Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-04-24 13:02 -0400 (Thu, 24 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
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: 2025-04-22 13:40 -0400 (Tue, 22 Apr 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 24.04.1 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

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: 2025-04-23 03:32:06 -0400 (Wed, 23 Apr 2025)
EndedAt: 2025-04-23 03:49:06 -0400 (Wed, 23 Apr 2025)
EllapsedTime: 1019.5 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 4.5.0 RC (2025-04-04 r88126 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_from_output   50.36   1.97   62.92
maaslin_plot_results               48.25   2.50   60.47
maaslin_contrast_test              30.12   1.55   43.88
maaslin3                           29.71   1.26   44.81
maaslin_write_results              22.25   2.04   31.98
maaslin_write_results_lefse_format 21.58   1.36   30.47
maaslin_fit                        19.49   1.97   28.86
* 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 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
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")
2025-04-23 03:41:24.011258 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:41:24.172661 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:41:24.346553 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:41:24.401608 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:41:24.494065 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:41:24.663003 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:41:24.696686 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:41:24.733751 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:41:24.931865 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:41:24.958532 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:41:25.074537 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:41:25.168202 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:41:25.210681 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:41:25.295572 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:41:25.407117 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:41:45.848472 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:41:45.953878 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:41:46.146447 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:41:46.198371 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:41:46.256776 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:41:46.419686 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:41:46.446678 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:41:46.477337 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:41:46.622141 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:41:46.647769 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:41:46.722298 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:41:46.812501 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:41:46.851166 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:41:46.945476 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:41:47.064117 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:42:12.396165 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:42:12.534085 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:42:12.667615 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:42:12.731563 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:42:12.791803 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:42:12.941557 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:42:12.97097 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:42:13.013037 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:42:13.214879 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:42:13.239383 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:42:13.328119 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:42:13.416739 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:42:13.444496 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:42:13.519687 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:42:13.668473 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:42:31.622637 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:42:31.768863 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:42:31.935424 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:42:31.995543 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:42:32.133779 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:42:32.262202 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:42:32.285813 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:42:32.328288 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:42:32.480249 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:42:32.518495 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:42:32.636279 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:42:32.740691 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:42:32.777312 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:42:32.875813 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:42:33.012556 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:42:33.37963 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_linear.rds
2025-04-23 03:42:33.48995 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_linear.rds
2025-04-23 03:42:33.606385 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_logistic.rds
2025-04-23 03:42:34.009844 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_logistic.rds
2025-04-23 03:42:56.393575 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:42:56.50623 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:42:56.629236 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:42:56.686989 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:42:56.747764 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:42:56.8499 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:42:56.870067 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:42:56.897229 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:42:57.087342 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:42:57.11738 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:42:57.218589 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:42:57.319208 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:42:57.360298 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:42:57.431937 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:42:57.585644 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:43:16.064037 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:43:16.168293 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:43:16.276603 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:43:16.337607 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:43:16.421188 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:43:16.577768 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:43:16.604517 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:43:16.647284 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:43:16.849176 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:43:16.87342 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:43:16.994933 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:43:17.091737 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:43:17.126873 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:43:17.2258 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:43:17.356583 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:43:17.67689 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_linear.rds
2025-04-23 03:43:17.799273 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_linear.rds
2025-04-23 03:43:17.919046 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_logistic.rds
2025-04-23 03:43:18.283391 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_logistic.rds
2025-04-23 03:43:40.582809 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:43:40.706568 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:43:41.360809 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:43:41.422372 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:43:41.519212 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:43:41.657586 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:43:41.686816 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:43:41.726135 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:43:41.871806 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:43:41.907683 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:43:41.9953 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:43:42.073098 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:43:42.105246 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:43:42.183634 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:43:42.314486 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:43:58.216249 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:43:58.40064 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:43:58.549159 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:43:58.652042 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:43:58.755676 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:43:58.890651 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:43:58.924726 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:43:58.963014 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:43:59.12164 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:43:59.159293 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:43:59.320288 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:43:59.414328 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:43:59.457532 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:43:59.565694 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:43:59.815592 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:44:00.097503 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_linear.rds
2025-04-23 03:44:00.326526 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_linear.rds
2025-04-23 03:44:00.437972 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/residuals_logistic.rds
2025-04-23 03:44:00.763207 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c446b304e/fits/fitted_logistic.rds
2025-04-23 03:44:26.567767 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:44:26.713531 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:44:26.867352 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:44:26.928451 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:44:27.037838 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:44:27.17586 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:44:27.200947 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:44:27.243208 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:44:27.367792 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:44:27.391819 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:44:27.466134 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:44:27.55906 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:44:27.603101 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:44:27.674059 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:44:27.805015 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:44:45.602743 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:44:45.755923 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:44:45.886052 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:44:45.927433 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:44:46.012705 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:44:46.157311 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:44:46.18192 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:44:46.229107 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:44:46.441337 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:44:46.469543 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:44:46.590806 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:44:46.685266 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:44:46.725843 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:44:46.82298 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:44:46.97652 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:45:25.057685 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:45:38.498178 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:46:09.574406 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:46:23.986363 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:46:24.953408 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_linear.rds
2025-04-23 03:46:25.065532 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_linear.rds
2025-04-23 03:46:25.132628 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_logistic.rds
2025-04-23 03:46:25.269148 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_logistic.rds
2025-04-23 03:46:49.368253 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:46:57.308207 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:46:57.82228 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_linear.rds
2025-04-23 03:46:57.931124 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_linear.rds
2025-04-23 03:46:57.999418 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_logistic.rds
2025-04-23 03:46:58.115395 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_logistic.rds
2025-04-23 03:47:19.716911 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:47:29.077057 WARNING::Fitting problem for feature 124 returning NA
2025-04-23 03:47:29.605622 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_linear.rds
2025-04-23 03:47:29.699286 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_linear.rds
2025-04-23 03:47:29.782473 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_logistic.rds
2025-04-23 03:47:29.900743 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_logistic.rds
2025-04-23 03:47:49.223665 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:47:49.386643 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:47:49.549707 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:47:49.611369 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:47:49.696836 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:47:49.866445 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:47:49.897559 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:47:49.93619 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:47:50.129635 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:47:50.160684 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:47:50.280456 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:47:50.361529 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:47:50.403574 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:47:50.499157 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:47:50.637079 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:48:07.452241 WARNING::Fitting problem for feature 50 returning NA
2025-04-23 03:48:07.590636 WARNING::Fitting problem for feature 62 returning NA
2025-04-23 03:48:07.700918 WARNING::Fitting problem for feature 74 returning NA
2025-04-23 03:48:07.743838 WARNING::Fitting problem for feature 78 returning NA
2025-04-23 03:48:07.802811 WARNING::Fitting problem for feature 84 returning NA
2025-04-23 03:48:07.95184 WARNING::Fitting problem for feature 96 returning NA
2025-04-23 03:48:07.989647 WARNING::Fitting problem for feature 97 returning NA
2025-04-23 03:48:08.020705 WARNING::Fitting problem for feature 99 returning NA
2025-04-23 03:48:08.189866 WARNING::Fitting problem for feature 114 returning NA
2025-04-23 03:48:08.21619 WARNING::Fitting problem for feature 115 returning NA
2025-04-23 03:48:08.307723 WARNING::Fitting problem for feature 123 returning NA
2025-04-23 03:48:08.381967 WARNING::Fitting problem for feature 130 returning NA
2025-04-23 03:48:08.4166 WARNING::Fitting problem for feature 132 returning NA
2025-04-23 03:48:08.498974 WARNING::Fitting problem for feature 139 returning NA
2025-04-23 03:48:08.619921 WARNING::Fitting problem for feature 150 returning NA
2025-04-23 03:48:08.97665 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_linear.rds
2025-04-23 03:48:09.077382 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_linear.rds
2025-04-23 03:48:09.162511 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/residuals_logistic.rds
2025-04-23 03:48:09.506344 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c49fe48a1/fits/fitted_logistic.rds
2025-04-23 03:48:30.949396 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-04-23 03:48:30.96541 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-04-23 03:48:30.976624 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-04-23 03:48:31.041821 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-04-23 03:48:31.063647 ERROR::Effect name not found in metadata: d
2025-04-23 03:48:31.076272 ERROR::No user formula provided
2025-04-23 03:48:31.139798 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-04-23 03:48:31.158001 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-04-23 03:48:35.637711 INFO::Writing function arguments to log file
2025-04-23 03:48:36.327001 INFO::Verifying options selected are valid
2025-04-23 03:48:38.924482 INFO::Writing function arguments to log file
2025-04-23 03:48:39.424271 INFO::Verifying options selected are valid
2025-04-23 03:48:39.447312 INFO::Determining format of input files
2025-04-23 03:48:39.469603 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-23 03:48:39.516581 INFO::Running selected normalization method: TSS
2025-04-23 03:48:39.537006 INFO::Creating output feature tables folder
2025-04-23 03:48:39.557356 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/features/data_norm.tsv
2025-04-23 03:48:39.598697 INFO::Filter data based on min abundance and min prevalence
2025-04-23 03:48:39.617259 INFO::Total samples in data: 16
2025-04-23 03:48:39.637707 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-04-23 03:48:39.672539 INFO::Total filtered features: 0
2025-04-23 03:48:39.690465 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-23 03:48:39.707175 INFO::Total features filtered by non-zero variance filtering: 0
2025-04-23 03:48:39.722141 INFO::Filtered feature names from variance filtering:
2025-04-23 03:48:39.738471 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/features/filtered_data.tsv
2025-04-23 03:48:39.758689 INFO::Running selected transform method: LOG
2025-04-23 03:48:39.776516 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/features/data_transformed.tsv
2025-04-23 03:48:39.808587 INFO::Applying z-score to standardize continuous metadata
2025-04-23 03:48:39.836294 INFO::Running the linear model component
2025-04-23 03:48:40.466502 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:40.494573 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:40.522276 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:40.556703 INFO::Counting total values for each feature
2025-04-23 03:48:40.575653 INFO::Running the logistic model component
2025-04-23 03:48:41.097482 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:41.130045 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:41.16386 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:41.203409 INFO::Counting total values for each feature
2025-04-23 03:48:41.22927 INFO::Re-running abundances for warn_prevalence
2025-04-23 03:48:41.254111 INFO::Running selected normalization method: TSS
2025-04-23 03:48:41.271792 INFO::Running selected transform method: LOG
2025-04-23 03:48:41.801486 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:41.831145 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:41.863785 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:42.045256 INFO::Creating fits folder
2025-04-23 03:48:42.065186 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/fits/residuals_linear.rds
2025-04-23 03:48:42.106171 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/fits/fitted_linear.rds
2025-04-23 03:48:42.139946 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/fits/residuals_logistic.rds
2025-04-23 03:48:42.181023 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/fits/fitted_logistic.rds
2025-04-23 03:48:42.213867 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/all_results.tsv
2025-04-23 03:48:42.246788 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\Rtmp6LNIsw\fileb41c58e37442/significant_results.tsv
2025-04-23 03:48:42.278414 INFO::Creating output figures folder
2025-04-23 03:48:42.296028 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/figures/summary_plot.pdf
2025-04-23 03:48:44.043597 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/figures
2025-04-23 03:48:44.065206 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-23 03:48:44.089968 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-23 03:48:44.623297 INFO::Writing summary plot of
                        significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/figures/summary_plot.pdf
2025-04-23 03:48:46.054548 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c58e37442/figures
2025-04-23 03:48:46.057334 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-23 03:48:46.065726 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-23 03:48:46.501748 INFO::Running the linear model component
2025-04-23 03:48:46.523201 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:46.531536 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:46.539566 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:46.551845 INFO::Counting total values for each feature
2025-04-23 03:48:46.555216 INFO::Running the logistic model component
2025-04-23 03:48:46.578128 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:46.590487 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:46.602094 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:46.617283 INFO::Counting total values for each feature
2025-04-23 03:48:46.620999 INFO::Re-running abundances for warn_prevalence
2025-04-23 03:48:46.622728 INFO::Running selected normalization method: TSS
2025-04-23 03:48:46.625394 INFO::Running selected transform method: LOG
2025-04-23 03:48:46.647692 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:46.656232 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:46.664085 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:46.795999 INFO::Creating output folder
2025-04-23 03:48:46.798259 INFO::Creating output figures folder
2025-04-23 03:48:46.80091 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c1c6e66f0/figures/summary_plot.pdf
2025-04-23 03:48:48.475993 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c1c6e66f0/figures
2025-04-23 03:48:48.478447 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-23 03:48:48.485593 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-23 03:48:49.726132 INFO::Applying z-score to standardize continuous metadata
2025-04-23 03:48:49.73406 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-04-23 03:48:49.735194 INFO::Bypass z-score application to metadata
2025-04-23 03:48:49.738014 INFO::Bypass z-score application to metadata
2025-04-23 03:48:49.852294 INFO::Determining format of input files
2025-04-23 03:48:49.854388 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-23 03:48:49.856322 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-04-23 03:48:49.868709 INFO::Determining format of input files
2025-04-23 03:48:49.870914 INFO::Input format is data samples as columns and metadata samples as rows
2025-04-23 03:48:49.87355 INFO::Input format is feature_specific_covariate samples as columns
2025-04-23 03:48:49.886648 INFO::Determining format of input files
2025-04-23 03:48:49.888728 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-23 03:48:49.890915 INFO::Input format is feature_specific_covariate samples as columns
2025-04-23 03:48:49.894104 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-04-23 03:48:49.895832 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-04-23 03:48:49.936922 INFO::Running selected transform method: LOG
2025-04-23 03:48:49.938541 INFO::Creating output feature tables folder
2025-04-23 03:48:49.940261 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c44b16da1/features/data_transformed.tsv
2025-04-23 03:48:49.958435 INFO::Running selected transform method: LOG
2025-04-23 03:48:49.960952 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c44b16da1/features/data_transformed.tsv
2025-04-23 03:48:49.982563 INFO::Running selected transform method: PLOG
2025-04-23 03:48:49.985947 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c44b16da1/features/data_transformed.tsv
2025-04-23 03:48:50.007921 INFO::Running selected transform method: NONE
2025-04-23 03:48:50.009989 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c44b16da1/features/data_transformed.tsv
2025-04-23 03:48:50.061894 INFO::Running the linear model component
2025-04-23 03:48:50.076465 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:50.081831 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:50.086967 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:50.094894 INFO::Counting total values for each feature
2025-04-23 03:48:50.096902 INFO::Running the logistic model component
2025-04-23 03:48:50.109117 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:50.116335 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:50.123084 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:50.132725 INFO::Counting total values for each feature
2025-04-23 03:48:50.135052 INFO::Re-running abundances for warn_prevalence
2025-04-23 03:48:50.136166 INFO::Running selected normalization method: TSS
2025-04-23 03:48:50.137829 INFO::Running selected transform method: LOG
2025-04-23 03:48:50.150975 INFO::Fitting model to feature number 1, a
2025-04-23 03:48:50.156247 INFO::Fitting model to feature number 2, b
2025-04-23 03:48:50.161356 INFO::Fitting model to feature number 3, c
2025-04-23 03:48:50.264905 INFO::Creating output folder
2025-04-23 03:48:50.266447 INFO::Creating fits folder
2025-04-23 03:48:50.267855 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c48f34708/fits/residuals_linear.rds
2025-04-23 03:48:50.283473 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c48f34708/fits/fitted_linear.rds
2025-04-23 03:48:50.298286 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c48f34708/fits/residuals_logistic.rds
2025-04-23 03:48:50.31466 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c48f34708/fits/fitted_logistic.rds
2025-04-23 03:48:50.336138 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6LNIsw\fileb41c48f34708/all_results.tsv
2025-04-23 03:48:50.35745 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\Rtmp6LNIsw\fileb41c48f34708/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
 407.26   14.18  460.40

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin329.71 1.2644.81
maaslin_check_arguments0.30.00.3
maaslin_check_formula0.290.021.08
maaslin_compute_formula0.320.031.00
maaslin_contrast_test30.12 1.5543.88
maaslin_filter1.700.092.60
maaslin_fit19.49 1.9728.86
maaslin_log_arguments0.340.030.83
maaslin_normalize0.830.061.42
maaslin_plot_results48.25 2.5060.47
maaslin_plot_results_from_output50.36 1.9762.92
maaslin_process_metadata1.500.132.51
maaslin_read_data0.220.000.92
maaslin_reorder_data0.300.030.90
maaslin_transform2.430.143.37
maaslin_write_results22.25 2.0431.98
maaslin_write_results_lefse_format21.58 1.3630.47
preprocess_dna_mtx000
preprocess_taxa_mtx0.020.000.02