Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1155/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.0.0  (landing page)
William Nickols
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: 7584c46
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on palomino7

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.

raw results


Summary

Package: maaslin3
Version: 1.0.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_1.0.0.tar.gz
StartedAt: 2025-08-15 03:40:53 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 03:56:05 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 911.3 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'maaslin3/DESCRIPTION' ... OK
* this is package 'maaslin3' version '1.0.0'
* 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 whether package 'maaslin3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
maaslin_plot_results               49.52   2.49   52.53
maaslin_plot_results_from_output   48.59   1.40   50.72
maaslin3                           29.87   1.06   31.08
maaslin_contrast_test              27.22   1.86   29.08
maaslin_write_results              21.67   1.69   23.38
maaslin_write_results_lefse_format 21.79   1.45   23.31
maaslin_fit                        19.54   1.69   21.22
* 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'maaslin3' ...
** this is package 'maaslin3' version '1.0.0'
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
2025-08-15 03:48:52.853006 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:48:52.941985 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:48:53.037536 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:48:53.069036 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:48:53.129081 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:48:53.215678 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:48:53.222563 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:48:53.237046 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:48:53.35862 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:48:53.367647 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:48:53.452926 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:48:53.506755 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:48:53.521091 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:48:53.569203 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:48:53.661762 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:49:13.555931 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:49:13.710112 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:49:13.900417 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:49:13.944482 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:49:14.009843 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:49:14.155487 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:49:14.166172 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:49:14.188137 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:49:14.382509 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:49:14.393949 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:49:14.494089 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:49:14.57459 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:49:14.597526 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:49:14.673636 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:49:14.8095 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:49:38.560092 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:49:38.721227 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:49:38.824424 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:49:38.869576 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:49:38.938434 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:49:39.068097 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:49:39.075168 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:49:39.089833 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:49:39.225374 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:49:39.239106 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:49:39.385181 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:49:39.465455 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:49:39.488425 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:49:39.541981 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:49:39.649273 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:49:59.118012 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:49:59.277408 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:49:59.441143 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:49:59.487466 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:49:59.559825 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:49:59.680112 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:49:59.687523 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:49:59.70368 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:49:59.830126 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:49:59.837951 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:49:59.907923 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:49:59.966148 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:49:59.984061 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:50:00.062411 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:50:00.178685 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:50:00.455438 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_linear.rds
2025-08-15 03:50:00.515695 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_linear.rds
2025-08-15 03:50:00.589325 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_logistic.rds
2025-08-15 03:50:00.952936 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_logistic.rds
2025-08-15 03:50:22.263749 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:50:22.425314 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:50:22.560219 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:50:22.608357 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:50:22.657932 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:50:22.779718 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:50:22.790424 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:50:22.810124 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:50:23.006203 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:50:23.020286 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:50:23.127481 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:50:23.217082 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:50:23.243485 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:50:23.32076 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:50:23.435908 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:50:41.319192 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:50:41.418654 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:50:41.520772 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:50:41.550072 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:50:41.595012 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:50:41.699005 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:50:41.706553 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:50:41.725127 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:50:41.880335 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:50:41.88876 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:50:41.957118 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:50:42.013114 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:50:42.029446 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:50:42.084728 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:50:42.232964 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:50:42.543636 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_linear.rds
2025-08-15 03:50:42.612399 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_linear.rds
2025-08-15 03:50:42.682812 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_logistic.rds
2025-08-15 03:50:43.065929 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_logistic.rds
2025-08-15 03:51:05.099288 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:51:05.258145 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:51:05.411664 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:51:05.457404 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:51:05.528138 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:51:05.679537 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:51:05.691379 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:51:05.716587 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:51:05.933996 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:51:05.943788 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:51:06.008665 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:51:06.059379 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:51:06.084122 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:51:06.16193 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:51:06.286745 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:51:24.115083 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:51:24.210797 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:51:24.306872 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:51:24.338811 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:51:24.390982 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:51:24.494046 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:51:24.501871 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:51:24.518278 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:51:24.658446 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:51:24.665938 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:51:24.736186 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:51:24.870566 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:51:24.896212 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:51:24.963443 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:51:25.049114 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:51:25.251252 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_linear.rds
2025-08-15 03:51:25.305534 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_linear.rds
2025-08-15 03:51:25.359164 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/residuals_logistic.rds
2025-08-15 03:51:25.615963 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60032842b7b/fits/fitted_logistic.rds
2025-08-15 03:51:47.212504 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:51:47.349699 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:51:47.496951 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:51:47.52781 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:51:47.580801 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:51:47.766228 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:51:47.778408 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:51:47.802419 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:51:47.984028 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:51:48.000737 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:51:48.08093 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:51:48.132155 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:51:48.148428 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:51:48.198283 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:51:48.283524 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:52:05.77965 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:52:05.91545 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:52:06.005566 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:52:06.03321 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:52:06.075122 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:52:06.172911 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:52:06.180063 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:52:06.194853 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:52:06.372321 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:52:06.383873 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:52:06.472169 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:52:06.551445 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:52:06.576074 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:52:06.657648 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:52:06.802632 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:52:32.565032 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:52:49.57054 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:53:16.257542 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:53:32.024113 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:53:33.11276 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_linear.rds
2025-08-15 03:53:33.183462 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_linear.rds
2025-08-15 03:53:33.230793 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_logistic.rds
2025-08-15 03:53:33.321538 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_logistic.rds
2025-08-15 03:53:58.562578 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:54:07.05706 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:54:07.637865 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_linear.rds
2025-08-15 03:54:07.710197 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_linear.rds
2025-08-15 03:54:07.746098 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_logistic.rds
2025-08-15 03:54:07.810948 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_logistic.rds
2025-08-15 03:54:28.796715 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:54:37.215343 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 03:54:37.569582 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_linear.rds
2025-08-15 03:54:37.623232 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_linear.rds
2025-08-15 03:54:37.657873 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_logistic.rds
2025-08-15 03:54:37.721774 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_logistic.rds
2025-08-15 03:54:57.568918 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:54:57.728798 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:54:57.886413 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:54:57.932053 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:54:58.003821 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:54:58.156166 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:54:58.168352 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:54:58.191665 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:54:58.37542 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:54:58.389736 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:54:58.476691 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:54:58.537581 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:54:58.554965 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:54:58.607111 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:54:58.707717 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:55:15.667517 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 03:55:15.802571 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 03:55:15.941456 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 03:55:15.982128 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 03:55:16.04569 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 03:55:16.183865 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 03:55:16.194488 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 03:55:16.21716 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 03:55:16.388078 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 03:55:16.399081 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 03:55:16.491839 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 03:55:16.566339 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 03:55:16.589348 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 03:55:16.720654 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 03:55:16.807858 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 03:55:17.175163 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_linear.rds
2025-08-15 03:55:17.25081 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_linear.rds
2025-08-15 03:55:17.320104 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/residuals_logistic.rds
2025-08-15 03:55:17.620446 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600792dbad/fits/fitted_logistic.rds
2025-08-15 03:55:36.662231 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-15 03:55:36.680006 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-15 03:55:36.691949 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-15 03:55:36.779927 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-15 03:55:36.809446 ERROR::Effect name not found in metadata: d
2025-08-15 03:55:36.829773 ERROR::No user formula provided
2025-08-15 03:55:36.88787 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-15 03:55:36.908729 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-15 03:55:41.018455 INFO::Writing function arguments to log file
2025-08-15 03:55:41.066348 INFO::Verifying options selected are valid
2025-08-15 03:55:43.455731 INFO::Writing function arguments to log file
2025-08-15 03:55:43.492968 INFO::Verifying options selected are valid
2025-08-15 03:55:43.494837 INFO::Determining format of input files
2025-08-15 03:55:43.49661 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 03:55:43.500996 INFO::Running selected normalization method: TSS
2025-08-15 03:55:43.503351 INFO::Creating output feature tables folder
2025-08-15 03:55:43.506272 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/features/data_norm.tsv
2025-08-15 03:55:43.510157 INFO::Filter data based on min abundance and min prevalence
2025-08-15 03:55:43.512689 INFO::Total samples in data: 16
2025-08-15 03:55:43.515129 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-15 03:55:43.518912 INFO::Total filtered features: 0
2025-08-15 03:55:43.521483 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-15 03:55:43.523773 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-15 03:55:43.525595 INFO::Filtered feature names from variance filtering:
2025-08-15 03:55:43.527456 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/features/filtered_data.tsv
2025-08-15 03:55:43.530287 INFO::Running selected transform method: LOG
2025-08-15 03:55:43.532342 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/features/data_transformed.tsv
2025-08-15 03:55:43.536417 INFO::Applying z-score to standardize continuous metadata
2025-08-15 03:55:43.54478 INFO::Running the linear model component
2025-08-15 03:55:43.576631 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:43.582761 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:43.588973 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:43.59792 INFO::Counting total values for each feature
2025-08-15 03:55:43.600658 INFO::Running the logistic model component
2025-08-15 03:55:43.63792 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:43.647614 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:43.66128 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:43.678451 INFO::Counting total values for each feature
2025-08-15 03:55:43.68207 INFO::Re-running abundances for warn_prevalence
2025-08-15 03:55:43.684098 INFO::Running selected normalization method: TSS
2025-08-15 03:55:43.687086 INFO::Running selected transform method: LOG
2025-08-15 03:55:43.735064 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:43.741378 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:43.747634 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:43.863289 INFO::Creating fits folder
2025-08-15 03:55:43.865527 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/fits/residuals_linear.rds
2025-08-15 03:55:43.867908 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/fits/fitted_linear.rds
2025-08-15 03:55:43.871431 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/fits/residuals_logistic.rds
2025-08-15 03:55:43.87501 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/fits/fitted_logistic.rds
2025-08-15 03:55:43.880852 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/all_results.tsv
2025-08-15 03:55:43.88584 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/significant_results.tsv
2025-08-15 03:55:43.888909 INFO::Creating output figures folder
2025-08-15 03:55:43.891304 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/figures/summary_plot.pdf
2025-08-15 03:55:45.386907 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/figures
2025-08-15 03:55:45.391 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 03:55:45.40033 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 03:55:45.964725 INFO::Writing summary plot of
                        significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/figures/summary_plot.pdf
2025-08-15 03:55:47.551455 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6007ff632bd/figures
2025-08-15 03:55:47.554539 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 03:55:47.562818 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 03:55:48.034502 INFO::Running the linear model component
2025-08-15 03:55:48.058907 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:48.068405 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:48.076676 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:48.089635 INFO::Counting total values for each feature
2025-08-15 03:55:48.093101 INFO::Running the logistic model component
2025-08-15 03:55:48.116033 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:48.128125 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:48.139475 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:48.155398 INFO::Counting total values for each feature
2025-08-15 03:55:48.159432 INFO::Re-running abundances for warn_prevalence
2025-08-15 03:55:48.16133 INFO::Running selected normalization method: TSS
2025-08-15 03:55:48.1642 INFO::Running selected transform method: LOG
2025-08-15 03:55:48.187136 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:48.196327 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:48.204957 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:48.37694 INFO::Creating output folder
2025-08-15 03:55:48.37941 INFO::Creating output figures folder
2025-08-15 03:55:48.382517 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60044972d00/figures/summary_plot.pdf
2025-08-15 03:55:50.035938 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec60044972d00/figures
2025-08-15 03:55:50.03792 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 03:55:50.044084 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 03:55:51.284506 INFO::Applying z-score to standardize continuous metadata
2025-08-15 03:55:51.29804 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-15 03:55:51.299992 INFO::Bypass z-score application to metadata
2025-08-15 03:55:51.304831 INFO::Bypass z-score application to metadata
2025-08-15 03:55:51.371083 INFO::Determining format of input files
2025-08-15 03:55:51.372376 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 03:55:51.373539 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-15 03:55:51.381167 INFO::Determining format of input files
2025-08-15 03:55:51.382571 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-15 03:55:51.384151 INFO::Input format is feature_specific_covariate samples as columns
2025-08-15 03:55:51.392459 INFO::Determining format of input files
2025-08-15 03:55:51.393802 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 03:55:51.395218 INFO::Input format is feature_specific_covariate samples as columns
2025-08-15 03:55:51.397239 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-15 03:55:51.39832 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-15 03:55:51.414626 INFO::Running selected transform method: LOG
2025-08-15 03:55:51.416842 INFO::Creating output feature tables folder
2025-08-15 03:55:51.418696 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600349e244f/features/data_transformed.tsv
2025-08-15 03:55:51.423956 INFO::Running selected transform method: LOG
2025-08-15 03:55:51.425543 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600349e244f/features/data_transformed.tsv
2025-08-15 03:55:51.443737 INFO::Running selected transform method: PLOG
2025-08-15 03:55:51.447344 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600349e244f/features/data_transformed.tsv
2025-08-15 03:55:51.459765 INFO::Running selected transform method: NONE
2025-08-15 03:55:51.462003 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec600349e244f/features/data_transformed.tsv
2025-08-15 03:55:51.497324 INFO::Running the linear model component
2025-08-15 03:55:51.511298 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:51.517238 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:51.523547 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:51.531992 INFO::Counting total values for each feature
2025-08-15 03:55:51.534068 INFO::Running the logistic model component
2025-08-15 03:55:51.546977 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:51.554513 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:51.561584 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:51.571478 INFO::Counting total values for each feature
2025-08-15 03:55:51.573902 INFO::Re-running abundances for warn_prevalence
2025-08-15 03:55:51.575069 INFO::Running selected normalization method: TSS
2025-08-15 03:55:51.576821 INFO::Running selected transform method: LOG
2025-08-15 03:55:51.589653 INFO::Fitting model to feature number 1, a
2025-08-15 03:55:51.595325 INFO::Fitting model to feature number 2, b
2025-08-15 03:55:51.600763 INFO::Fitting model to feature number 3, c
2025-08-15 03:55:51.718549 INFO::Creating output folder
2025-08-15 03:55:51.720995 INFO::Creating fits folder
2025-08-15 03:55:51.723346 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/fits/residuals_linear.rds
2025-08-15 03:55:51.726087 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/fits/fitted_linear.rds
2025-08-15 03:55:51.728621 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/fits/residuals_logistic.rds
2025-08-15 03:55:51.731252 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/fits/fitted_logistic.rds
2025-08-15 03:55:51.736022 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/all_results.tsv
2025-08-15 03:55:51.740062 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp0YIbDl\filec6003a4378ff/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
 419.93   14.15  434.79

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin329.87 1.0631.08
maaslin_check_arguments0.210.000.20
maaslin_check_formula0.250.020.28
maaslin_compute_formula0.280.000.29
maaslin_contrast_test27.22 1.8629.08
maaslin_filter1.410.061.49
maaslin_fit19.54 1.6921.22
maaslin_log_arguments0.210.000.21
maaslin_normalize0.840.010.86
maaslin_plot_results49.52 2.4952.53
maaslin_plot_results_from_output48.59 1.4050.72
maaslin_process_metadata1.770.031.80
maaslin_read_data0.230.020.25
maaslin_reorder_data0.200.030.23
maaslin_transform2.220.032.27
maaslin_write_results21.67 1.6923.38
maaslin_write_results_lefse_format21.79 1.4523.31
preprocess_dna_mtx000
preprocess_taxa_mtx0.010.000.01