Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1155/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.0.2 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.0.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.2.tar.gz |
StartedAt: 2025-10-16 00:37:19 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 00:58:59 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 1299.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maaslin3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘maaslin3/DESCRIPTION’ ... OK * this is package ‘maaslin3’ version ‘1.0.2’ * 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 43.365 0.324 43.640 maaslin_plot_results_from_output 43.345 0.274 43.624 maaslin3 20.188 0.697 20.891 maaslin_contrast_test 18.889 0.517 19.406 maaslin_write_results_lefse_format 14.173 0.162 14.337 maaslin_write_results 13.760 0.216 13.976 maaslin_fit 13.269 0.256 13.527 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.0.2’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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") 2025-10-16 00:43:27.928971 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:43:28.014118 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:43:28.097584 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:43:28.126502 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:43:28.160753 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:43:28.235462 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:43:28.240927 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:43:28.25298 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:43:28.35503 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:43:28.360457 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:43:28.425966 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:43:28.467104 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:43:28.478909 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:43:28.518708 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:43:28.586466 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:43:43.446772 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:43:43.519314 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:43:43.590058 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:43:43.610916 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:43:43.644146 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:43:43.716414 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:43:43.721483 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:43:43.732966 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:43:43.836597 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:43:43.841879 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:43:43.889215 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:43:43.927757 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:43:43.939284 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:43:43.978281 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:43:44.046813 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:44:09.809814 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:44:09.883671 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:44:09.957144 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:44:09.978433 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:44:10.011559 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:44:10.084174 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:44:10.089366 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:44:10.100766 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:44:10.192146 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:44:10.197455 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:44:10.245654 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:44:10.284667 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:44:10.296179 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:44:10.335327 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:44:10.402632 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:44:23.898532 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:44:23.977103 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:44:24.051228 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:44:24.073084 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:44:24.108542 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:44:24.187228 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:44:24.19282 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:44:24.204835 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:44:24.299279 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:44:24.304798 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:44:24.354586 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:44:24.395962 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:44:24.408595 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:44:24.450926 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:44:24.522529 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:44:24.773354 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds 2025-10-16 00:44:24.835275 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds 2025-10-16 00:44:24.899169 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds 2025-10-16 00:44:25.201896 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds 2025-10-16 00:44:47.047393 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:44:47.124804 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:44:47.222709 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:44:47.244831 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:44:47.279281 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:44:47.355289 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:44:47.360848 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:44:47.372779 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:44:47.468866 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:44:47.474697 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:44:47.52769 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:44:47.571237 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:44:47.584002 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:44:47.624853 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:44:47.692801 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:44:59.658001 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:44:59.733392 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:44:59.807222 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:44:59.828955 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:44:59.863396 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:44:59.938242 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:44:59.943776 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:44:59.956006 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:45:00.05282 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:45:00.058297 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:45:00.109123 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:45:00.149206 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:45:00.161404 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:45:00.203733 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:45:00.273145 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:45:00.48747 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds 2025-10-16 00:45:00.547933 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds 2025-10-16 00:45:00.610199 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds 2025-10-16 00:45:00.909578 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds 2025-10-16 00:45:22.199674 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:45:22.278542 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:45:22.356085 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:45:22.378966 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:45:22.413531 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:45:22.491283 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:45:22.497177 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:45:22.509892 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:45:22.608751 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:45:22.614597 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:45:22.66633 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:45:22.707252 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:45:22.719852 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:45:22.761224 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:45:22.830833 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:45:34.699212 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:45:34.773088 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:45:34.844772 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:45:34.866201 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:45:34.900453 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:45:34.976869 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:45:34.982372 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:45:34.994449 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:45:35.090441 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:45:35.095886 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:45:35.144898 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:45:35.183872 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:45:35.195287 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:45:35.234831 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:45:35.305102 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:45:35.505888 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds 2025-10-16 00:45:35.567317 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds 2025-10-16 00:45:35.630955 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds 2025-10-16 00:45:35.933055 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds 2025-10-16 00:45:58.292433 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:45:58.370115 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:45:58.44529 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:45:58.467252 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:45:58.502973 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:45:58.580893 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:45:58.586522 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:45:58.59846 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:45:58.69497 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:45:58.700552 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:45:58.749681 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:45:58.789207 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:45:58.80104 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:45:58.840762 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:45:58.908344 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:46:09.716013 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:46:09.792307 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:46:09.867885 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:46:09.889211 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:46:09.924502 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:46:10.030828 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:46:10.036726 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:46:10.050222 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:46:10.15046 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:46:10.155997 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:46:10.204351 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:46:10.244653 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:46:10.256461 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:46:10.297306 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:46:10.367104 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:46:35.457211 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:46:44.388302 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:47:09.639057 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:47:19.745395 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:47:20.385418 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds 2025-10-16 00:47:20.447539 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds 2025-10-16 00:47:20.486083 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds 2025-10-16 00:47:20.554762 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds 2025-10-16 00:47:43.410675 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:47:48.551482 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:47:48.853454 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds 2025-10-16 00:47:48.914668 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds 2025-10-16 00:47:48.953101 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds 2025-10-16 00:47:49.021828 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds 2025-10-16 00:48:07.750064 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:48:14.401747 WARNING::Fitting problem for feature 124 returning NA 2025-10-16 00:48:14.754454 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds 2025-10-16 00:48:14.816572 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds 2025-10-16 00:48:14.855939 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds 2025-10-16 00:48:14.927253 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds 2025-10-16 00:48:33.112132 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:48:33.188617 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:48:33.261088 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:48:33.282268 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:48:33.316085 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:48:33.391202 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:48:33.396629 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:48:33.408442 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:48:33.501194 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:48:33.506523 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:48:33.556701 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:48:33.597066 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:48:33.608799 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:48:33.650341 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:48:33.719317 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:48:45.809977 WARNING::Fitting problem for feature 50 returning NA 2025-10-16 00:48:45.884612 WARNING::Fitting problem for feature 62 returning NA 2025-10-16 00:48:45.957936 WARNING::Fitting problem for feature 74 returning NA 2025-10-16 00:48:45.979483 WARNING::Fitting problem for feature 78 returning NA 2025-10-16 00:48:46.013835 WARNING::Fitting problem for feature 84 returning NA 2025-10-16 00:48:46.088512 WARNING::Fitting problem for feature 96 returning NA 2025-10-16 00:48:46.093849 WARNING::Fitting problem for feature 97 returning NA 2025-10-16 00:48:46.106204 WARNING::Fitting problem for feature 99 returning NA 2025-10-16 00:48:46.19997 WARNING::Fitting problem for feature 114 returning NA 2025-10-16 00:48:46.205439 WARNING::Fitting problem for feature 115 returning NA 2025-10-16 00:48:46.255108 WARNING::Fitting problem for feature 123 returning NA 2025-10-16 00:48:46.294992 WARNING::Fitting problem for feature 130 returning NA 2025-10-16 00:48:46.306641 WARNING::Fitting problem for feature 132 returning NA 2025-10-16 00:48:46.346238 WARNING::Fitting problem for feature 139 returning NA 2025-10-16 00:48:46.417391 WARNING::Fitting problem for feature 150 returning NA 2025-10-16 00:48:46.680358 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds 2025-10-16 00:48:46.741288 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds 2025-10-16 00:48:46.804548 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds 2025-10-16 00:48:47.10457 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds 2025-10-16 00:49:07.629554 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-10-16 00:49:07.647648 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-10-16 00:49:07.660264 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-10-16 00:49:07.713413 ERROR::No fixed, group, or ordered effects included in formula. 2025-10-16 00:49:07.742869 ERROR::Effect name not found in metadata: d 2025-10-16 00:49:07.75503 ERROR::No user formula provided 2025-10-16 00:49:07.784824 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-10-16 00:49:07.796365 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-10-16 00:49:10.847891 INFO::Writing function arguments to log file 2025-10-16 00:49:10.86244 INFO::Verifying options selected are valid 2025-10-16 00:49:13.21307 INFO::Writing function arguments to log file 2025-10-16 00:49:13.225396 INFO::Verifying options selected are valid 2025-10-16 00:49:13.226607 INFO::Determining format of input files 2025-10-16 00:49:13.227654 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-16 00:49:13.230076 INFO::Running selected normalization method: TSS 2025-10-16 00:49:13.231608 INFO::Creating output feature tables folder 2025-10-16 00:49:13.232655 INFO::Writing normalized data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/data_norm.tsv 2025-10-16 00:49:13.234169 INFO::Filter data based on min abundance, min prevalence, and max prevalence 2025-10-16 00:49:13.235137 INFO::Total samples in data: 16 2025-10-16 00:49:13.236025 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-10-16 00:49:13.236915 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000 2025-10-16 00:49:13.238896 INFO::Total filtered features: 0 2025-10-16 00:49:13.239904 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering: 2025-10-16 00:49:13.241184 INFO::Total features filtered by non-zero variance filtering: 0 2025-10-16 00:49:13.242262 INFO::Filtered feature names from variance filtering: 2025-10-16 00:49:13.243246 INFO::Writing filtered data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/filtered_data.tsv 2025-10-16 00:49:13.245081 INFO::Running selected transform method: LOG 2025-10-16 00:49:13.246656 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/data_transformed.tsv 2025-10-16 00:49:13.248767 INFO::Applying z-score to standardize continuous metadata 2025-10-16 00:49:13.256234 INFO::Running the linear model component 2025-10-16 00:49:13.272408 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:13.277585 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:13.281999 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:13.289166 INFO::Counting total values for each feature 2025-10-16 00:49:13.291046 INFO::Running the logistic model component 2025-10-16 00:49:13.304709 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:13.311308 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:13.317551 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:13.326595 INFO::Counting total values for each feature 2025-10-16 00:49:13.328822 INFO::Re-running abundances for warn_prevalence 2025-10-16 00:49:13.329812 INFO::Running selected normalization method: TSS 2025-10-16 00:49:13.331333 INFO::Running selected transform method: LOG 2025-10-16 00:49:13.346045 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:13.350614 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:13.354941 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:13.43898 INFO::Creating fits folder 2025-10-16 00:49:13.440251 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/residuals_linear.rds 2025-10-16 00:49:13.441474 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/fitted_linear.rds 2025-10-16 00:49:13.442715 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/residuals_logistic.rds 2025-10-16 00:49:13.443892 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/fitted_logistic.rds 2025-10-16 00:49:13.447195 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpXly8xD/file1b21ef56207d00/all_results.tsv 2025-10-16 00:49:13.448878 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/RtmpXly8xD/file1b21ef56207d00/significant_results.tsv 2025-10-16 00:49:13.450263 INFO::Creating output figures folder 2025-10-16 00:49:13.451658 INFO::Writing summary plot of significant results to file: /tmp/RtmpXly8xD/file1b21ef56207d00/figures/summary_plot.pdf 2025-10-16 00:49:15.062141 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef56207d00/figures 2025-10-16 00:49:15.064114 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-16 00:49:15.069203 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-16 00:49:15.661414 INFO::Writing summary plot of significant results to file: /tmp/RtmpXly8xD/file1b21ef56207d00/figures/summary_plot.pdf 2025-10-16 00:49:17.294886 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef56207d00/figures 2025-10-16 00:49:17.296494 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-16 00:49:17.301346 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-16 00:49:17.814097 INFO::Running the linear model component 2025-10-16 00:49:17.823075 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:17.827521 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:17.831644 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:17.838508 INFO::Counting total values for each feature 2025-10-16 00:49:17.840169 INFO::Running the logistic model component 2025-10-16 00:49:17.848443 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:17.854645 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:17.860464 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:17.871871 INFO::Counting total values for each feature 2025-10-16 00:49:17.874542 INFO::Re-running abundances for warn_prevalence 2025-10-16 00:49:17.875434 INFO::Running selected normalization method: TSS 2025-10-16 00:49:17.876844 INFO::Running selected transform method: LOG 2025-10-16 00:49:17.885333 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:17.889604 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:17.893677 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:17.980216 INFO::Creating output folder 2025-10-16 00:49:17.98123 INFO::Creating output figures folder 2025-10-16 00:49:17.982522 INFO::Writing summary plot of significant results to file: /tmp/RtmpXly8xD/file1b21ef6c09e5a9/figures/summary_plot.pdf 2025-10-16 00:49:19.614304 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef6c09e5a9/figures 2025-10-16 00:49:19.616034 INFO::Plotting associations from most to least significant, grouped by metadata 2025-10-16 00:49:19.621122 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-10-16 00:49:20.61461 INFO::Applying z-score to standardize continuous metadata 2025-10-16 00:49:20.622468 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-10-16 00:49:20.623382 INFO::Bypass z-score application to metadata 2025-10-16 00:49:20.625841 INFO::Bypass z-score application to metadata 2025-10-16 00:49:20.643385 INFO::Determining format of input files 2025-10-16 00:49:20.644438 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-16 00:49:20.645344 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-10-16 00:49:20.65212 INFO::Determining format of input files 2025-10-16 00:49:20.653119 INFO::Input format is data samples as columns and metadata samples as rows 2025-10-16 00:49:20.654398 INFO::Input format is feature_specific_covariate samples as columns 2025-10-16 00:49:20.661954 INFO::Determining format of input files 2025-10-16 00:49:20.662884 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-16 00:49:20.663926 INFO::Input format is feature_specific_covariate samples as columns 2025-10-16 00:49:20.665565 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-10-16 00:49:20.666363 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-10-16 00:49:20.677031 INFO::Running selected transform method: LOG 2025-10-16 00:49:20.678191 INFO::Creating output feature tables folder 2025-10-16 00:49:20.679107 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv 2025-10-16 00:49:20.682883 INFO::Running selected transform method: LOG 2025-10-16 00:49:20.683914 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv 2025-10-16 00:49:20.687422 INFO::Running selected transform method: PLOG 2025-10-16 00:49:20.688964 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv 2025-10-16 00:49:20.691634 INFO::Running selected transform method: NONE 2025-10-16 00:49:20.692383 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv 2025-10-16 00:49:20.699265 INFO::Running the linear model component 2025-10-16 00:49:20.707609 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:20.711758 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:20.715669 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:20.722476 INFO::Counting total values for each feature 2025-10-16 00:49:20.724125 INFO::Running the logistic model component 2025-10-16 00:49:20.732356 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:20.7384 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:20.744703 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:20.75364 INFO::Counting total values for each feature 2025-10-16 00:49:20.755637 INFO::Re-running abundances for warn_prevalence 2025-10-16 00:49:20.756402 INFO::Running selected normalization method: TSS 2025-10-16 00:49:20.757775 INFO::Running selected transform method: LOG 2025-10-16 00:49:20.766273 INFO::Fitting model to feature number 1, a 2025-10-16 00:49:20.770378 INFO::Fitting model to feature number 2, b 2025-10-16 00:49:20.774318 INFO::Fitting model to feature number 3, c 2025-10-16 00:49:20.903385 INFO::Creating output folder 2025-10-16 00:49:20.904734 INFO::Creating fits folder 2025-10-16 00:49:20.905846 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/residuals_linear.rds 2025-10-16 00:49:20.906988 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/fitted_linear.rds 2025-10-16 00:49:20.908135 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/residuals_logistic.rds 2025-10-16 00:49:20.909271 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/fitted_logistic.rds 2025-10-16 00:49:20.912226 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpXly8xD/file1b21ef78b962a0/all_results.tsv 2025-10-16 00:49:20.91408 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/RtmpXly8xD/file1b21ef78b962a0/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 359.207 5.137 364.338
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 20.188 | 0.697 | 20.891 | |
maaslin_check_arguments | 0.139 | 0.009 | 0.148 | |
maaslin_check_formula | 0.138 | 0.004 | 0.142 | |
maaslin_compute_formula | 0.149 | 0.003 | 0.152 | |
maaslin_contrast_test | 18.889 | 0.517 | 19.406 | |
maaslin_filter | 0.441 | 0.010 | 0.450 | |
maaslin_fit | 13.269 | 0.256 | 13.527 | |
maaslin_log_arguments | 0.128 | 0.004 | 0.133 | |
maaslin_normalize | 0.266 | 0.007 | 0.274 | |
maaslin_plot_results | 43.365 | 0.324 | 43.640 | |
maaslin_plot_results_from_output | 43.345 | 0.274 | 43.624 | |
maaslin_process_metadata | 0.440 | 0.011 | 0.451 | |
maaslin_read_data | 0.130 | 0.002 | 0.132 | |
maaslin_reorder_data | 0.166 | 0.003 | 0.169 | |
maaslin_transform | 0.548 | 0.013 | 0.561 | |
maaslin_write_results | 13.760 | 0.216 | 13.976 | |
maaslin_write_results_lefse_format | 14.173 | 0.162 | 14.337 | |
preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
preprocess_taxa_mtx | 0.005 | 0.000 | 0.004 | |