William Nickols
| Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: e862fe9 |
| git_last_commit_date: 2025-03-17 23:20:44 -0400 (Mon, 17 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 1142/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.13 (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. |
| Package: maaslin3 |
| Version: 0.99.13 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.13.tar.gz |
| StartedAt: 2025-03-18 21:48:07 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 22:00:54 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 767.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.13.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘0.99.13’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 41.040 1.455 42.862
maaslin_plot_results 40.724 1.215 42.241
maaslin3 22.755 1.079 24.067
maaslin_contrast_test 21.783 1.171 23.322
maaslin_write_results_lefse_format 16.725 0.750 17.626
maaslin_write_results 15.912 0.942 16.998
maaslin_fit 14.560 0.678 15.366
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘0.99.13’ ** 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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-03-18 21:55:00.056116 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:55:00.158984 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:55:00.272051 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:55:00.315879 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:55:00.362267 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:55:00.464786 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:55:00.472664 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:55:00.485225 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:55:00.63236 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:55:00.639335 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:55:00.709159 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:55:00.76325 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:55:00.777692 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:55:00.841242 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:55:00.922432 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:55:19.027769 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:55:19.126764 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:55:19.209061 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:55:19.235298 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:55:19.318404 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:55:19.421043 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:55:19.429394 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:55:19.445759 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:55:19.560465 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:55:19.567683 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:55:19.630959 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:55:19.68277 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:55:19.699276 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:55:19.750084 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:55:19.836945 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:55:23.454 R[56895:440462428] XType: com.apple.fonts is not accessible.
2025-03-18 21:55:23.454 R[56895:440462428] XType: XTFontStaticRegistry is enabled.
2025-03-18 21:55:40.869572 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:55:40.96865 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:55:41.063592 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:55:41.089286 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:55:41.122953 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:55:41.209293 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:55:41.215412 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:55:41.22904 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:55:41.358651 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:55:41.365976 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:55:41.441962 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:55:41.495854 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:55:41.513484 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:55:41.569035 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:55:41.711415 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:55:56.859009 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:55:56.950397 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:55:57.028043 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:55:57.054251 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:55:57.103051 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:55:57.189211 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:55:57.195016 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:55:57.208881 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:55:57.340826 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:55:57.347981 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:55:57.413802 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:55:57.469564 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:55:57.485545 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:55:57.540336 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:55:57.633781 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:55:57.869115 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_linear.rds
2025-03-18 21:55:57.933771 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_linear.rds
2025-03-18 21:55:58.008115 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_logistic.rds
2025-03-18 21:55:58.36029 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_logistic.rds
2025-03-18 21:56:16.726401 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:56:16.835968 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:56:16.940657 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:56:16.969076 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:56:17.01436 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:56:17.118045 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:56:17.125822 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:56:17.143617 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:56:17.281338 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:56:17.28952 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:56:17.360831 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:56:17.420992 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:56:17.440467 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:56:17.507364 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:56:17.643724 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:56:32.542823 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:56:32.646426 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:56:32.749923 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:56:32.775972 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:56:32.817089 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:56:32.918186 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:56:32.926107 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:56:32.941697 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:56:33.082077 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:56:33.08861 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:56:33.159104 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:56:33.216243 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:56:33.23407 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:56:33.293017 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:56:33.391269 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:56:33.655691 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_linear.rds
2025-03-18 21:56:33.725 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_linear.rds
2025-03-18 21:56:33.803002 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_logistic.rds
2025-03-18 21:56:34.158775 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_logistic.rds
2025-03-18 21:56:52.451188 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:56:52.545868 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:56:52.632133 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:56:52.65453 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:56:52.695907 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:56:52.78568 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:56:52.794086 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:56:52.80935 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:56:52.940806 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:56:52.948542 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:56:53.01639 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:56:53.072064 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:56:53.084947 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:56:53.142736 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:56:53.228056 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:57:06.291548 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:57:06.368866 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:57:06.44949 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:57:06.471233 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:57:06.513554 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:57:06.595866 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:57:06.601319 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:57:06.615425 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:57:06.724191 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:57:06.730746 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:57:06.787947 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:57:06.839073 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:57:06.853078 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:57:06.903188 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:57:06.981532 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:57:07.224317 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_linear.rds
2025-03-18 21:57:07.292075 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_linear.rds
2025-03-18 21:57:07.359526 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/residuals_logistic.rds
2025-03-18 21:57:07.717977 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f4a1552b2/fits/fitted_logistic.rds
2025-03-18 21:57:25.755999 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:57:25.86119 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:57:25.957823 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:57:25.987443 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:57:26.031774 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:57:26.147473 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:57:26.156039 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:57:26.173067 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:57:26.29939 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:57:26.306935 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:57:26.378238 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:57:26.42787 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:57:26.444182 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:57:26.499192 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:57:26.594236 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:57:39.997834 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:57:40.089097 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:57:40.229841 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:57:40.251513 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:57:40.290677 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:57:40.391508 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:57:40.397968 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:57:40.413103 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:57:40.527163 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:57:40.534018 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:57:40.595262 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:57:40.631427 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:57:40.643522 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:57:40.688258 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:57:40.764258 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 21:58:01.944742 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:58:12.882797 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:58:36.215023 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:58:47.138201 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:58:47.90157 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_linear.rds
2025-03-18 21:58:47.974088 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_linear.rds
2025-03-18 21:58:48.016868 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_logistic.rds
2025-03-18 21:58:48.091841 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_logistic.rds
2025-03-18 21:59:08.26828 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:59:15.562954 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:59:15.892693 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_linear.rds
2025-03-18 21:59:15.958139 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_linear.rds
2025-03-18 21:59:16.00297 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_logistic.rds
2025-03-18 21:59:16.07676 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_logistic.rds
2025-03-18 21:59:32.323757 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:59:38.449729 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 21:59:38.863625 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_linear.rds
2025-03-18 21:59:38.931303 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_linear.rds
2025-03-18 21:59:38.970641 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_logistic.rds
2025-03-18 21:59:39.040312 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_logistic.rds
2025-03-18 21:59:55.809898 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 21:59:55.90426 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 21:59:56.000762 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 21:59:56.034932 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 21:59:56.084307 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 21:59:56.19499 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 21:59:56.20239 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 21:59:56.218065 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 21:59:56.378651 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 21:59:56.387469 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 21:59:56.463 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 21:59:56.517676 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 21:59:56.533073 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 21:59:56.582718 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 21:59:56.707194 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 22:00:09.887047 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 22:00:09.990604 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 22:00:10.089689 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 22:00:10.118969 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 22:00:10.164936 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 22:00:10.268128 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 22:00:10.276385 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 22:00:10.290768 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 22:00:10.412498 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 22:00:10.421306 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 22:00:10.483432 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 22:00:10.542111 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 22:00:10.609304 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 22:00:10.66123 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 22:00:10.756204 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 22:00:11.039951 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_linear.rds
2025-03-18 22:00:11.105862 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_linear.rds
2025-03-18 22:00:11.178231 WARNING::Deleting existing residuals file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/residuals_logistic.rds
2025-03-18 22:00:11.530176 WARNING::Deleting existing fitted file: /tmp/RtmpXFsTmV/filede3f22d2b992/fits/fitted_logistic.rds
2025-03-18 22:00:29.165106 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-03-18 22:00:29.189737 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-03-18 22:00:29.204308 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-03-18 22:00:29.27762 ERROR::No fixed, group, or
ordered effects included in formula.
2025-03-18 22:00:29.298923 ERROR::Effect name not found in metadata: d
2025-03-18 22:00:29.313072 ERROR::No user formula provided
2025-03-18 22:00:29.350004 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-03-18 22:00:29.367153 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-03-18 22:00:32.648452 INFO::Writing function arguments to log file
2025-03-18 22:00:32.671765 INFO::Verifying options selected are valid
2025-03-18 22:00:34.730393 INFO::Writing function arguments to log file
2025-03-18 22:00:34.750029 INFO::Verifying options selected are valid
2025-03-18 22:00:34.75165 INFO::Determining format of input files
2025-03-18 22:00:34.753029 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 22:00:34.757029 INFO::Running selected normalization method: TSS
2025-03-18 22:00:34.759731 INFO::Creating output feature tables folder
2025-03-18 22:00:34.760936 INFO::Writing normalized data to file /tmp/RtmpXFsTmV/filede3f16761ccc/features/data_norm.tsv
2025-03-18 22:00:34.763124 INFO::Filter data based on min abundance and min prevalence
2025-03-18 22:00:34.764138 INFO::Total samples in data: 16
2025-03-18 22:00:34.765176 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-03-18 22:00:34.767997 INFO::Total filtered features: 0
2025-03-18 22:00:34.769518 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 22:00:34.771034 INFO::Total features filtered by non-zero variance filtering: 0
2025-03-18 22:00:34.772592 INFO::Filtered feature names from variance filtering:
2025-03-18 22:00:34.774097 INFO::Writing filtered data to file /tmp/RtmpXFsTmV/filede3f16761ccc/features/filtered_data.tsv
2025-03-18 22:00:34.776728 INFO::Running selected transform method: LOG
2025-03-18 22:00:34.778643 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXFsTmV/filede3f16761ccc/features/data_transformed.tsv
2025-03-18 22:00:34.781147 INFO::Applying z-score to standardize continuous metadata
2025-03-18 22:00:34.787649 INFO::Running the linear model component
2025-03-18 22:00:34.817066 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:34.824309 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:34.831757 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:34.842089 INFO::Counting total values for each feature
2025-03-18 22:00:34.845216 INFO::Running the logistic model component
2025-03-18 22:00:34.874004 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:34.882443 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:34.889261 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:34.902924 INFO::Counting total values for each feature
2025-03-18 22:00:34.906742 INFO::Re-running abundances for warn_prevalence
2025-03-18 22:00:34.908125 INFO::Running selected normalization method: TSS
2025-03-18 22:00:34.910856 INFO::Running selected transform method: LOG
2025-03-18 22:00:34.941611 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:34.948294 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:34.954445 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:35.092485 INFO::Creating fits folder
2025-03-18 22:00:35.094193 INFO::Writing residuals to file /tmp/RtmpXFsTmV/filede3f16761ccc/fits/residuals_linear.rds
2025-03-18 22:00:35.095708 INFO::Writing fitted values to file /tmp/RtmpXFsTmV/filede3f16761ccc/fits/fitted_linear.rds
2025-03-18 22:00:35.097422 INFO::Writing residuals to file /tmp/RtmpXFsTmV/filede3f16761ccc/fits/residuals_logistic.rds
2025-03-18 22:00:35.098779 INFO::Writing fitted values to file /tmp/RtmpXFsTmV/filede3f16761ccc/fits/fitted_logistic.rds
2025-03-18 22:00:35.102372 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpXFsTmV/filede3f16761ccc/all_results.tsv
2025-03-18 22:00:35.104371 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/RtmpXFsTmV/filede3f16761ccc/significant_results.tsv
2025-03-18 22:00:35.106871 INFO::Creating output figures folder
2025-03-18 22:00:35.109125 INFO::Writing summary plot of significant
results to file: /tmp/RtmpXFsTmV/filede3f16761ccc/figures/summary_plot.pdf
2025-03-18 22:00:36.591013 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXFsTmV/filede3f16761ccc/figures
2025-03-18 22:00:36.592954 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 22:00:36.600233 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 22:00:37.04307 INFO::Writing summary plot of
significant results to file: /tmp/RtmpXFsTmV/filede3f16761ccc/figures/summary_plot.pdf
2025-03-18 22:00:38.525849 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXFsTmV/filede3f16761ccc/figures
2025-03-18 22:00:38.52795 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 22:00:38.535318 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 22:00:39.011881 INFO::Running the linear model component
2025-03-18 22:00:39.02446 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:39.030283 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:39.036602 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:39.04558 INFO::Counting total values for each feature
2025-03-18 22:00:39.04732 INFO::Running the logistic model component
2025-03-18 22:00:39.061159 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:39.06716 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:39.073987 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:39.086982 INFO::Counting total values for each feature
2025-03-18 22:00:39.090321 INFO::Re-running abundances for warn_prevalence
2025-03-18 22:00:39.091403 INFO::Running selected normalization method: TSS
2025-03-18 22:00:39.09269 INFO::Running selected transform method: LOG
2025-03-18 22:00:39.107974 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:39.113142 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:39.118759 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:39.242255 INFO::Creating output folder
2025-03-18 22:00:39.243757 INFO::Creating output figures folder
2025-03-18 22:00:39.245559 INFO::Writing summary plot of significant
results to file: /tmp/RtmpXFsTmV/filede3fc4449b7/figures/summary_plot.pdf
2025-03-18 22:00:40.758754 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXFsTmV/filede3fc4449b7/figures
2025-03-18 22:00:40.760589 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 22:00:40.764845 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 22:00:41.802697 INFO::Applying z-score to standardize continuous metadata
2025-03-18 22:00:41.812194 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-03-18 22:00:41.813038 INFO::Bypass z-score application to metadata
2025-03-18 22:00:41.815735 INFO::Bypass z-score application to metadata
2025-03-18 22:00:41.840314 INFO::Determining format of input files
2025-03-18 22:00:41.841296 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 22:00:41.842099 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-03-18 22:00:41.852362 INFO::Determining format of input files
2025-03-18 22:00:41.853972 INFO::Input format is data samples as columns and metadata samples as rows
2025-03-18 22:00:41.855634 INFO::Input format is feature_specific_covariate samples as columns
2025-03-18 22:00:41.868119 INFO::Determining format of input files
2025-03-18 22:00:41.869613 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 22:00:41.871132 INFO::Input format is feature_specific_covariate samples as columns
2025-03-18 22:00:41.873505 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-03-18 22:00:41.87463 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-03-18 22:00:41.889843 INFO::Running selected transform method: LOG
2025-03-18 22:00:41.891514 INFO::Creating output feature tables folder
2025-03-18 22:00:41.89312 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXFsTmV/filede3f227f419a/features/data_transformed.tsv
2025-03-18 22:00:41.897234 INFO::Running selected transform method: LOG
2025-03-18 22:00:41.898279 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXFsTmV/filede3f227f419a/features/data_transformed.tsv
2025-03-18 22:00:41.90366 INFO::Running selected transform method: PLOG
2025-03-18 22:00:41.905918 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXFsTmV/filede3f227f419a/features/data_transformed.tsv
2025-03-18 22:00:41.909398 INFO::Running selected transform method: NONE
2025-03-18 22:00:41.910509 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXFsTmV/filede3f227f419a/features/data_transformed.tsv
2025-03-18 22:00:41.921348 INFO::Running the linear model component
2025-03-18 22:00:41.932098 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:41.936174 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:41.941575 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:41.950347 INFO::Counting total values for each feature
2025-03-18 22:00:41.951972 INFO::Running the logistic model component
2025-03-18 22:00:41.962108 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:41.968292 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:41.974002 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:41.982095 INFO::Counting total values for each feature
2025-03-18 22:00:41.984829 INFO::Re-running abundances for warn_prevalence
2025-03-18 22:00:41.986035 INFO::Running selected normalization method: TSS
2025-03-18 22:00:41.987888 INFO::Running selected transform method: LOG
2025-03-18 22:00:42.004275 INFO::Fitting model to feature number 1, a
2025-03-18 22:00:42.008462 INFO::Fitting model to feature number 2, b
2025-03-18 22:00:42.013765 INFO::Fitting model to feature number 3, c
2025-03-18 22:00:42.11896 INFO::Creating output folder
2025-03-18 22:00:42.120661 INFO::Creating fits folder
2025-03-18 22:00:42.122148 INFO::Writing residuals to file /tmp/RtmpXFsTmV/filede3f50abf727/fits/residuals_linear.rds
2025-03-18 22:00:42.123996 INFO::Writing fitted values to file /tmp/RtmpXFsTmV/filede3f50abf727/fits/fitted_linear.rds
2025-03-18 22:00:42.125763 INFO::Writing residuals to file /tmp/RtmpXFsTmV/filede3f50abf727/fits/residuals_logistic.rds
2025-03-18 22:00:42.127554 INFO::Writing fitted values to file /tmp/RtmpXFsTmV/filede3f50abf727/fits/fitted_logistic.rds
2025-03-18 22:00:42.131927 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpXFsTmV/filede3f50abf727/all_results.tsv
2025-03-18 22:00:42.151203 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/RtmpXFsTmV/filede3f50abf727/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
345.352 7.943 355.724
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 22.755 | 1.079 | 24.067 | |
| maaslin_check_arguments | 0.191 | 0.006 | 0.202 | |
| maaslin_check_formula | 0.176 | 0.011 | 0.189 | |
| maaslin_compute_formula | 0.191 | 0.012 | 0.206 | |
| maaslin_contrast_test | 21.783 | 1.171 | 23.322 | |
| maaslin_filter | 0.552 | 0.045 | 0.604 | |
| maaslin_fit | 14.560 | 0.678 | 15.366 | |
| maaslin_log_arguments | 0.168 | 0.010 | 0.181 | |
| maaslin_normalize | 0.348 | 0.026 | 0.379 | |
| maaslin_plot_results | 40.724 | 1.215 | 42.241 | |
| maaslin_plot_results_from_output | 41.040 | 1.455 | 42.862 | |
| maaslin_process_metadata | 0.647 | 0.044 | 0.698 | |
| maaslin_read_data | 0.168 | 0.010 | 0.181 | |
| maaslin_reorder_data | 0.176 | 0.011 | 0.188 | |
| maaslin_transform | 0.818 | 0.101 | 0.932 | |
| maaslin_write_results | 15.912 | 0.942 | 16.998 | |
| maaslin_write_results_lefse_format | 16.725 | 0.750 | 17.626 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.006 | |