Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-11 11:44 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
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: 2025-08-07 13:40 -0400 (Thu, 07 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 24.04.2 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 merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.0.0.tar.gz
StartedAt: 2025-08-08 05:37:14 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 06:02:18 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 1504.1 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 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               82.692  1.824  86.775
maaslin_plot_results_from_output   81.278  1.214  87.603
maaslin_contrast_test              42.018  1.653  47.110
maaslin3                           42.002  1.594  47.219
maaslin_write_results_lefse_format 37.519  0.698  40.286
maaslin_write_results              32.672  1.088  36.591
maaslin_fit                        30.271  0.839  32.324
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
2025-08-08 05:50:32.245984 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:50:32.471943 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:50:32.711737 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:50:32.785375 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:50:32.884186 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:50:33.095448 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:50:33.110549 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:50:33.14657 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:50:33.473585 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:50:33.487625 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:50:33.631103 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:50:33.778785 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:50:33.809902 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:50:33.920103 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:50:34.117067 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:51:08.792522 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:51:09.003651 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:51:09.215595 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:51:09.280521 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:51:09.379594 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:51:09.618335 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:51:09.632908 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:51:09.665488 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:51:09.933231 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:51:09.948192 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:51:10.080862 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:51:10.193604 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:51:10.231996 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:51:10.346949 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:51:10.543698 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:51:19.192 R[14200:302858682] XType: com.apple.fonts is not accessible.
2025-08-08 05:51:19.192 R[14200:302858682] XType: XTFontStaticRegistry is enabled.
2025-08-08 05:51:51.372723 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:51:51.579188 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:51:51.781523 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:51:51.84115 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:51:51.931494 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:51:52.1366 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:51:52.150542 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:51:52.18245 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:51:52.45676 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:51:52.472311 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:51:52.609067 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:51:52.730932 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:51:52.763517 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:51:52.883532 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:51:53.123283 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:52:22.351839 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:52:22.555795 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:52:22.760115 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:52:22.817978 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:52:22.912526 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:52:23.116863 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:52:23.13124 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:52:23.163065 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:52:23.417466 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:52:23.433168 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:52:23.571374 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:52:23.685998 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:52:23.719603 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:52:23.829484 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:52:24.020236 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:52:24.609681 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_linear.rds
2025-08-08 05:52:24.719436 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_linear.rds
2025-08-08 05:52:24.835469 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_logistic.rds
2025-08-08 05:52:25.451614 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_logistic.rds
2025-08-08 05:53:01.80124 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:53:02.012828 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:53:02.22231 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:53:02.284605 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:53:02.38301 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:53:02.611647 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:53:02.627278 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:53:02.66455 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:53:03.027292 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:53:03.042112 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:53:03.189133 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:53:03.30721 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:53:03.341942 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:53:03.456704 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:53:03.665006 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:53:33.267151 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:53:33.493335 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:53:33.711957 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:53:33.772373 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:53:33.922851 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:53:34.135387 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:53:34.149972 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:53:34.182404 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:53:34.445205 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:53:34.461458 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:53:34.599463 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:53:34.712106 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:53:34.745301 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:53:34.858439 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:53:35.054569 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:53:35.612392 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_linear.rds
2025-08-08 05:53:35.721128 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_linear.rds
2025-08-08 05:53:35.845923 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_logistic.rds
2025-08-08 05:53:36.454999 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_logistic.rds
2025-08-08 05:54:13.044758 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:54:13.248665 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:54:13.454257 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:54:13.513043 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:54:13.605177 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:54:13.806411 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:54:13.82102 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:54:13.855166 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:54:14.104221 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:54:14.118604 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:54:14.256501 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:54:14.362824 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:54:14.394229 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:54:14.503903 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:54:14.695877 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:54:43.233176 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:54:43.439285 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:54:43.718168 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:54:43.77617 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:54:43.865468 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:54:44.068788 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:54:44.082608 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:54:44.115577 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:54:44.371083 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:54:44.386356 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:54:44.513292 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:54:44.620281 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:54:44.650839 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:54:44.756871 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:54:44.93674 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:54:45.442919 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_linear.rds
2025-08-08 05:54:45.545028 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_linear.rds
2025-08-08 05:54:45.649649 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/residuals_logistic.rds
2025-08-08 05:54:46.211972 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file37786edd12ec/fits/fitted_logistic.rds
2025-08-08 05:55:21.580932 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:55:21.795194 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:55:21.997869 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:55:22.054931 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:55:22.141017 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:55:22.341993 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:55:22.356272 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:55:22.3872 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:55:22.643305 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:55:22.658132 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:55:22.790555 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:55:22.900684 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:55:22.932532 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:55:23.040042 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:55:23.220448 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:55:52.810496 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 05:55:53.021823 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 05:55:53.224217 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 05:55:53.281869 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 05:55:53.372945 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 05:55:53.570198 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 05:55:53.584426 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 05:55:53.614936 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 05:55:53.936218 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 05:55:53.95047 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 05:55:54.080982 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 05:55:54.189898 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 05:55:54.222685 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 05:55:54.328817 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 05:55:54.509281 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 05:56:35.704161 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:56:56.904559 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:57:41.307761 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:58:00.91836 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:58:02.528523 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_linear.rds
2025-08-08 05:58:02.762006 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_linear.rds
2025-08-08 05:58:02.884339 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_logistic.rds
2025-08-08 05:58:03.051728 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_logistic.rds
2025-08-08 05:58:43.563888 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:58:56.55255 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:58:57.46933 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_linear.rds
2025-08-08 05:58:57.581716 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_linear.rds
2025-08-08 05:58:57.65139 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_logistic.rds
2025-08-08 05:58:57.790228 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_logistic.rds
2025-08-08 05:59:35.443784 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:59:48.727504 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 05:59:49.588047 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_linear.rds
2025-08-08 05:59:49.692905 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_linear.rds
2025-08-08 05:59:49.761979 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_logistic.rds
2025-08-08 05:59:49.896428 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_logistic.rds
2025-08-08 06:00:20.976898 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 06:00:21.220661 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 06:00:21.43096 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 06:00:21.49124 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 06:00:21.586035 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 06:00:21.825264 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 06:00:21.840112 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 06:00:21.872427 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 06:00:22.177143 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 06:00:22.191303 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 06:00:22.332257 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 06:00:22.445654 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 06:00:22.487021 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 06:00:22.607074 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 06:00:22.808094 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 06:00:51.721262 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 06:00:51.93614 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 06:00:52.141518 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 06:00:52.200835 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 06:00:52.29431 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 06:00:52.506628 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 06:00:52.521245 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 06:00:52.594413 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 06:00:52.858968 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 06:00:52.87398 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 06:00:53.013526 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 06:00:53.125319 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 06:00:53.155916 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 06:00:53.268599 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 06:00:53.469181 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 06:00:54.208615 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_linear.rds
2025-08-08 06:00:54.315961 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_linear.rds
2025-08-08 06:00:54.428255 WARNING::Deleting existing residuals file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/residuals_logistic.rds
2025-08-08 06:00:55.041736 WARNING::Deleting existing fitted file: /tmp/RtmpQCQ2RN/file377816da0c5e/fits/fitted_logistic.rds
2025-08-08 06:01:29.34819 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-08 06:01:29.39196 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-08 06:01:29.422017 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-08 06:01:29.560173 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-08 06:01:29.604599 ERROR::Effect name not found in metadata: d
2025-08-08 06:01:29.636039 ERROR::No user formula provided
2025-08-08 06:01:29.717121 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-08 06:01:29.746701 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-08 06:01:39.414472 INFO::Writing function arguments to log file
2025-08-08 06:01:39.453842 INFO::Verifying options selected are valid
2025-08-08 06:01:43.751301 INFO::Writing function arguments to log file
2025-08-08 06:01:43.799809 INFO::Verifying options selected are valid
2025-08-08 06:01:43.803213 INFO::Determining format of input files
2025-08-08 06:01:43.806473 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 06:01:43.814391 INFO::Running selected normalization method: TSS
2025-08-08 06:01:43.822787 INFO::Creating output feature tables folder
2025-08-08 06:01:43.826962 INFO::Writing normalized data to file /tmp/RtmpQCQ2RN/file37786416694c/features/data_norm.tsv
2025-08-08 06:01:43.831575 INFO::Filter data based on min abundance and min prevalence
2025-08-08 06:01:43.874722 INFO::Total samples in data: 16
2025-08-08 06:01:43.877355 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-08 06:01:43.882025 INFO::Total filtered features: 0
2025-08-08 06:01:43.884776 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-08 06:01:43.887934 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-08 06:01:43.890819 INFO::Filtered feature names from variance filtering:
2025-08-08 06:01:43.893675 INFO::Writing filtered data to file /tmp/RtmpQCQ2RN/file37786416694c/features/filtered_data.tsv
2025-08-08 06:01:43.898419 INFO::Running selected transform method: LOG
2025-08-08 06:01:43.902116 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQCQ2RN/file37786416694c/features/data_transformed.tsv
2025-08-08 06:01:43.906893 INFO::Applying z-score to standardize continuous metadata
2025-08-08 06:01:43.920468 INFO::Running the linear model component
2025-08-08 06:01:43.962064 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:43.973401 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:43.986535 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:44.00674 INFO::Counting total values for each feature
2025-08-08 06:01:44.012507 INFO::Running the logistic model component
2025-08-08 06:01:44.062326 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:44.079593 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:44.098997 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:44.122397 INFO::Counting total values for each feature
2025-08-08 06:01:44.128551 INFO::Re-running abundances for warn_prevalence
2025-08-08 06:01:44.131244 INFO::Running selected normalization method: TSS
2025-08-08 06:01:44.135232 INFO::Running selected transform method: LOG
2025-08-08 06:01:44.18272 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:44.194296 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:44.207778 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:44.433522 INFO::Creating fits folder
2025-08-08 06:01:44.436772 INFO::Writing residuals to file /tmp/RtmpQCQ2RN/file37786416694c/fits/residuals_linear.rds
2025-08-08 06:01:44.440116 INFO::Writing fitted values to file /tmp/RtmpQCQ2RN/file37786416694c/fits/fitted_linear.rds
2025-08-08 06:01:44.443107 INFO::Writing residuals to file /tmp/RtmpQCQ2RN/file37786416694c/fits/residuals_logistic.rds
2025-08-08 06:01:44.445351 INFO::Writing fitted values to file /tmp/RtmpQCQ2RN/file37786416694c/fits/fitted_logistic.rds
2025-08-08 06:01:44.452254 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpQCQ2RN/file37786416694c/all_results.tsv
2025-08-08 06:01:44.458533 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/RtmpQCQ2RN/file37786416694c/significant_results.tsv
2025-08-08 06:01:44.462522 INFO::Creating output figures folder
2025-08-08 06:01:44.466168 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpQCQ2RN/file37786416694c/figures/summary_plot.pdf
2025-08-08 06:01:47.448276 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQCQ2RN/file37786416694c/figures
2025-08-08 06:01:47.452568 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 06:01:47.46583 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 06:01:48.389683 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpQCQ2RN/file37786416694c/figures/summary_plot.pdf
2025-08-08 06:01:51.338123 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQCQ2RN/file37786416694c/figures
2025-08-08 06:01:51.342347 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 06:01:51.359948 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 06:01:52.237626 INFO::Running the linear model component
2025-08-08 06:01:52.259984 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:52.270255 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:52.281172 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:52.297664 INFO::Counting total values for each feature
2025-08-08 06:01:52.301624 INFO::Running the logistic model component
2025-08-08 06:01:52.323292 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:52.336202 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:52.349238 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:52.369736 INFO::Counting total values for each feature
2025-08-08 06:01:52.374783 INFO::Re-running abundances for warn_prevalence
2025-08-08 06:01:52.376805 INFO::Running selected normalization method: TSS
2025-08-08 06:01:52.38029 INFO::Running selected transform method: LOG
2025-08-08 06:01:52.403011 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:52.413381 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:52.42343 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:52.628433 INFO::Creating output folder
2025-08-08 06:01:52.631128 INFO::Creating output figures folder
2025-08-08 06:01:52.634415 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpQCQ2RN/file377876b2bf97/figures/summary_plot.pdf
2025-08-08 06:01:55.641323 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQCQ2RN/file377876b2bf97/figures
2025-08-08 06:01:55.645084 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 06:01:55.65852 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 06:01:57.793967 INFO::Applying z-score to standardize continuous metadata
2025-08-08 06:01:57.813183 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-08 06:01:57.815079 INFO::Bypass z-score application to metadata
2025-08-08 06:01:57.821702 INFO::Bypass z-score application to metadata
2025-08-08 06:01:57.866844 INFO::Determining format of input files
2025-08-08 06:01:57.868781 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 06:01:57.870714 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-08 06:01:57.887968 INFO::Determining format of input files
2025-08-08 06:01:57.890465 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-08 06:01:57.893871 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 06:01:57.912842 INFO::Determining format of input files
2025-08-08 06:01:57.915204 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 06:01:57.917733 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 06:01:57.92186 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-08 06:01:57.923889 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-08 06:01:57.952781 INFO::Running selected transform method: LOG
2025-08-08 06:01:57.95536 INFO::Creating output feature tables folder
2025-08-08 06:01:57.957903 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQCQ2RN/file377824df3e88/features/data_transformed.tsv
2025-08-08 06:01:57.967274 INFO::Running selected transform method: LOG
2025-08-08 06:01:57.96986 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQCQ2RN/file377824df3e88/features/data_transformed.tsv
2025-08-08 06:01:57.978444 INFO::Running selected transform method: PLOG
2025-08-08 06:01:57.982538 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQCQ2RN/file377824df3e88/features/data_transformed.tsv
2025-08-08 06:01:57.989275 INFO::Running selected transform method: NONE
2025-08-08 06:01:57.991342 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQCQ2RN/file377824df3e88/features/data_transformed.tsv
2025-08-08 06:01:58.008817 INFO::Running the linear model component
2025-08-08 06:01:58.030692 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:58.040969 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:58.051493 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:58.068476 INFO::Counting total values for each feature
2025-08-08 06:01:58.072863 INFO::Running the logistic model component
2025-08-08 06:01:58.094587 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:58.109803 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:58.124813 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:58.145762 INFO::Counting total values for each feature
2025-08-08 06:01:58.150745 INFO::Re-running abundances for warn_prevalence
2025-08-08 06:01:58.152647 INFO::Running selected normalization method: TSS
2025-08-08 06:01:58.155706 INFO::Running selected transform method: LOG
2025-08-08 06:01:58.181627 INFO::Fitting model to feature number 1, a
2025-08-08 06:01:58.192082 INFO::Fitting model to feature number 2, b
2025-08-08 06:01:58.203876 INFO::Fitting model to feature number 3, c
2025-08-08 06:01:58.433181 INFO::Creating output folder
2025-08-08 06:01:58.435415 INFO::Creating fits folder
2025-08-08 06:01:58.438026 INFO::Writing residuals to file /tmp/RtmpQCQ2RN/file37783c8265a1/fits/residuals_linear.rds
2025-08-08 06:01:58.440873 INFO::Writing fitted values to file /tmp/RtmpQCQ2RN/file37783c8265a1/fits/fitted_linear.rds
2025-08-08 06:01:58.443654 INFO::Writing residuals to file /tmp/RtmpQCQ2RN/file37783c8265a1/fits/residuals_logistic.rds
2025-08-08 06:01:58.446713 INFO::Writing fitted values to file /tmp/RtmpQCQ2RN/file37783c8265a1/fits/fitted_logistic.rds
2025-08-08 06:01:58.453457 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpQCQ2RN/file37783c8265a1/all_results.tsv
2025-08-08 06:01:58.457773 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/RtmpQCQ2RN/file37783c8265a1/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
671.333  12.340 710.014

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin342.002 1.59447.219
maaslin_check_arguments0.2560.0070.306
maaslin_check_formula0.2980.0160.349
maaslin_compute_formula0.2990.0150.315
maaslin_contrast_test42.018 1.65347.110
maaslin_filter1.2000.0801.547
maaslin_fit30.271 0.83932.324
maaslin_log_arguments0.2850.0130.299
maaslin_normalize0.6560.0400.741
maaslin_plot_results82.692 1.82486.775
maaslin_plot_results_from_output81.278 1.21487.603
maaslin_process_metadata1.2060.0731.292
maaslin_read_data0.2850.0130.299
maaslin_reorder_data0.3480.0230.374
maaslin_transform2.4530.2882.886
maaslin_write_results32.672 1.08836.591
maaslin_write_results_lefse_format37.519 0.69840.286
preprocess_dna_mtx0.0090.0010.010
preprocess_taxa_mtx0.0100.0010.011