Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-16 12:07 -0400 (Thu, 16 Oct 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" | 4867 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4655 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4600 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1161/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.1.2 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: maaslin3 |
Version: 1.1.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz |
StartedAt: 2025-10-14 09:45:17 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 10:02:21 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 1023.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maaslin3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maaslin3/DESCRIPTION’ ... OK * this is package ‘maaslin3’ version ‘1.1.2’ * 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 loading without being on the library search path ... 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 64.679 0.218 65.109 maaslin_plot_results_from_output 63.309 0.311 63.769 maaslin3 30.097 1.407 31.621 maaslin_contrast_test 28.105 0.806 29.031 maaslin_write_results_lefse_format 24.479 0.148 24.673 maaslin_write_results 21.317 0.147 21.507 maaslin_fit 20.934 0.166 21.171 * 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.2’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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") 2025-10-14 09:53:48.297085 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:53:48.424959 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:53:48.585802 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:53:48.620207 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:53:48.674399 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:53:48.79429 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:53:48.802334 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:53:48.820374 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:53:48.983509 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:53:48.991772 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:53:49.069968 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:53:49.132951 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:53:49.151603 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:53:49.226261 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:53:49.337507 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:54:12.88805 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:54:13.013297 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:54:13.156977 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:54:13.192475 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:54:13.248775 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:54:13.386393 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:54:13.395186 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:54:13.414061 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:54:13.568444 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:54:13.576724 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:54:13.656493 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:54:13.72243 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:54:13.741549 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:54:13.805711 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:54:13.919706 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:54:46.333664 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:54:46.479977 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:54:46.617046 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:54:46.65536 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:54:46.716466 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:54:46.85537 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:54:46.870664 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:54:46.893278 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:54:47.078006 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:54:47.088839 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:54:47.19061 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:54:47.276253 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:54:47.301285 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:54:47.384802 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:54:47.519313 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:55:08.718434 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:55:08.869421 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:55:08.99246 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:55:09.02753 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:55:09.083964 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:55:09.209343 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:55:09.217748 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:55:09.236501 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:55:09.407585 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:55:09.416338 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:55:09.498194 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:55:09.563775 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:55:09.582569 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:55:09.649014 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:55:09.762383 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:55:10.069611 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds 2025-10-14 09:55:10.138572 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds 2025-10-14 09:55:10.209023 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds 2025-10-14 09:55:10.556324 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds 2025-10-14 09:55:39.629239 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:55:39.761089 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:55:39.88938 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:55:39.928332 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:55:39.988298 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:55:40.119736 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:55:40.128604 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:55:40.14881 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:55:40.306417 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:55:40.31494 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:55:40.395253 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:55:40.460352 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:55:40.479476 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:55:40.543883 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:55:41.65153 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:56:02.175 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:56:02.302835 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:56:02.42597 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:56:02.461846 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:56:02.519103 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:56:02.649408 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:56:02.658679 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:56:02.679338 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:56:02.837207 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:56:02.845752 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:56:02.926301 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:56:02.992115 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:56:03.014222 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:56:03.089232 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:56:03.216391 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:56:03.588884 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds 2025-10-14 09:56:03.65829 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds 2025-10-14 09:56:03.729579 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds 2025-10-14 09:56:04.079816 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds 2025-10-14 09:56:33.697616 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:56:33.827116 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:56:33.954521 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:56:33.992677 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:56:34.053371 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:56:34.185914 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:56:34.195143 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:56:34.215683 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:56:34.382472 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:56:34.391449 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:56:34.478294 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:56:34.554528 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:56:34.575792 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:56:34.649282 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:56:34.782635 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:56:53.087259 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:56:53.209674 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:56:53.330537 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:56:53.365752 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:56:53.423108 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:56:53.55208 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:56:53.560529 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:56:53.579888 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:56:53.744286 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:56:53.753075 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:56:53.875915 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:56:53.944489 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:56:53.964252 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:56:54.03243 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:56:54.147333 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:56:54.443198 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds 2025-10-14 09:56:54.51169 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds 2025-10-14 09:56:54.581745 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds 2025-10-14 09:56:54.928529 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds 2025-10-14 09:57:23.615538 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:57:23.740283 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:57:23.862448 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:57:23.897909 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:57:23.953274 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:57:24.076608 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:57:24.085098 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:57:24.104428 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:57:24.264537 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:57:24.273528 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:57:24.393174 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:57:24.460793 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:57:24.480629 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:57:24.545641 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:57:24.655801 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:57:44.137084 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 09:57:44.263083 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 09:57:44.386384 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 09:57:44.422069 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 09:57:44.478827 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 09:57:44.605676 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 09:57:44.614208 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 09:57:44.633589 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 09:57:44.789282 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 09:57:44.797781 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 09:57:44.877542 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 09:57:44.94268 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 09:57:44.961549 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 09:57:45.025102 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 09:57:45.137948 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 09:58:18.180562 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 09:58:32.918088 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 09:59:07.352095 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 09:59:21.189008 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 09:59:22.185082 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds 2025-10-14 09:59:22.251775 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds 2025-10-14 09:59:22.294461 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds 2025-10-14 09:59:22.371411 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds 2025-10-14 09:59:53.799718 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 10:00:03.258312 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 10:00:03.748904 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds 2025-10-14 10:00:03.81826 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds 2025-10-14 10:00:03.861795 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds 2025-10-14 10:00:03.940302 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds 2025-10-14 10:00:30.097598 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 10:00:39.577579 WARNING::Fitting problem for feature 124 returning NA 2025-10-14 10:00:40.074272 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds 2025-10-14 10:00:40.144403 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds 2025-10-14 10:00:40.18807 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds 2025-10-14 10:00:40.266353 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds 2025-10-14 10:01:05.529715 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 10:01:05.702811 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 10:01:05.835103 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 10:01:05.872494 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 10:01:05.930542 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 10:01:06.05835 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 10:01:06.067145 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 10:01:06.086759 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 10:01:06.25198 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 10:01:06.261712 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 10:01:06.351758 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 10:01:06.420875 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 10:01:06.440938 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 10:01:06.510011 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 10:01:06.630306 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 10:01:26.676891 WARNING::Fitting problem for feature 50 returning NA 2025-10-14 10:01:26.804905 WARNING::Fitting problem for feature 62 returning NA 2025-10-14 10:01:26.929374 WARNING::Fitting problem for feature 74 returning NA 2025-10-14 10:01:26.964231 WARNING::Fitting problem for feature 78 returning NA 2025-10-14 10:01:27.05984 WARNING::Fitting problem for feature 84 returning NA 2025-10-14 10:01:27.193214 WARNING::Fitting problem for feature 96 returning NA 2025-10-14 10:01:27.202337 WARNING::Fitting problem for feature 97 returning NA 2025-10-14 10:01:27.223058 WARNING::Fitting problem for feature 99 returning NA 2025-10-14 10:01:27.389796 WARNING::Fitting problem for feature 114 returning NA 2025-10-14 10:01:27.398533 WARNING::Fitting problem for feature 115 returning NA 2025-10-14 10:01:27.482452 WARNING::Fitting problem for feature 123 returning NA 2025-10-14 10:01:27.550028 WARNING::Fitting problem for feature 130 returning NA 2025-10-14 10:01:27.57172 WARNING::Fitting problem for feature 132 returning NA 2025-10-14 10:01:27.641235 WARNING::Fitting problem for feature 139 returning NA 2025-10-14 10:01:27.758743 WARNING::Fitting problem for feature 150 returning NA 2025-10-14 10:01:28.117198 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds 2025-10-14 10:01:28.178528 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds 2025-10-14 10:01:28.241173 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds 2025-10-14 10:01:28.531533 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds 2025-10-14 10:01:56.736264 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-10-14 10:01:56.762645 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-10-14 10:01:56.780509 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-10-14 10:01:56.864037 ERROR::No fixed, group, or ordered effects included in formula. 2025-10-14 10:01:56.89053 ERROR::Effect name not found in metadata: d 2025-10-14 10:01:56.908221 ERROR::No user formula provided 2025-10-14 10:01:56.95452 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-10-14 10:01:56.972581 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-10-14 10:02:01.885631 INFO::Writing function arguments to log file 2025-10-14 10:02:01.907919 INFO::Verifying options selected are valid 2025-10-14 10:02:05.284496 INFO::Writing function arguments to log file 2025-10-14 10:02:05.303212 INFO::Verifying options selected are valid 2025-10-14 10:02:05.304849 INFO::Determining format of input files 2025-10-14 10:02:05.306279 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 10:02:05.30987 INFO::Running selected normalization method: TSS 2025-10-14 10:02:05.312136 INFO::Creating output feature tables folder 2025-10-14 10:02:05.313661 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/data_norm.tsv 2025-10-14 10:02:05.31585 INFO::Filter data based on min abundance, min prevalence, and max prevalence 2025-10-14 10:02:05.317282 INFO::Total samples in data: 16 2025-10-14 10:02:05.3186 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-10-14 10:02:05.319921 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000 2025-10-14 10:02:05.32286 INFO::Total filtered features: 0 2025-10-14 10:02:05.324429 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering: 2025-10-14 10:02:05.326158 INFO::Total features filtered by non-zero variance filtering: 0 2025-10-14 10:02:05.32759 INFO::Filtered feature names from variance filtering: 2025-10-14 10:02:05.328895 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/filtered_data.tsv 2025-10-14 10:02:05.331013 INFO::Running selected transform method: LOG 2025-10-14 10:02:05.332767 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/data_transformed.tsv 2025-10-14 10:02:05.335182 INFO::Applying z-score to standardize continuous metadata 2025-10-14 10:02:05.343103 INFO::Running the linear model component 2025-10-14 10:02:05.365825 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:05.373042 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:05.379718 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:05.390758 INFO::Counting total values for each feature 2025-10-14 10:02:05.393728 INFO::Running the logistic model component 2025-10-14 10:02:05.415276 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:05.425072 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:05.434768 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:05.448476 INFO::Counting total values for each feature 2025-10-14 10:02:05.451855 INFO::Re-running abundances for warn_prevalence 2025-10-14 10:02:05.453251 INFO::Running selected normalization method: TSS 2025-10-14 10:02:05.455514 INFO::Running selected transform method: LOG 2025-10-14 10:02:05.477154 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:05.483813 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:05.490406 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:05.624229 INFO::Creating fits folder 2025-10-14 10:02:05.625926 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/residuals_linear.rds 2025-10-14 10:02:05.627508 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/fitted_linear.rds 2025-10-14 10:02:05.629241 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/residuals_logistic.rds 2025-10-14 10:02:05.630901 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/fitted_logistic.rds 2025-10-14 10:02:05.634773 INFO::Writing all the results to file (ordered by increasing individual q-values): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/all_results.tsv 2025-10-14 10:02:05.637223 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): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/significant_results.tsv 2025-10-14 10:02:05.639103 INFO::Creating output figures folder 2025-10-14 10:02:05.641176 INFO::Writing summary plot of significant results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures/summary_plot.pdf 2025-10-14 10:02:07.956454 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures 2025-10-14 10:02:07.959217 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 10:02:07.967029 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 10:02:08.697423 INFO::Writing summary plot of significant results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures/summary_plot.pdf 2025-10-14 10:02:11.029326 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures 2025-10-14 10:02:11.031615 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 10:02:11.039185 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 10:02:11.805944 INFO::Running the linear model component 2025-10-14 10:02:11.820549 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:11.827154 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:11.833642 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:11.844691 INFO::Counting total values for each feature 2025-10-14 10:02:11.847363 INFO::Running the logistic model component 2025-10-14 10:02:11.860875 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:11.870121 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:11.879117 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:11.892144 INFO::Counting total values for each feature 2025-10-14 10:02:11.895255 INFO::Re-running abundances for warn_prevalence 2025-10-14 10:02:11.896409 INFO::Running selected normalization method: TSS 2025-10-14 10:02:11.89841 INFO::Running selected transform method: LOG 2025-10-14 10:02:11.91217 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:11.918413 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:11.924649 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:12.058478 INFO::Creating output folder 2025-10-14 10:02:12.059975 INFO::Creating output figures folder 2025-10-14 10:02:12.061994 INFO::Writing summary plot of significant results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc73e0b5123/figures/summary_plot.pdf 2025-10-14 10:02:14.371514 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc73e0b5123/figures 2025-10-14 10:02:14.373952 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-14 10:02:14.381267 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-14 10:02:15.791193 INFO::Applying z-score to standardize continuous metadata 2025-10-14 10:02:15.803452 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-10-14 10:02:15.804833 INFO::Bypass z-score application to metadata 2025-10-14 10:02:15.808721 INFO::Bypass z-score application to metadata 2025-10-14 10:02:15.835512 INFO::Determining format of input files 2025-10-14 10:02:15.836896 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 10:02:15.838207 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-10-14 10:02:15.849337 INFO::Determining format of input files 2025-10-14 10:02:15.850919 INFO::Input format is data samples as columns and metadata samples as rows 2025-10-14 10:02:15.852904 INFO::Input format is feature_specific_covariate samples as columns 2025-10-14 10:02:15.865185 INFO::Determining format of input files 2025-10-14 10:02:15.866692 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-14 10:02:15.868326 INFO::Input format is feature_specific_covariate samples as columns 2025-10-14 10:02:15.870905 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-10-14 10:02:15.872149 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-10-14 10:02:15.888927 INFO::Running selected transform method: LOG 2025-10-14 10:02:15.890733 INFO::Creating output feature tables folder 2025-10-14 10:02:15.892142 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv 2025-10-14 10:02:15.898092 INFO::Running selected transform method: LOG 2025-10-14 10:02:15.899848 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv 2025-10-14 10:02:15.905668 INFO::Running selected transform method: PLOG 2025-10-14 10:02:15.908335 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv 2025-10-14 10:02:15.912719 INFO::Running selected transform method: NONE 2025-10-14 10:02:15.914041 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv 2025-10-14 10:02:15.945352 INFO::Running the linear model component 2025-10-14 10:02:15.962193 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:15.969451 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:15.977077 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:15.989004 INFO::Counting total values for each feature 2025-10-14 10:02:15.991767 INFO::Running the logistic model component 2025-10-14 10:02:16.006598 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:16.016795 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:16.026833 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:16.04172 INFO::Counting total values for each feature 2025-10-14 10:02:16.045143 INFO::Re-running abundances for warn_prevalence 2025-10-14 10:02:16.04655 INFO::Running selected normalization method: TSS 2025-10-14 10:02:16.049024 INFO::Running selected transform method: LOG 2025-10-14 10:02:16.064149 INFO::Fitting model to feature number 1, a 2025-10-14 10:02:16.071319 INFO::Fitting model to feature number 2, b 2025-10-14 10:02:16.078565 INFO::Fitting model to feature number 3, c 2025-10-14 10:02:16.225574 INFO::Creating output folder 2025-10-14 10:02:16.22716 INFO::Creating fits folder 2025-10-14 10:02:16.228654 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/residuals_linear.rds 2025-10-14 10:02:16.230343 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/fitted_linear.rds 2025-10-14 10:02:16.232209 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/residuals_logistic.rds 2025-10-14 10:02:16.234081 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/fitted_logistic.rds 2025-10-14 10:02:16.238351 INFO::Writing all the results to file (ordered by increasing individual q-values): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/all_results.tsv 2025-10-14 10:02:16.241095 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): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 513.330 7.416 522.369
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 30.097 | 1.407 | 31.621 | |
maaslin_check_arguments | 0.183 | 0.004 | 0.188 | |
maaslin_check_formula | 0.206 | 0.000 | 0.207 | |
maaslin_compute_formula | 0.210 | 0.004 | 0.215 | |
maaslin_contrast_test | 28.105 | 0.806 | 29.031 | |
maaslin_filter | 0.664 | 0.009 | 0.675 | |
maaslin_fit | 20.934 | 0.166 | 21.171 | |
maaslin_log_arguments | 0.194 | 0.004 | 0.199 | |
maaslin_normalize | 0.371 | 0.008 | 0.381 | |
maaslin_plot_results | 64.679 | 0.218 | 65.109 | |
maaslin_plot_results_from_output | 63.309 | 0.311 | 63.769 | |
maaslin_process_metadata | 0.643 | 0.017 | 0.660 | |
maaslin_read_data | 0.194 | 0.000 | 0.195 | |
maaslin_reorder_data | 0.197 | 0.004 | 0.203 | |
maaslin_transform | 0.769 | 0.004 | 0.774 | |
maaslin_write_results | 21.317 | 0.147 | 21.507 | |
maaslin_write_results_lefse_format | 24.479 | 0.148 | 24.673 | |
preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
preprocess_taxa_mtx | 0.003 | 0.003 | 0.006 | |