Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1147/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 2025-08-08 21:58:53 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 22:11:57 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 783.9 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 (2025-06-13) * 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 42.399 1.261 44.083 maaslin_plot_results 41.957 1.081 43.365 maaslin3 23.967 1.088 25.338 maaslin_contrast_test 20.144 1.026 21.479 maaslin_write_results 16.758 0.797 17.740 maaslin_write_results_lefse_format 16.990 0.530 17.636 maaslin_fit 14.958 0.858 15.991 * 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 (2025-06-13) -- "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 22:05:53.433081 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:05:53.526094 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:05:53.633827 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:05:53.656709 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:05:53.711229 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:05:53.818249 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:05:53.825659 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:05:53.840436 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:05:53.980845 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:05:53.988813 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:05:54.046975 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:05:54.100771 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:05:54.114426 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:05:54.168558 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:05:54.272198 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:06:12.178327 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:06:12.282607 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:06:12.38085 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:06:12.409467 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:06:12.451714 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:06:12.546857 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:06:12.570639 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:06:12.585329 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:06:12.708112 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:06:12.715018 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:06:12.773585 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:06:12.821695 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:06:12.836119 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:06:12.890238 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:06:12.988063 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:06:16.619 R[41882:417872624] XType: com.apple.fonts is not accessible. 2025-08-08 22:06:16.620 R[41882:417872624] XType: XTFontStaticRegistry is enabled. 2025-08-08 22:06:33.481587 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:06:33.609075 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:06:33.713122 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:06:33.741098 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:06:33.791123 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:06:33.894061 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:06:33.901222 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:06:33.917301 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:06:34.049336 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:06:34.056716 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:06:34.182249 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:06:34.237414 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:06:34.253903 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:06:34.3135 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:06:34.406389 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:06:50.2349 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:06:50.326328 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:06:50.410807 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:06:50.433067 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:06:50.474465 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:06:50.560043 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:06:50.566486 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:06:50.581356 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:06:50.754742 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:06:50.762457 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:06:50.827061 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:06:50.884082 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:06:50.903423 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:06:50.959106 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:06:51.042517 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:06:51.290812 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds 2025-08-08 22:06:51.363712 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds 2025-08-08 22:06:51.429973 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds 2025-08-08 22:06:51.776411 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds 2025-08-08 22:07:11.541757 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:07:11.664379 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:07:11.760956 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:07:11.788222 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:07:11.832882 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:07:11.929877 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:07:11.937033 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:07:11.957088 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:07:12.089495 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:07:12.097359 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:07:12.180819 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:07:12.244359 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:07:12.260667 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:07:12.321856 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:07:12.432424 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:07:27.611478 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:07:27.715335 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:07:27.803085 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:07:27.826838 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:07:27.874588 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:07:27.961399 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:07:27.968202 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:07:27.985113 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:07:28.121299 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:07:28.128207 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:07:28.188705 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:07:28.24316 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:07:28.258695 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:07:28.317938 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:07:28.416695 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:07:28.69321 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds 2025-08-08 22:07:28.760942 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds 2025-08-08 22:07:28.833342 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds 2025-08-08 22:07:29.193722 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds 2025-08-08 22:07:48.279435 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:07:48.38293 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:07:48.494007 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:07:48.529661 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:07:48.588127 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:07:48.710232 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:07:48.719991 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:07:48.738795 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:07:48.893322 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:07:48.90158 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:07:48.971765 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:07:49.026222 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:07:49.040526 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:07:49.138859 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:07:49.22876 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:08:03.00125 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:08:03.103792 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:08:03.198738 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:08:03.224718 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:08:03.271592 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:08:03.36215 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:08:03.369242 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:08:03.385501 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:08:03.493096 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:08:03.49999 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:08:03.564443 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:08:03.614164 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:08:03.628393 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:08:03.678351 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:08:03.770669 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:08:04.011483 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds 2025-08-08 22:08:04.078734 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds 2025-08-08 22:08:04.149321 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds 2025-08-08 22:08:04.504071 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds 2025-08-08 22:08:23.180601 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:08:23.27411 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:08:23.377335 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:08:23.409545 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:08:23.460815 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:08:23.563003 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:08:23.570468 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:08:23.587416 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:08:23.712439 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:08:23.719574 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:08:23.78424 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:08:23.838348 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:08:23.853854 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:08:23.949987 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:08:24.031817 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:08:38.120865 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:08:38.277355 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:08:38.363238 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:08:38.394998 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:08:38.44104 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:08:38.546181 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:08:38.555172 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:08:38.57403 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:08:38.72363 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:08:38.732796 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:08:38.801738 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:08:38.854124 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:08:38.87218 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:08:38.92442 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:08:39.019439 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:09:01.300377 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:09:13.296213 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:09:36.283152 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:09:47.321437 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:09:48.047578 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds 2025-08-08 22:09:48.121365 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds 2025-08-08 22:09:48.165598 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds 2025-08-08 22:09:48.243186 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds 2025-08-08 22:10:08.689741 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:10:14.76974 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:10:15.147543 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds 2025-08-08 22:10:15.222559 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds 2025-08-08 22:10:15.266221 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds 2025-08-08 22:10:15.341852 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds 2025-08-08 22:10:33.111742 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:10:39.39463 WARNING::Fitting problem for feature 124 returning NA 2025-08-08 22:10:39.766618 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds 2025-08-08 22:10:39.833208 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds 2025-08-08 22:10:39.872701 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds 2025-08-08 22:10:39.949107 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds 2025-08-08 22:10:56.905286 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:10:56.993294 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:10:57.086713 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:10:57.114151 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:10:57.160282 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:10:57.253725 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:10:57.260202 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:10:57.274453 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:10:57.405228 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:10:57.414005 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:10:57.474922 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:10:57.532105 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:10:57.550513 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:10:57.60276 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:10:57.68745 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:11:11.292389 WARNING::Fitting problem for feature 50 returning NA 2025-08-08 22:11:11.388987 WARNING::Fitting problem for feature 62 returning NA 2025-08-08 22:11:11.485024 WARNING::Fitting problem for feature 74 returning NA 2025-08-08 22:11:11.514261 WARNING::Fitting problem for feature 78 returning NA 2025-08-08 22:11:11.559162 WARNING::Fitting problem for feature 84 returning NA 2025-08-08 22:11:11.649423 WARNING::Fitting problem for feature 96 returning NA 2025-08-08 22:11:11.655405 WARNING::Fitting problem for feature 97 returning NA 2025-08-08 22:11:11.673567 WARNING::Fitting problem for feature 99 returning NA 2025-08-08 22:11:11.796527 WARNING::Fitting problem for feature 114 returning NA 2025-08-08 22:11:11.803154 WARNING::Fitting problem for feature 115 returning NA 2025-08-08 22:11:11.875547 WARNING::Fitting problem for feature 123 returning NA 2025-08-08 22:11:11.928698 WARNING::Fitting problem for feature 130 returning NA 2025-08-08 22:11:11.944281 WARNING::Fitting problem for feature 132 returning NA 2025-08-08 22:11:11.991454 WARNING::Fitting problem for feature 139 returning NA 2025-08-08 22:11:12.082912 WARNING::Fitting problem for feature 150 returning NA 2025-08-08 22:11:12.483289 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds 2025-08-08 22:11:12.554627 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds 2025-08-08 22:11:12.628802 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds 2025-08-08 22:11:12.986611 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds 2025-08-08 22:11:31.026067 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-08-08 22:11:31.045544 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-08-08 22:11:31.061889 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-08-08 22:11:31.132434 ERROR::No fixed, group, or ordered effects included in formula. 2025-08-08 22:11:31.153024 ERROR::Effect name not found in metadata: d 2025-08-08 22:11:31.165361 ERROR::No user formula provided 2025-08-08 22:11:31.199111 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-08-08 22:11:31.213678 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-08-08 22:11:34.827343 INFO::Writing function arguments to log file 2025-08-08 22:11:34.852511 INFO::Verifying options selected are valid 2025-08-08 22:11:36.929193 INFO::Writing function arguments to log file 2025-08-08 22:11:36.948331 INFO::Verifying options selected are valid 2025-08-08 22:11:36.95002 INFO::Determining format of input files 2025-08-08 22:11:36.951408 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-08 22:11:36.954087 INFO::Running selected normalization method: TSS 2025-08-08 22:11:36.955975 INFO::Creating output feature tables folder 2025-08-08 22:11:36.957377 INFO::Writing normalized data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/data_norm.tsv 2025-08-08 22:11:36.959829 INFO::Filter data based on min abundance and min prevalence 2025-08-08 22:11:36.961244 INFO::Total samples in data: 16 2025-08-08 22:11:36.96266 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-08-08 22:11:36.965325 INFO::Total filtered features: 0 2025-08-08 22:11:36.966772 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-08 22:11:36.96848 INFO::Total features filtered by non-zero variance filtering: 0 2025-08-08 22:11:36.969486 INFO::Filtered feature names from variance filtering: 2025-08-08 22:11:36.970417 INFO::Writing filtered data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/filtered_data.tsv 2025-08-08 22:11:36.972866 INFO::Running selected transform method: LOG 2025-08-08 22:11:36.974599 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/data_transformed.tsv 2025-08-08 22:11:36.977178 INFO::Applying z-score to standardize continuous metadata 2025-08-08 22:11:36.983204 INFO::Running the linear model component 2025-08-08 22:11:37.004759 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:37.011434 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:37.017626 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:37.025365 INFO::Counting total values for each feature 2025-08-08 22:11:37.028327 INFO::Running the logistic model component 2025-08-08 22:11:37.047262 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:37.056815 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:37.06346 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:37.075399 INFO::Counting total values for each feature 2025-08-08 22:11:37.078773 INFO::Re-running abundances for warn_prevalence 2025-08-08 22:11:37.079943 INFO::Running selected normalization method: TSS 2025-08-08 22:11:37.08154 INFO::Running selected transform method: LOG 2025-08-08 22:11:37.103373 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:37.109529 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:37.114977 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:37.229179 INFO::Creating fits folder 2025-08-08 22:11:37.231317 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/residuals_linear.rds 2025-08-08 22:11:37.233802 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/fitted_linear.rds 2025-08-08 22:11:37.236483 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/residuals_logistic.rds 2025-08-08 22:11:37.238691 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/fitted_logistic.rds 2025-08-08 22:11:37.242927 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpvHGJYs/filea39a7e347ab/all_results.tsv 2025-08-08 22:11:37.245408 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/RtmpvHGJYs/filea39a7e347ab/significant_results.tsv 2025-08-08 22:11:37.248132 INFO::Creating output figures folder 2025-08-08 22:11:37.249776 INFO::Writing summary plot of significant results to file: /tmp/RtmpvHGJYs/filea39a7e347ab/figures/summary_plot.pdf 2025-08-08 22:11:38.654003 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a7e347ab/figures 2025-08-08 22:11:38.656287 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-08 22:11:38.661412 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-08 22:11:39.107873 INFO::Writing summary plot of significant results to file: /tmp/RtmpvHGJYs/filea39a7e347ab/figures/summary_plot.pdf 2025-08-08 22:11:40.615314 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a7e347ab/figures 2025-08-08 22:11:40.617561 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-08 22:11:40.622128 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-08 22:11:41.083936 INFO::Running the linear model component 2025-08-08 22:11:41.097769 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:41.104402 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:41.109086 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:41.119594 INFO::Counting total values for each feature 2025-08-08 22:11:41.122343 INFO::Running the logistic model component 2025-08-08 22:11:41.132395 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:41.138547 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:41.144203 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:41.152546 INFO::Counting total values for each feature 2025-08-08 22:11:41.154698 INFO::Re-running abundances for warn_prevalence 2025-08-08 22:11:41.156015 INFO::Running selected normalization method: TSS 2025-08-08 22:11:41.158156 INFO::Running selected transform method: LOG 2025-08-08 22:11:41.172559 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:41.177388 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:41.18309 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:41.29612 INFO::Creating output folder 2025-08-08 22:11:41.297817 INFO::Creating output figures folder 2025-08-08 22:11:41.299968 INFO::Writing summary plot of significant results to file: /tmp/RtmpvHGJYs/filea39a45016b4a/figures/summary_plot.pdf 2025-08-08 22:11:42.744556 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a45016b4a/figures 2025-08-08 22:11:42.746853 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-08 22:11:42.753188 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-08 22:11:43.910851 INFO::Applying z-score to standardize continuous metadata 2025-08-08 22:11:43.921971 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-08-08 22:11:43.923429 INFO::Bypass z-score application to metadata 2025-08-08 22:11:43.927392 INFO::Bypass z-score application to metadata 2025-08-08 22:11:43.953092 INFO::Determining format of input files 2025-08-08 22:11:43.954468 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-08 22:11:43.955945 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-08-08 22:11:43.967094 INFO::Determining format of input files 2025-08-08 22:11:43.968663 INFO::Input format is data samples as columns and metadata samples as rows 2025-08-08 22:11:43.970556 INFO::Input format is feature_specific_covariate samples as columns 2025-08-08 22:11:43.9816 INFO::Determining format of input files 2025-08-08 22:11:43.982644 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-08 22:11:43.9841 INFO::Input format is feature_specific_covariate samples as columns 2025-08-08 22:11:43.985893 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 22:11:43.986591 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 22:11:44.000399 INFO::Running selected transform method: LOG 2025-08-08 22:11:44.002231 INFO::Creating output feature tables folder 2025-08-08 22:11:44.003901 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv 2025-08-08 22:11:44.010055 INFO::Running selected transform method: LOG 2025-08-08 22:11:44.011229 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv 2025-08-08 22:11:44.015675 INFO::Running selected transform method: PLOG 2025-08-08 22:11:44.017153 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv 2025-08-08 22:11:44.02165 INFO::Running selected transform method: NONE 2025-08-08 22:11:44.022617 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv 2025-08-08 22:11:44.033955 INFO::Running the linear model component 2025-08-08 22:11:44.042351 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:44.046588 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:44.051269 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:44.060933 INFO::Counting total values for each feature 2025-08-08 22:11:44.063733 INFO::Running the logistic model component 2025-08-08 22:11:44.072385 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:44.080824 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:44.088059 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:44.098879 INFO::Counting total values for each feature 2025-08-08 22:11:44.102133 INFO::Re-running abundances for warn_prevalence 2025-08-08 22:11:44.103692 INFO::Running selected normalization method: TSS 2025-08-08 22:11:44.105618 INFO::Running selected transform method: LOG 2025-08-08 22:11:44.117872 INFO::Fitting model to feature number 1, a 2025-08-08 22:11:44.122918 INFO::Fitting model to feature number 2, b 2025-08-08 22:11:44.127754 INFO::Fitting model to feature number 3, c 2025-08-08 22:11:44.237956 INFO::Creating output folder 2025-08-08 22:11:44.239122 INFO::Creating fits folder 2025-08-08 22:11:44.240115 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/residuals_linear.rds 2025-08-08 22:11:44.241326 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/fitted_linear.rds 2025-08-08 22:11:44.242457 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/residuals_logistic.rds 2025-08-08 22:11:44.243717 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/fitted_logistic.rds 2025-08-08 22:11:44.247778 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpvHGJYs/filea39a223b5152/all_results.tsv 2025-08-08 22:11:44.250586 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/RtmpvHGJYs/filea39a223b5152/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 353.534 8.214 364.378
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 23.967 | 1.088 | 25.338 | |
maaslin_check_arguments | 0.173 | 0.004 | 0.180 | |
maaslin_check_formula | 0.171 | 0.011 | 0.185 | |
maaslin_compute_formula | 0.188 | 0.014 | 0.205 | |
maaslin_contrast_test | 20.144 | 1.026 | 21.479 | |
maaslin_filter | 1.413 | 0.298 | 1.750 | |
maaslin_fit | 14.958 | 0.858 | 15.991 | |
maaslin_log_arguments | 0.172 | 0.011 | 0.193 | |
maaslin_normalize | 0.352 | 0.025 | 0.380 | |
maaslin_plot_results | 41.957 | 1.081 | 43.365 | |
maaslin_plot_results_from_output | 42.399 | 1.261 | 44.083 | |
maaslin_process_metadata | 0.658 | 0.044 | 0.711 | |
maaslin_read_data | 0.170 | 0.011 | 0.185 | |
maaslin_reorder_data | 0.182 | 0.012 | 0.197 | |
maaslin_transform | 0.813 | 0.074 | 0.906 | |
maaslin_write_results | 16.758 | 0.797 | 17.740 | |
maaslin_write_results_lefse_format | 16.990 | 0.530 | 17.636 | |
preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
preprocess_taxa_mtx | 0.004 | 0.001 | 0.005 | |