William Nickols
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 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" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 1145/2313 | 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 | | ||||||||
| 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-08-01 07:59:30 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 08:14:51 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 920.2 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_1.1.0.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 ‘1.1.0’
* 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 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_from_output 51.895 0.291 52.331
maaslin_plot_results 51.266 0.307 51.706
maaslin_contrast_test 27.773 0.275 28.118
maaslin3 27.391 0.603 28.062
maaslin_write_results_lefse_format 24.280 0.107 24.444
maaslin_write_results 22.244 0.164 22.468
maaslin_fit 20.295 0.096 20.438
* 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 ‘1.1.0’ ** 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 4.5.0 (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")
2025-08-01 08:07:30.377882 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:07:30.5193 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:07:30.661291 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:07:30.699546 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:07:30.770581 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:07:30.898836 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:07:30.906975 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:07:30.92579 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:07:31.09709 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:07:31.105365 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:07:31.189991 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:07:31.258968 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:07:31.27824 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:07:31.34518 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:07:31.471839 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:07:54.013854 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:07:54.144295 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:07:54.288551 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:07:54.329649 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:07:54.395119 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:07:54.556974 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:07:54.565754 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:07:54.585664 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:07:54.751018 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:07:54.759784 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:07:54.845679 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:07:54.917645 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:07:54.940468 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:07:55.008927 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:07:55.122987 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:08:18.931133 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:08:19.082614 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:08:19.204596 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:08:19.239655 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:08:19.295298 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:08:19.420646 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:08:19.429092 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:08:19.447919 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:08:19.607457 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:08:19.61653 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:08:19.735201 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:08:19.808663 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:08:19.829083 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:08:19.900594 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:08:20.018132 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:08:41.508583 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:08:41.656594 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:08:41.780996 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:08:41.817075 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:08:41.874894 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:08:42.011143 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:08:42.020384 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:08:42.041483 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:08:42.21903 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:08:42.229094 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:08:42.320812 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:08:42.389587 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:08:42.409166 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:08:42.476943 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:08:42.596414 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:08:42.879915 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_linear.rds
2025-08-01 08:08:42.948533 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_linear.rds
2025-08-01 08:08:43.019022 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_logistic.rds
2025-08-01 08:08:43.364689 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_logistic.rds
2025-08-01 08:09:06.243301 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:09:06.393048 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:09:06.542715 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:09:06.588463 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:09:06.660707 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:09:06.821155 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:09:06.832053 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:09:06.857643 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:09:07.07436 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:09:07.086522 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:09:07.204923 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:09:07.281506 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:09:07.303433 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:09:07.409544 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:09:07.527626 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:09:29.466192 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:09:29.599858 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:09:29.727573 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:09:29.764425 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:09:29.823894 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:09:29.957459 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:09:29.966216 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:09:29.986212 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:09:30.161261 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:09:30.171627 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:09:30.272688 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:09:30.35489 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:09:30.379373 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:09:30.460387 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:09:30.606623 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:09:30.925929 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_linear.rds
2025-08-01 08:09:30.995881 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_linear.rds
2025-08-01 08:09:31.0681 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_logistic.rds
2025-08-01 08:09:31.417407 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_logistic.rds
2025-08-01 08:09:54.320844 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:09:54.454517 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:09:54.58145 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:09:54.619338 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:09:54.683551 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:09:54.817395 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:09:54.826471 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:09:54.847478 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:09:55.029181 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:09:55.038901 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:09:55.136616 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:09:55.213476 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:09:55.236387 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:09:55.355788 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:09:55.474767 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:10:16.498865 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:10:16.627557 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:10:16.795991 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:10:16.834506 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:10:16.89788 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:10:17.034281 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:10:17.043173 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:10:17.063109 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:10:17.25069 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:10:17.261889 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:10:17.361134 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:10:17.440601 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:10:17.463873 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:10:17.543408 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:10:17.681226 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:10:18.011855 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_linear.rds
2025-08-01 08:10:18.074527 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_linear.rds
2025-08-01 08:10:18.139061 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/residuals_logistic.rds
2025-08-01 08:10:18.435692 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803a0aa31c/fits/fitted_logistic.rds
2025-08-01 08:10:41.381953 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:10:41.541133 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:10:41.70888 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:10:41.751696 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:10:41.813614 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:10:41.954342 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:10:41.96294 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:10:41.983799 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:10:42.163582 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:10:42.173442 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:10:42.268475 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:10:42.345762 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:10:42.367118 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:10:42.442214 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:10:42.574457 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:11:03.05991 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:11:03.236665 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:11:03.369679 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:11:03.407686 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:11:03.47898 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:11:03.630547 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:11:03.640545 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:11:03.662974 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:11:03.848969 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:11:03.858951 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:11:03.956539 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:11:04.032496 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:11:04.053763 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:11:04.128188 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:11:04.255728 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:11:30.629647 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:11:43.920409 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:12:10.4663 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:12:24.997004 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:12:25.97141 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_linear.rds
2025-08-01 08:12:26.03548 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_linear.rds
2025-08-01 08:12:26.077583 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_logistic.rds
2025-08-01 08:12:26.153939 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_logistic.rds
2025-08-01 08:12:49.871949 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:12:58.901264 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:12:59.402243 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_linear.rds
2025-08-01 08:12:59.469424 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_linear.rds
2025-08-01 08:12:59.512173 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_logistic.rds
2025-08-01 08:12:59.590518 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_logistic.rds
2025-08-01 08:13:19.132426 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:13:28.048252 WARNING::Fitting problem for feature 124 returning NA
2025-08-01 08:13:28.580974 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_linear.rds
2025-08-01 08:13:28.651141 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_linear.rds
2025-08-01 08:13:28.695507 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_logistic.rds
2025-08-01 08:13:28.775684 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_logistic.rds
2025-08-01 08:13:47.266833 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:13:47.395699 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:13:47.521677 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:13:47.558686 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:13:47.615814 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:13:47.743829 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:13:47.753322 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:13:47.773321 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:13:47.93448 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:13:47.943365 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:13:48.029868 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:13:48.096915 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:13:48.117749 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:13:48.237899 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:13:48.371617 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:14:07.507744 WARNING::Fitting problem for feature 50 returning NA
2025-08-01 08:14:07.641228 WARNING::Fitting problem for feature 62 returning NA
2025-08-01 08:14:07.767541 WARNING::Fitting problem for feature 74 returning NA
2025-08-01 08:14:07.805325 WARNING::Fitting problem for feature 78 returning NA
2025-08-01 08:14:07.864498 WARNING::Fitting problem for feature 84 returning NA
2025-08-01 08:14:07.994213 WARNING::Fitting problem for feature 96 returning NA
2025-08-01 08:14:08.003246 WARNING::Fitting problem for feature 97 returning NA
2025-08-01 08:14:08.023822 WARNING::Fitting problem for feature 99 returning NA
2025-08-01 08:14:08.195421 WARNING::Fitting problem for feature 114 returning NA
2025-08-01 08:14:08.204862 WARNING::Fitting problem for feature 115 returning NA
2025-08-01 08:14:08.290835 WARNING::Fitting problem for feature 123 returning NA
2025-08-01 08:14:08.363198 WARNING::Fitting problem for feature 130 returning NA
2025-08-01 08:14:08.383841 WARNING::Fitting problem for feature 132 returning NA
2025-08-01 08:14:08.454257 WARNING::Fitting problem for feature 139 returning NA
2025-08-01 08:14:08.622538 WARNING::Fitting problem for feature 150 returning NA
2025-08-01 08:14:09.00508 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_linear.rds
2025-08-01 08:14:09.071425 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_linear.rds
2025-08-01 08:14:09.139431 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/residuals_logistic.rds
2025-08-01 08:14:09.468433 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWsFOCU/filed48034d2b773a/fits/fitted_logistic.rds
2025-08-01 08:14:29.444829 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-01 08:14:29.472405 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-01 08:14:29.491465 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-01 08:14:29.569633 ERROR::No fixed, group, or
ordered effects included in formula.
2025-08-01 08:14:29.595658 ERROR::Effect name not found in metadata: d
2025-08-01 08:14:29.614771 ERROR::No user formula provided
2025-08-01 08:14:29.661865 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-01 08:14:29.680133 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-08-01 08:14:34.619757 INFO::Writing function arguments to log file
2025-08-01 08:14:34.647652 INFO::Verifying options selected are valid
2025-08-01 08:14:37.202155 INFO::Writing function arguments to log file
2025-08-01 08:14:37.223554 INFO::Verifying options selected are valid
2025-08-01 08:14:37.225379 INFO::Determining format of input files
2025-08-01 08:14:37.227116 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-01 08:14:37.231175 INFO::Running selected normalization method: TSS
2025-08-01 08:14:37.233596 INFO::Creating output feature tables folder
2025-08-01 08:14:37.235279 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/features/data_norm.tsv
2025-08-01 08:14:37.237634 INFO::Filter data based on min abundance and min prevalence
2025-08-01 08:14:37.239214 INFO::Total samples in data: 16
2025-08-01 08:14:37.240687 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-01 08:14:37.243935 INFO::Total filtered features: 0
2025-08-01 08:14:37.245729 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-01 08:14:37.247828 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-01 08:14:37.249589 INFO::Filtered feature names from variance filtering:
2025-08-01 08:14:37.251218 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/features/filtered_data.tsv
2025-08-01 08:14:37.253744 INFO::Running selected transform method: LOG
2025-08-01 08:14:37.255818 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/features/data_transformed.tsv
2025-08-01 08:14:37.25865 INFO::Applying z-score to standardize continuous metadata
2025-08-01 08:14:37.266577 INFO::Running the linear model component
2025-08-01 08:14:37.291141 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:37.298422 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:37.305582 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:37.317005 INFO::Counting total values for each feature
2025-08-01 08:14:37.320008 INFO::Running the logistic model component
2025-08-01 08:14:37.343713 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:37.353851 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:37.363902 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:37.378201 INFO::Counting total values for each feature
2025-08-01 08:14:37.381782 INFO::Re-running abundances for warn_prevalence
2025-08-01 08:14:37.383593 INFO::Running selected normalization method: TSS
2025-08-01 08:14:37.386319 INFO::Running selected transform method: LOG
2025-08-01 08:14:37.412647 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:37.420499 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:37.428307 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:37.564886 INFO::Creating fits folder
2025-08-01 08:14:37.566715 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/fits/residuals_linear.rds
2025-08-01 08:14:37.568429 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/fits/fitted_linear.rds
2025-08-01 08:14:37.570333 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/fits/residuals_logistic.rds
2025-08-01 08:14:37.572148 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/fits/fitted_logistic.rds
2025-08-01 08:14:37.576185 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/all_results.tsv
2025-08-01 08:14:37.578797 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/RtmpWsFOCU/filed4803502a2949/significant_results.tsv
2025-08-01 08:14:37.580912 INFO::Creating output figures folder
2025-08-01 08:14:37.583232 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/figures/summary_plot.pdf
2025-08-01 08:14:39.261093 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/figures
2025-08-01 08:14:39.263771 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-01 08:14:39.271141 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-01 08:14:39.797416 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/figures/summary_plot.pdf
2025-08-01 08:14:41.537843 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWsFOCU/filed4803502a2949/figures
2025-08-01 08:14:41.540008 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-01 08:14:41.54721 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-01 08:14:42.047082 INFO::Running the linear model component
2025-08-01 08:14:42.079531 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:42.085906 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:42.092011 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:42.102592 INFO::Counting total values for each feature
2025-08-01 08:14:42.1051 INFO::Running the logistic model component
2025-08-01 08:14:42.118897 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:42.127961 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:42.13763 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:42.150429 INFO::Counting total values for each feature
2025-08-01 08:14:42.153388 INFO::Re-running abundances for warn_prevalence
2025-08-01 08:14:42.154564 INFO::Running selected normalization method: TSS
2025-08-01 08:14:42.156516 INFO::Running selected transform method: LOG
2025-08-01 08:14:42.170386 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:42.176427 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:42.182444 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:42.311192 INFO::Creating output folder
2025-08-01 08:14:42.312525 INFO::Creating output figures folder
2025-08-01 08:14:42.314358 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpWsFOCU/filed48033103849e/figures/summary_plot.pdf
2025-08-01 08:14:44.0186 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWsFOCU/filed48033103849e/figures
2025-08-01 08:14:44.020966 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-01 08:14:44.028214 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-01 08:14:45.236915 INFO::Applying z-score to standardize continuous metadata
2025-08-01 08:14:45.248814 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-01 08:14:45.250203 INFO::Bypass z-score application to metadata
2025-08-01 08:14:45.25435 INFO::Bypass z-score application to metadata
2025-08-01 08:14:45.282831 INFO::Determining format of input files
2025-08-01 08:14:45.28432 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-01 08:14:45.285858 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-01 08:14:45.297903 INFO::Determining format of input files
2025-08-01 08:14:45.299582 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-01 08:14:45.301779 INFO::Input format is feature_specific_covariate samples as columns
2025-08-01 08:14:45.314785 INFO::Determining format of input files
2025-08-01 08:14:45.316381 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-01 08:14:45.318191 INFO::Input format is feature_specific_covariate samples as columns
2025-08-01 08:14:45.320987 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-01 08:14:45.322347 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-01 08:14:45.339912 INFO::Running selected transform method: LOG
2025-08-01 08:14:45.341697 INFO::Creating output feature tables folder
2025-08-01 08:14:45.343192 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWsFOCU/filed480361838a2f/features/data_transformed.tsv
2025-08-01 08:14:45.349368 INFO::Running selected transform method: LOG
2025-08-01 08:14:45.351159 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWsFOCU/filed480361838a2f/features/data_transformed.tsv
2025-08-01 08:14:45.356972 INFO::Running selected transform method: PLOG
2025-08-01 08:14:45.359622 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWsFOCU/filed480361838a2f/features/data_transformed.tsv
2025-08-01 08:14:45.364331 INFO::Running selected transform method: NONE
2025-08-01 08:14:45.365732 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWsFOCU/filed480361838a2f/features/data_transformed.tsv
2025-08-01 08:14:45.377465 INFO::Running the linear model component
2025-08-01 08:14:45.392728 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:45.400256 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:45.407407 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:45.418993 INFO::Counting total values for each feature
2025-08-01 08:14:45.421883 INFO::Running the logistic model component
2025-08-01 08:14:45.437966 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:45.449301 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:45.46031 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:45.476001 INFO::Counting total values for each feature
2025-08-01 08:14:45.479557 INFO::Re-running abundances for warn_prevalence
2025-08-01 08:14:45.48108 INFO::Running selected normalization method: TSS
2025-08-01 08:14:45.483639 INFO::Running selected transform method: LOG
2025-08-01 08:14:45.500219 INFO::Fitting model to feature number 1, a
2025-08-01 08:14:45.508302 INFO::Fitting model to feature number 2, b
2025-08-01 08:14:45.516195 INFO::Fitting model to feature number 3, c
2025-08-01 08:14:45.663597 INFO::Creating output folder
2025-08-01 08:14:45.665168 INFO::Creating fits folder
2025-08-01 08:14:45.666716 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWsFOCU/filed48031c1dc59c/fits/residuals_linear.rds
2025-08-01 08:14:45.668361 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWsFOCU/filed48031c1dc59c/fits/fitted_linear.rds
2025-08-01 08:14:45.670309 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWsFOCU/filed48031c1dc59c/fits/residuals_logistic.rds
2025-08-01 08:14:45.672192 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWsFOCU/filed48031c1dc59c/fits/fitted_logistic.rds
2025-08-01 08:14:45.676517 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpWsFOCU/filed48031c1dc59c/all_results.tsv
2025-08-01 08:14:45.679093 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/RtmpWsFOCU/filed48031c1dc59c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
443.933 4.535 449.676
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 27.391 | 0.603 | 28.062 | |
| maaslin_check_arguments | 0.196 | 0.008 | 0.204 | |
| maaslin_check_formula | 0.189 | 0.016 | 0.205 | |
| maaslin_compute_formula | 0.208 | 0.000 | 0.209 | |
| maaslin_contrast_test | 27.773 | 0.275 | 28.118 | |
| maaslin_filter | 0.667 | 0.032 | 0.700 | |
| maaslin_fit | 20.295 | 0.096 | 20.438 | |
| maaslin_log_arguments | 0.185 | 0.008 | 0.192 | |
| maaslin_normalize | 0.360 | 0.012 | 0.372 | |
| maaslin_plot_results | 51.266 | 0.307 | 51.706 | |
| maaslin_plot_results_from_output | 51.895 | 0.291 | 52.331 | |
| maaslin_process_metadata | 0.627 | 0.012 | 0.641 | |
| maaslin_read_data | 0.200 | 0.004 | 0.205 | |
| maaslin_reorder_data | 0.216 | 0.000 | 0.216 | |
| maaslin_transform | 0.786 | 0.012 | 0.800 | |
| maaslin_write_results | 22.244 | 0.164 | 22.468 | |
| maaslin_write_results_lefse_format | 24.280 | 0.107 | 24.444 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |