/features/data_transformed.tsv
2025-06-17 09:14:20.858279 INFO::Running selected transform method: LOG
2025-06-17 09:14:20.859883 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c6425c164/features/data_transformed.tsv
2025-06-17 09:14:20.865592 INFO::Running selected transform method: PLOG
2025-06-17 09:14:20.868196 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c6425c164/features/data_transformed.tsv
2025-06-17 09:14:20.872638 INFO::Running selected transform method: NONE
2025-06-17 09:14:20.873955 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c6425c164/features/data_transformed.tsv
2025-06-17 09:14:20.88384 INFO::Running the linear model component
2025-06-17 09:14:20.89745 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:20.903926 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:20.910769 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:20.921853 INFO::Counting total values for each feature
2025-06-17 09:14:20.924364 INFO::Running the logistic model component
2025-06-17 09:14:20.937735 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:20.946859 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:20.955668 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:20.96876 INFO::Counting total values for each feature
2025-06-17 09:14:20.971674 INFO::Re-running abundances for warn_prevalence
2025-06-17 09:14:20.972856 INFO::Running selected normalization method: TSS
2025-06-17 09:14:20.975015 INFO::Running selected transform method: LOG
2025-06-17 09:14:20.988526 INFO::Fitting model to feature number 1, a
2025-06-17 09:14:20.995311 INFO::Fitting model to feature number 2, b
2025-06-17 09:14:21.002361 INFO::Fitting model to feature number 3, c
2025-06-17 09:14:21.14377 INFO::Creating output folder
2025-06-17 09:14:21.145419 INFO::Creating fits folder
2025-06-17 09:14:21.146858 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c57add640/fits/residuals_linear.rds
2025-06-17 09:14:21.148432 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c57add640/fits/fitted_linear.rds
2025-06-17 09:14:21.150254 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c57add640/fits/residuals_logistic.rds
2025-06-17 09:14:21.152035 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c57add640/fits/fitted_logistic.rds
2025-06-17 09:14:21.156259 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpRYvTvd/file30fb7c57add640/all_results.tsv
2025-06-17 09:14:21.158849 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/RtmpRYvTvd/file30fb7c57add640/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
430.955   4.269 436.196

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin329.065 0.69729.855
maaslin_check_arguments0.1880.0000.188
maaslin_check_formula0.2060.0000.207
maaslin_compute_formula0.2040.0040.209
maaslin_contrast_test30.877 0.39531.365
maaslin_filter0.6370.0200.658
maaslin_fit21.772 0.21122.047
maaslin_log_arguments0.1880.0090.197
maaslin_normalize0.3720.0080.381
maaslin_plot_results52.437 0.25152.823
maaslin_plot_results_from_output51.073 0.28751.459
maaslin_process_metadata0.6420.0000.643
maaslin_read_data0.1970.0000.197
maaslin_reorder_data0.2070.0000.207
maaslin_transform0.8000.0120.812
maaslin_write_results22.348 0.21622.609
maaslin_write_results_lefse_format23.573 0.10023.730
preprocess_dna_mtx0.0050.0000.005
preprocess_taxa_mtx0.0060.0000.006