William Nickols
| Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7584c46 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4667 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1.0.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2025-04-17 08:12:31 -0000 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 08:28:48 -0000 (Thu, 17 Apr 2025) |
| EllapsedTime: 977.3 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.0’
* 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 54.604 0.299 55.058
maaslin_plot_results_from_output 54.065 0.348 54.556
maaslin3 33.175 0.563 33.829
maaslin_contrast_test 29.965 0.335 30.364
maaslin_write_results_lefse_format 26.394 0.168 26.619
maaslin_write_results 22.830 0.152 23.029
maaslin_fit 22.339 0.088 22.476
* 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-devel_2025-02-19/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.0.0’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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")
2025-04-17 08:21:12.183091 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:21:12.318919 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:21:12.468347 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:21:12.509438 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:21:12.581352 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:21:12.712289 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:21:12.721145 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:21:12.74138 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:21:12.920925 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:21:12.929904 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:21:13.014847 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:21:13.083512 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:21:13.103577 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:21:13.171309 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:21:13.302549 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:21:40.55793 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:21:40.686949 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:21:40.813817 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:21:40.8526 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:21:40.914613 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:21:41.078754 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:21:41.087595 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:21:41.107764 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:21:41.282374 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:21:41.291414 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:21:41.379911 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:21:41.448174 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:21:41.468166 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:21:41.538187 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:21:41.657751 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:22:05.543108 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:22:05.693191 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:22:05.820309 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:22:05.856209 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:22:05.913425 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:22:06.038084 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:22:06.046479 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:22:06.065712 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:22:06.223732 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:22:06.232398 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:22:06.355578 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:22:06.425183 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:22:06.444969 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:22:06.512925 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:22:06.639953 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:22:29.234326 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:22:29.368982 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:22:29.495687 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:22:29.531481 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:22:29.588309 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:22:29.712781 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:22:29.721237 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:22:29.740716 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:22:29.893936 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:22:29.902218 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:22:29.982272 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:22:30.04651 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:22:30.065402 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:22:30.138232 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:22:30.266569 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:22:30.634729 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_linear.rds
2025-04-17 08:22:30.698364 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_linear.rds
2025-04-17 08:22:30.76332 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_logistic.rds
2025-04-17 08:22:31.077816 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_logistic.rds
2025-04-17 08:22:52.867341 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:22:52.999357 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:22:53.128748 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:22:53.166171 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:22:53.224904 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:22:53.358463 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:22:53.367639 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:22:53.388362 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:22:53.551573 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:22:53.56093 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:22:53.645663 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:22:53.716283 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:22:53.736902 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:22:53.807508 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:22:53.927595 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:23:16.161693 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:23:16.292329 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:23:16.423046 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:23:16.460442 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:23:16.519987 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:23:16.647519 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:23:16.656339 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:23:16.676215 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:23:16.838182 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:23:16.846918 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:23:16.929665 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:23:16.995164 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:23:17.014497 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:23:17.081541 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:23:17.197508 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:23:17.49598 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_linear.rds
2025-04-17 08:23:17.564276 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_linear.rds
2025-04-17 08:23:17.631371 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_logistic.rds
2025-04-17 08:23:17.974569 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_logistic.rds
2025-04-17 08:23:40.197645 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:23:40.342455 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:23:40.480987 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:23:40.518154 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:23:40.577958 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:23:40.71085 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:23:40.719483 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:23:40.739327 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:23:40.905223 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:23:40.914285 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:23:41.002124 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:23:41.071902 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:23:41.091888 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:23:41.160793 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:23:41.27843 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:24:02.669047 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:24:02.810006 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:24:02.950582 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:24:02.990177 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:24:03.051457 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:24:03.190251 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:24:03.199646 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:24:03.22141 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:24:03.403579 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:24:03.412865 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:24:03.501162 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:24:03.572236 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:24:03.592743 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:24:03.661598 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:24:03.783609 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:24:04.090269 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_linear.rds
2025-04-17 08:24:04.159125 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_linear.rds
2025-04-17 08:24:04.230896 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/residuals_logistic.rds
2025-04-17 08:24:04.564656 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e051d4552d7/fits/fitted_logistic.rds
2025-04-17 08:24:26.41603 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:24:26.550078 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:24:26.688032 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:24:26.728063 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:24:26.790959 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:24:26.929378 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:24:26.938307 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:24:26.958945 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:24:27.131129 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:24:27.140275 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:24:27.226995 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:24:27.297825 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:24:27.318995 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:24:27.391827 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:24:27.521304 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:24:50.302514 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:24:50.434057 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:24:50.62887 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:24:50.667814 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:24:50.729916 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:24:50.864289 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:24:50.87323 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:24:50.894048 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:24:51.063504 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:24:51.072755 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:24:51.160239 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:24:51.231098 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:24:51.251613 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:24:51.321901 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:24:51.444053 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:25:17.38693 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:25:32.560699 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:25:59.073431 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:26:14.294111 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:26:15.248966 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_linear.rds
2025-04-17 08:26:15.318752 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_linear.rds
2025-04-17 08:26:15.362889 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_logistic.rds
2025-04-17 08:26:15.444662 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_logistic.rds
2025-04-17 08:26:39.060672 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:26:47.730647 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:26:48.412822 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_linear.rds
2025-04-17 08:26:48.481743 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_linear.rds
2025-04-17 08:26:48.525848 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_logistic.rds
2025-04-17 08:26:48.607711 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_logistic.rds
2025-04-17 08:27:09.738641 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:27:18.682791 WARNING::Fitting problem for feature 124 returning NA
2025-04-17 08:27:19.178392 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_linear.rds
2025-04-17 08:27:19.242672 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_linear.rds
2025-04-17 08:27:19.285711 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_logistic.rds
2025-04-17 08:27:19.367576 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_logistic.rds
2025-04-17 08:27:39.380089 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:27:39.514633 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:27:39.648223 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:27:39.688775 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:27:39.78765 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:27:39.917469 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:27:39.926085 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:27:39.94585 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:27:40.109975 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:27:40.119042 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:27:40.205167 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:27:40.272478 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:27:40.29197 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:27:40.36021 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:27:40.476526 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:28:00.403387 WARNING::Fitting problem for feature 50 returning NA
2025-04-17 08:28:00.535064 WARNING::Fitting problem for feature 62 returning NA
2025-04-17 08:28:00.661786 WARNING::Fitting problem for feature 74 returning NA
2025-04-17 08:28:00.698717 WARNING::Fitting problem for feature 78 returning NA
2025-04-17 08:28:00.757332 WARNING::Fitting problem for feature 84 returning NA
2025-04-17 08:28:00.887706 WARNING::Fitting problem for feature 96 returning NA
2025-04-17 08:28:00.896462 WARNING::Fitting problem for feature 97 returning NA
2025-04-17 08:28:00.91642 WARNING::Fitting problem for feature 99 returning NA
2025-04-17 08:28:01.083272 WARNING::Fitting problem for feature 114 returning NA
2025-04-17 08:28:01.092399 WARNING::Fitting problem for feature 115 returning NA
2025-04-17 08:28:01.178155 WARNING::Fitting problem for feature 123 returning NA
2025-04-17 08:28:01.247661 WARNING::Fitting problem for feature 130 returning NA
2025-04-17 08:28:01.267729 WARNING::Fitting problem for feature 132 returning NA
2025-04-17 08:28:01.336157 WARNING::Fitting problem for feature 139 returning NA
2025-04-17 08:28:01.4533 WARNING::Fitting problem for feature 150 returning NA
2025-04-17 08:28:01.825836 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_linear.rds
2025-04-17 08:28:01.894475 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_linear.rds
2025-04-17 08:28:01.964904 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/residuals_logistic.rds
2025-04-17 08:28:02.309736 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpspnAV9/file285e0523e21497/fits/fitted_logistic.rds
2025-04-17 08:28:25.675837 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-04-17 08:28:25.703546 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-04-17 08:28:25.722936 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-04-17 08:28:25.807577 ERROR::No fixed, group, or
ordered effects included in formula.
2025-04-17 08:28:25.834768 ERROR::Effect name not found in metadata: d
2025-04-17 08:28:25.853433 ERROR::No user formula provided
2025-04-17 08:28:25.900999 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-04-17 08:28:25.91948 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-04-17 08:28:31.061543 INFO::Writing function arguments to log file
2025-04-17 08:28:31.083285 INFO::Verifying options selected are valid
2025-04-17 08:28:33.728361 INFO::Writing function arguments to log file
2025-04-17 08:28:33.747255 INFO::Verifying options selected are valid
2025-04-17 08:28:33.748883 INFO::Determining format of input files
2025-04-17 08:28:33.750387 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-17 08:28:33.753966 INFO::Running selected normalization method: TSS
2025-04-17 08:28:33.756243 INFO::Creating output feature tables folder
2025-04-17 08:28:33.757857 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/features/data_norm.tsv
2025-04-17 08:28:33.760183 INFO::Filter data based on min abundance and min prevalence
2025-04-17 08:28:33.76165 INFO::Total samples in data: 16
2025-04-17 08:28:33.763061 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-04-17 08:28:33.788903 INFO::Total filtered features: 0
2025-04-17 08:28:33.790638 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-17 08:28:33.792382 INFO::Total features filtered by non-zero variance filtering: 0
2025-04-17 08:28:33.793815 INFO::Filtered feature names from variance filtering:
2025-04-17 08:28:33.795194 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/features/filtered_data.tsv
2025-04-17 08:28:33.797364 INFO::Running selected transform method: LOG
2025-04-17 08:28:33.799141 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/features/data_transformed.tsv
2025-04-17 08:28:33.801539 INFO::Applying z-score to standardize continuous metadata
2025-04-17 08:28:33.809117 INFO::Running the linear model component
2025-04-17 08:28:33.830846 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:33.837537 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:33.844225 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:33.855544 INFO::Counting total values for each feature
2025-04-17 08:28:33.858468 INFO::Running the logistic model component
2025-04-17 08:28:33.880314 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:33.890091 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:33.899707 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:33.913551 INFO::Counting total values for each feature
2025-04-17 08:28:33.916961 INFO::Re-running abundances for warn_prevalence
2025-04-17 08:28:33.918442 INFO::Running selected normalization method: TSS
2025-04-17 08:28:33.920793 INFO::Running selected transform method: LOG
2025-04-17 08:28:33.942917 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:33.949639 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:33.956426 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:34.092372 INFO::Creating fits folder
2025-04-17 08:28:34.094097 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/fits/residuals_linear.rds
2025-04-17 08:28:34.095781 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/fits/fitted_linear.rds
2025-04-17 08:28:34.097567 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/fits/residuals_logistic.rds
2025-04-17 08:28:34.099335 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/fits/fitted_logistic.rds
2025-04-17 08:28:34.103275 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/all_results.tsv
2025-04-17 08:28:34.105961 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/RtmpspnAV9/file285e05279a84f9/significant_results.tsv
2025-04-17 08:28:34.108039 INFO::Creating output figures folder
2025-04-17 08:28:34.110198 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/figures/summary_plot.pdf
2025-04-17 08:28:35.87899 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/figures
2025-04-17 08:28:35.882079 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-17 08:28:35.890479 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-17 08:28:36.449964 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/figures/summary_plot.pdf
2025-04-17 08:28:38.26988 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpspnAV9/file285e05279a84f9/figures
2025-04-17 08:28:38.27211 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-17 08:28:38.279603 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-17 08:28:38.841457 INFO::Running the linear model component
2025-04-17 08:28:38.856831 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:38.863999 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:38.871033 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:38.882812 INFO::Counting total values for each feature
2025-04-17 08:28:38.885624 INFO::Running the logistic model component
2025-04-17 08:28:38.900457 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:38.910817 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:38.921067 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:38.93565 INFO::Counting total values for each feature
2025-04-17 08:28:38.939027 INFO::Re-running abundances for warn_prevalence
2025-04-17 08:28:38.940357 INFO::Running selected normalization method: TSS
2025-04-17 08:28:38.942736 INFO::Running selected transform method: LOG
2025-04-17 08:28:38.957296 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:38.963996 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:38.970673 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:39.118198 INFO::Creating output folder
2025-04-17 08:28:39.119769 INFO::Creating output figures folder
2025-04-17 08:28:39.121979 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpspnAV9/file285e05416d82f/figures/summary_plot.pdf
2025-04-17 08:28:40.942522 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpspnAV9/file285e05416d82f/figures
2025-04-17 08:28:40.945226 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-17 08:28:40.953083 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-17 08:28:42.276206 INFO::Applying z-score to standardize continuous metadata
2025-04-17 08:28:42.287769 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-04-17 08:28:42.289079 INFO::Bypass z-score application to metadata
2025-04-17 08:28:42.292973 INFO::Bypass z-score application to metadata
2025-04-17 08:28:42.320016 INFO::Determining format of input files
2025-04-17 08:28:42.321478 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-17 08:28:42.322776 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-04-17 08:28:42.334017 INFO::Determining format of input files
2025-04-17 08:28:42.335675 INFO::Input format is data samples as columns and metadata samples as rows
2025-04-17 08:28:42.337787 INFO::Input format is feature_specific_covariate samples as columns
2025-04-17 08:28:42.350483 INFO::Determining format of input files
2025-04-17 08:28:42.352029 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-17 08:28:42.353725 INFO::Input format is feature_specific_covariate samples as columns
2025-04-17 08:28:42.356411 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-04-17 08:28:42.357724 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-04-17 08:28:42.374175 INFO::Running selected transform method: LOG
2025-04-17 08:28:42.375853 INFO::Creating output feature tables folder
2025-04-17 08:28:42.377182 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpspnAV9/file285e0511b142d0/features/data_transformed.tsv
2025-04-17 08:28:42.383113 INFO::Running selected transform method: LOG
2025-04-17 08:28:42.384833 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpspnAV9/file285e0511b142d0/features/data_transformed.tsv
2025-04-17 08:28:42.391113 INFO::Running selected transform method: PLOG
2025-04-17 08:28:42.393829 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpspnAV9/file285e0511b142d0/features/data_transformed.tsv
2025-04-17 08:28:42.398795 INFO::Running selected transform method: NONE
2025-04-17 08:28:42.400103 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpspnAV9/file285e0511b142d0/features/data_transformed.tsv
2025-04-17 08:28:42.411096 INFO::Running the linear model component
2025-04-17 08:28:42.424984 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:42.43154 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:42.438036 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:42.4488 INFO::Counting total values for each feature
2025-04-17 08:28:42.451488 INFO::Running the logistic model component
2025-04-17 08:28:42.465753 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:42.475228 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:42.484496 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:42.498027 INFO::Counting total values for each feature
2025-04-17 08:28:42.501202 INFO::Re-running abundances for warn_prevalence
2025-04-17 08:28:42.502486 INFO::Running selected normalization method: TSS
2025-04-17 08:28:42.504673 INFO::Running selected transform method: LOG
2025-04-17 08:28:42.519216 INFO::Fitting model to feature number 1, a
2025-04-17 08:28:42.525779 INFO::Fitting model to feature number 2, b
2025-04-17 08:28:42.532168 INFO::Fitting model to feature number 3, c
2025-04-17 08:28:42.671067 INFO::Creating output folder
2025-04-17 08:28:42.672515 INFO::Creating fits folder
2025-04-17 08:28:42.673862 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpspnAV9/file285e05575b5cae/fits/residuals_linear.rds
2025-04-17 08:28:42.67535 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpspnAV9/file285e05575b5cae/fits/fitted_linear.rds
2025-04-17 08:28:42.677098 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpspnAV9/file285e05575b5cae/fits/residuals_logistic.rds
2025-04-17 08:28:42.678809 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpspnAV9/file285e05575b5cae/fits/fitted_logistic.rds
2025-04-17 08:28:42.682804 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpspnAV9/file285e05575b5cae/all_results.tsv
2025-04-17 08:28:42.685265 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/RtmpspnAV9/file285e05575b5cae/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
459.722 5.050 466.046
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 33.175 | 0.563 | 33.829 | |
| maaslin_check_arguments | 0.188 | 0.000 | 0.189 | |
| maaslin_check_formula | 0.214 | 0.000 | 0.214 | |
| maaslin_compute_formula | 0.214 | 0.000 | 0.215 | |
| maaslin_contrast_test | 29.965 | 0.335 | 30.364 | |
| maaslin_filter | 0.662 | 0.004 | 0.668 | |
| maaslin_fit | 22.339 | 0.088 | 22.476 | |
| maaslin_log_arguments | 0.207 | 0.004 | 0.212 | |
| maaslin_normalize | 0.409 | 0.004 | 0.413 | |
| maaslin_plot_results | 54.604 | 0.299 | 55.058 | |
| maaslin_plot_results_from_output | 54.065 | 0.348 | 54.556 | |
| maaslin_process_metadata | 0.664 | 0.026 | 0.692 | |
| maaslin_read_data | 0.205 | 0.000 | 0.205 | |
| maaslin_reorder_data | 0.219 | 0.000 | 0.219 | |
| maaslin_transform | 0.789 | 0.020 | 0.811 | |
| maaslin_write_results | 22.830 | 0.152 | 23.029 | |
| maaslin_write_results_lefse_format | 26.394 | 0.168 | 26.619 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.006 | |