Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-11 12:05 -0400 (Thu, 11 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4539 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4474 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1150/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: maaslin3 |
Version: 1.1.0 |
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_1.1.0.tar.gz |
StartedAt: 2025-09-10 22:53:05 -0400 (Wed, 10 Sep 2025) |
EndedAt: 2025-09-10 23:06:10 -0400 (Wed, 10 Sep 2025) |
EllapsedTime: 784.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maaslin3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 ‘1.1.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maaslin3’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 43.447 1.068 45.043 maaslin_plot_results 42.040 1.108 43.489 maaslin3 23.410 1.028 24.657 maaslin_contrast_test 20.772 1.063 22.043 maaslin_write_results 17.244 0.900 18.414 maaslin_write_results_lefse_format 17.016 0.589 17.698 maaslin_fit 15.910 0.843 16.865 * 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
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 ‘1.1.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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") 2025-09-10 23:00:06.778989 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:00:06.879767 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:00:06.990706 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:00:07.019733 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:00:07.08141 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:00:07.183653 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:00:07.192269 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:00:07.211135 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:00:07.359045 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:00:07.367672 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:00:07.431958 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:00:07.482635 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:00:07.500923 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:00:07.562515 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:00:07.667418 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:00:25.651682 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:00:25.750726 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:00:25.836827 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:00:25.862159 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:00:25.910011 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:00:26.004756 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:00:26.010461 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:00:26.025531 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:00:26.154891 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:00:26.162952 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:00:26.251488 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:00:26.301467 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:00:26.316815 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:00:26.367524 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:00:26.443562 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:00:30.106 R[5236:255426489] XType: com.apple.fonts is not accessible. 2025-09-10 23:00:30.106 R[5236:255426489] XType: XTFontStaticRegistry is enabled. 2025-09-10 23:00:48.231368 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:00:48.326586 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:00:48.433999 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:00:48.46424 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:00:48.505443 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:00:48.602759 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:00:48.610437 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:00:48.627835 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:00:48.790748 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:00:48.799265 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:00:48.85878 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:00:48.911885 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:00:48.928004 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:00:48.974936 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:00:49.07064 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:01:04.896078 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:01:04.984573 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:01:05.073211 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:01:05.099699 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:01:05.146565 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:01:05.248453 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:01:05.255061 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:01:05.267027 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:01:05.401214 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:01:05.409248 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:01:05.476617 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:01:05.534831 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:01:05.551645 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:01:05.611272 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:01:05.726958 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:01:06.027147 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds 2025-09-10 23:01:06.091788 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds 2025-09-10 23:01:06.167234 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds 2025-09-10 23:01:06.536904 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds 2025-09-10 23:01:26.298998 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:01:26.407357 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:01:26.508376 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:01:26.538273 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:01:26.583104 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:01:26.68883 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:01:26.696886 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:01:26.714407 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:01:26.844852 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:01:26.853427 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:01:26.922752 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:01:26.98194 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:01:26.99846 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:01:27.057762 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:01:27.16696 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:01:42.463133 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:01:42.575639 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:01:42.679289 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:01:42.706312 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:01:42.739926 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:01:42.845578 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:01:42.853953 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:01:42.869406 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:01:42.987157 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:01:42.994471 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:01:43.067031 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:01:43.122895 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:01:43.138842 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:01:43.19397 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:01:43.29243 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:01:43.582963 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds 2025-09-10 23:01:43.718294 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds 2025-09-10 23:01:43.793854 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds 2025-09-10 23:01:44.145433 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds 2025-09-10 23:02:03.278246 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:02:03.375406 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:02:03.484043 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:02:03.513333 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:02:03.563165 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:02:03.66771 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:02:03.675455 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:02:03.693733 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:02:03.820675 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:02:03.828114 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:02:03.885396 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:02:03.977518 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:02:03.992448 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:02:04.041489 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:02:04.130164 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:02:17.993895 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:02:18.100763 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:02:18.208015 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:02:18.235919 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:02:18.284649 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:02:18.39649 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:02:18.405318 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:02:18.424611 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:02:18.554512 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:02:18.562462 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:02:18.630353 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:02:18.689241 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:02:18.706996 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:02:18.771611 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:02:18.87064 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:02:19.120211 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds 2025-09-10 23:02:19.192219 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds 2025-09-10 23:02:19.266722 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds 2025-09-10 23:02:19.618361 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds 2025-09-10 23:02:38.57046 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:02:38.671678 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:02:38.776765 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:02:38.809121 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:02:38.859639 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:02:38.966907 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:02:38.974763 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:02:38.990089 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:02:39.127696 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:02:39.135428 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:02:39.205234 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:02:39.264681 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:02:39.281161 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:02:39.33429 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:02:39.435022 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:02:53.904354 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:02:54.006104 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:02:54.109123 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:02:54.140189 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:02:54.183446 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:02:54.276205 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:02:54.282407 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:02:54.298066 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:02:54.419918 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:02:54.426812 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:02:54.48317 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:02:54.536612 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:02:54.554733 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:02:54.602152 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:02:54.6854 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:03:16.198707 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:03:27.286238 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:03:49.78866 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:00.875101 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:01.577348 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds 2025-09-10 23:04:01.648908 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds 2025-09-10 23:04:01.69332 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds 2025-09-10 23:04:01.76912 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds 2025-09-10 23:04:21.853251 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:28.930739 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:29.247639 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds 2025-09-10 23:04:29.310395 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds 2025-09-10 23:04:29.352395 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds 2025-09-10 23:04:29.425068 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds 2025-09-10 23:04:45.842886 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:53.153204 WARNING::Fitting problem for feature 124 returning NA 2025-09-10 23:04:53.555207 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds 2025-09-10 23:04:53.624911 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds 2025-09-10 23:04:53.669981 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds 2025-09-10 23:04:53.749994 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds 2025-09-10 23:05:10.411952 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:05:10.519777 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:05:10.65485 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:05:10.67934 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:05:10.726133 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:05:10.82941 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:05:10.837423 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:05:10.853149 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:05:10.974909 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:05:10.980826 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:05:11.053383 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:05:11.104269 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:05:11.122442 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:05:11.179837 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:05:11.26535 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:05:25.121184 WARNING::Fitting problem for feature 50 returning NA 2025-09-10 23:05:25.216528 WARNING::Fitting problem for feature 62 returning NA 2025-09-10 23:05:25.313283 WARNING::Fitting problem for feature 74 returning NA 2025-09-10 23:05:25.343298 WARNING::Fitting problem for feature 78 returning NA 2025-09-10 23:05:25.394296 WARNING::Fitting problem for feature 84 returning NA 2025-09-10 23:05:25.497205 WARNING::Fitting problem for feature 96 returning NA 2025-09-10 23:05:25.503999 WARNING::Fitting problem for feature 97 returning NA 2025-09-10 23:05:25.518107 WARNING::Fitting problem for feature 99 returning NA 2025-09-10 23:05:25.651665 WARNING::Fitting problem for feature 114 returning NA 2025-09-10 23:05:25.658418 WARNING::Fitting problem for feature 115 returning NA 2025-09-10 23:05:25.724381 WARNING::Fitting problem for feature 123 returning NA 2025-09-10 23:05:25.777028 WARNING::Fitting problem for feature 130 returning NA 2025-09-10 23:05:25.793872 WARNING::Fitting problem for feature 132 returning NA 2025-09-10 23:05:25.850821 WARNING::Fitting problem for feature 139 returning NA 2025-09-10 23:05:25.949632 WARNING::Fitting problem for feature 150 returning NA 2025-09-10 23:05:26.342716 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds 2025-09-10 23:05:26.40886 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds 2025-09-10 23:05:26.482834 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds 2025-09-10 23:05:26.840426 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds 2025-09-10 23:05:43.774256 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-09-10 23:05:43.790539 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-09-10 23:05:43.805175 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-09-10 23:05:43.872955 ERROR::No fixed, group, or ordered effects included in formula. 2025-09-10 23:05:43.892062 ERROR::Effect name not found in metadata: d 2025-09-10 23:05:43.909703 ERROR::No user formula provided 2025-09-10 23:05:43.950785 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-09-10 23:05:43.966253 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-09-10 23:05:47.477194 INFO::Writing function arguments to log file 2025-09-10 23:05:47.501391 INFO::Verifying options selected are valid 2025-09-10 23:05:49.579094 INFO::Writing function arguments to log file 2025-09-10 23:05:49.599077 INFO::Verifying options selected are valid 2025-09-10 23:05:49.601389 INFO::Determining format of input files 2025-09-10 23:05:49.603417 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-10 23:05:49.607746 INFO::Running selected normalization method: TSS 2025-09-10 23:05:49.609645 INFO::Creating output feature tables folder 2025-09-10 23:05:49.610993 INFO::Writing normalized data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/data_norm.tsv 2025-09-10 23:05:49.613011 INFO::Filter data based on min abundance and min prevalence 2025-09-10 23:05:49.614801 INFO::Total samples in data: 16 2025-09-10 23:05:49.615975 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-09-10 23:05:49.618753 INFO::Total filtered features: 0 2025-09-10 23:05:49.620421 INFO::Filtered feature names from abundance and prevalence filtering: 2025-09-10 23:05:49.622275 INFO::Total features filtered by non-zero variance filtering: 0 2025-09-10 23:05:49.623324 INFO::Filtered feature names from variance filtering: 2025-09-10 23:05:49.624446 INFO::Writing filtered data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/filtered_data.tsv 2025-09-10 23:05:49.626822 INFO::Running selected transform method: LOG 2025-09-10 23:05:49.62834 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/data_transformed.tsv 2025-09-10 23:05:49.630721 INFO::Applying z-score to standardize continuous metadata 2025-09-10 23:05:49.638083 INFO::Running the linear model component 2025-09-10 23:05:49.660918 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:49.666343 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:49.672158 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:49.682991 INFO::Counting total values for each feature 2025-09-10 23:05:49.6857 INFO::Running the logistic model component 2025-09-10 23:05:49.706331 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:49.713117 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:49.72018 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:49.72955 INFO::Counting total values for each feature 2025-09-10 23:05:49.732798 INFO::Re-running abundances for warn_prevalence 2025-09-10 23:05:49.73459 INFO::Running selected normalization method: TSS 2025-09-10 23:05:49.7372 INFO::Running selected transform method: LOG 2025-09-10 23:05:49.757181 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:49.761707 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:49.765821 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:49.888423 INFO::Creating fits folder 2025-09-10 23:05:49.890475 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/residuals_linear.rds 2025-09-10 23:05:49.892729 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/fitted_linear.rds 2025-09-10 23:05:49.894926 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/residuals_logistic.rds 2025-09-10 23:05:49.897155 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/fitted_logistic.rds 2025-09-10 23:05:49.901191 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpnQgYfL/file14746ab2aa81/all_results.tsv 2025-09-10 23:05:49.903698 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/RtmpnQgYfL/file14746ab2aa81/significant_results.tsv 2025-09-10 23:05:49.905346 INFO::Creating output figures folder 2025-09-10 23:05:49.90769 INFO::Writing summary plot of significant results to file: /tmp/RtmpnQgYfL/file14746ab2aa81/figures/summary_plot.pdf 2025-09-10 23:05:51.382715 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file14746ab2aa81/figures 2025-09-10 23:05:51.385777 INFO::Plotting associations from most to least significant, grouped by metadata 2025-09-10 23:05:51.393684 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-09-10 23:05:52.048574 INFO::Writing summary plot of significant results to file: /tmp/RtmpnQgYfL/file14746ab2aa81/figures/summary_plot.pdf 2025-09-10 23:05:53.617649 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file14746ab2aa81/figures 2025-09-10 23:05:53.619792 INFO::Plotting associations from most to least significant, grouped by metadata 2025-09-10 23:05:53.625205 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-09-10 23:05:54.146801 INFO::Running the linear model component 2025-09-10 23:05:54.160654 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:54.167069 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:54.173647 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:54.180857 INFO::Counting total values for each feature 2025-09-10 23:05:54.182552 INFO::Running the logistic model component 2025-09-10 23:05:54.196005 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:54.205481 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:54.211918 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:54.222856 INFO::Counting total values for each feature 2025-09-10 23:05:54.225673 INFO::Re-running abundances for warn_prevalence 2025-09-10 23:05:54.226883 INFO::Running selected normalization method: TSS 2025-09-10 23:05:54.228851 INFO::Running selected transform method: LOG 2025-09-10 23:05:54.239887 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:54.245775 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:54.251353 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:54.377382 INFO::Creating output folder 2025-09-10 23:05:54.379405 INFO::Creating output figures folder 2025-09-10 23:05:54.381012 INFO::Writing summary plot of significant results to file: /tmp/RtmpnQgYfL/file1474ed74ebf/figures/summary_plot.pdf 2025-09-10 23:05:55.928576 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file1474ed74ebf/figures 2025-09-10 23:05:55.931093 INFO::Plotting associations from most to least significant, grouped by metadata 2025-09-10 23:05:55.93806 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-09-10 23:05:56.988238 INFO::Applying z-score to standardize continuous metadata 2025-09-10 23:05:56.999796 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-09-10 23:05:57.001057 INFO::Bypass z-score application to metadata 2025-09-10 23:05:57.003665 INFO::Bypass z-score application to metadata 2025-09-10 23:05:57.032682 INFO::Determining format of input files 2025-09-10 23:05:57.033599 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-10 23:05:57.034363 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-09-10 23:05:57.044228 INFO::Determining format of input files 2025-09-10 23:05:57.045363 INFO::Input format is data samples as columns and metadata samples as rows 2025-09-10 23:05:57.047169 INFO::Input format is feature_specific_covariate samples as columns 2025-09-10 23:05:57.059339 INFO::Determining format of input files 2025-09-10 23:05:57.060445 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-10 23:05:57.061457 INFO::Input format is feature_specific_covariate samples as columns 2025-09-10 23:05:57.063517 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-09-10 23:05:57.064274 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-09-10 23:05:57.078544 INFO::Running selected transform method: LOG 2025-09-10 23:05:57.080387 INFO::Creating output feature tables folder 2025-09-10 23:05:57.082132 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv 2025-09-10 23:05:57.088899 INFO::Running selected transform method: LOG 2025-09-10 23:05:57.090626 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv 2025-09-10 23:05:57.096738 INFO::Running selected transform method: PLOG 2025-09-10 23:05:57.099339 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv 2025-09-10 23:05:57.104146 INFO::Running selected transform method: NONE 2025-09-10 23:05:57.105075 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv 2025-09-10 23:05:57.116259 INFO::Running the linear model component 2025-09-10 23:05:57.127864 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:57.132256 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:57.137348 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:57.145182 INFO::Counting total values for each feature 2025-09-10 23:05:57.147789 INFO::Running the logistic model component 2025-09-10 23:05:57.158792 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:57.16753 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:57.174918 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:57.185916 INFO::Counting total values for each feature 2025-09-10 23:05:57.189283 INFO::Re-running abundances for warn_prevalence 2025-09-10 23:05:57.190596 INFO::Running selected normalization method: TSS 2025-09-10 23:05:57.192228 INFO::Running selected transform method: LOG 2025-09-10 23:05:57.201657 INFO::Fitting model to feature number 1, a 2025-09-10 23:05:57.205893 INFO::Fitting model to feature number 2, b 2025-09-10 23:05:57.209846 INFO::Fitting model to feature number 3, c 2025-09-10 23:05:57.333424 INFO::Creating output folder 2025-09-10 23:05:57.335049 INFO::Creating fits folder 2025-09-10 23:05:57.336666 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/residuals_linear.rds 2025-09-10 23:05:57.338205 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/fitted_linear.rds 2025-09-10 23:05:57.339368 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/residuals_logistic.rds 2025-09-10 23:05:57.340658 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/fitted_logistic.rds 2025-09-10 23:05:57.343994 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpnQgYfL/file1474dd6ce3/all_results.tsv 2025-09-10 23:05:57.346474 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/RtmpnQgYfL/file1474dd6ce3/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 354.515 7.572 364.251
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 23.410 | 1.028 | 24.657 | |
maaslin_check_arguments | 0.181 | 0.003 | 0.185 | |
maaslin_check_formula | 0.176 | 0.009 | 0.187 | |
maaslin_compute_formula | 0.170 | 0.011 | 0.183 | |
maaslin_contrast_test | 20.772 | 1.063 | 22.043 | |
maaslin_filter | 0.618 | 0.048 | 0.672 | |
maaslin_fit | 15.910 | 0.843 | 16.865 | |
maaslin_log_arguments | 0.171 | 0.009 | 0.181 | |
maaslin_normalize | 0.372 | 0.024 | 0.399 | |
maaslin_plot_results | 42.040 | 1.108 | 43.489 | |
maaslin_plot_results_from_output | 43.447 | 1.068 | 45.043 | |
maaslin_process_metadata | 0.660 | 0.044 | 0.709 | |
maaslin_read_data | 0.179 | 0.011 | 0.195 | |
maaslin_reorder_data | 0.192 | 0.011 | 0.204 | |
maaslin_transform | 0.842 | 0.073 | 0.923 | |
maaslin_write_results | 17.244 | 0.900 | 18.414 | |
maaslin_write_results_lefse_format | 17.016 | 0.589 | 17.698 | |
preprocess_dna_mtx | 0.006 | 0.000 | 0.006 | |
preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |