William Nickols
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 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 2025-04-22 13:16 -0400 (Tue, 22 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" | 4831 |
| 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. |
| Package: maaslin3 |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2025-04-21 21:36:34 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 21:49:03 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 749.2 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘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 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 40.710 1.020 42.282
maaslin_plot_results 39.759 1.045 41.089
maaslin3 22.157 1.081 23.607
maaslin_contrast_test 20.514 1.100 21.837
maaslin_write_results_lefse_format 16.388 0.770 17.234
maaslin_write_results 15.880 0.870 16.872
maaslin_fit 14.486 0.591 15.159
* 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 ‘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 version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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")
2025-04-21 21:43:16.831171 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:43:16.912221 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:43:17.022454 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:43:17.051619 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:43:17.103693 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:43:17.191498 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:43:17.196811 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:43:17.209443 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:43:17.349648 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:43:17.356009 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:43:17.422486 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:43:17.468644 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:43:17.483017 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:43:17.533327 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:43:17.636484 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:43:34.726755 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:43:34.825613 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:43:34.916847 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:43:34.945709 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:43:34.992732 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:43:35.089137 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:43:35.116426 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:43:35.133283 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:43:35.263177 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:43:35.271542 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:43:35.331565 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:43:35.379299 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:43:35.394751 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:43:35.445239 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:43:35.524853 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:43:38.932 R[33535:728707552] XType: com.apple.fonts is not accessible.
2025-04-21 21:43:38.932 R[33535:728707552] XType: XTFontStaticRegistry is enabled.
2025-04-21 21:43:55.152001 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:43:55.307699 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:43:55.411163 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:43:55.440046 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:43:55.495417 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:43:55.591154 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:43:55.598815 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:43:55.617614 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:43:55.737161 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:43:55.745113 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:43:55.817112 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:43:56.687668 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:43:56.702031 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:43:56.753943 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:43:56.836843 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:44:11.490952 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:44:11.593159 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:44:11.698345 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:44:11.72719 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:44:11.776955 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:44:11.877727 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:44:11.884176 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:44:11.89976 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:44:12.021826 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:44:12.029754 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:44:12.093412 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:44:12.143505 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:44:12.161055 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:44:12.207313 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:44:12.294315 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:44:12.578634 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_linear.rds
2025-04-21 21:44:12.639404 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_linear.rds
2025-04-21 21:44:12.707148 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_logistic.rds
2025-04-21 21:44:13.036328 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_logistic.rds
2025-04-21 21:44:31.991675 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:44:32.096393 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:44:32.189314 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:44:32.217638 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:44:32.253374 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:44:32.331132 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:44:32.336946 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:44:32.348858 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:44:32.453976 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:44:32.46039 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:44:32.516852 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:44:32.562095 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:44:32.577629 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:44:32.622758 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:44:32.715684 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:44:46.834395 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:44:46.909644 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:44:46.997409 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:44:47.02768 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:44:47.068905 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:44:47.160551 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:44:47.168306 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:44:47.18062 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:44:47.304155 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:44:47.311489 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:44:47.370342 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:44:47.411646 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:44:47.429932 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:44:47.476599 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:44:47.560428 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:44:47.790472 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_linear.rds
2025-04-21 21:44:47.858174 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_linear.rds
2025-04-21 21:44:47.928826 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_logistic.rds
2025-04-21 21:44:48.261783 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_logistic.rds
2025-04-21 21:45:06.131237 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:45:06.23161 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:45:06.332658 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:45:06.35811 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:45:06.400208 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:45:06.499852 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:45:06.506487 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:45:06.523013 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:45:06.648801 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:45:06.656379 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:45:06.723956 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:45:06.774658 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:45:06.792196 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:45:06.845847 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:45:06.946892 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:45:20.328291 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:45:20.430279 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:45:20.527239 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:45:20.553226 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:45:20.590311 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:45:20.673096 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:45:20.678915 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:45:20.694259 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:45:20.807442 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:45:20.815782 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:45:20.8737 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:45:20.923078 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:45:20.936561 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:45:20.981868 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:45:21.068169 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:45:21.308729 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_linear.rds
2025-04-21 21:45:21.377721 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_linear.rds
2025-04-21 21:45:21.446136 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/residuals_logistic.rds
2025-04-21 21:45:21.795233 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff25f612c8/fits/fitted_logistic.rds
2025-04-21 21:45:40.055083 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:45:40.151336 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:45:40.24635 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:45:40.275542 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:45:40.318584 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:45:40.414318 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:45:40.42 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:45:40.433274 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:45:40.558946 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:45:40.566092 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:45:40.635773 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:45:40.689671 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:45:40.704863 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:45:40.765639 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:45:40.857948 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:45:54.505892 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:45:54.604565 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:45:54.787885 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:45:54.819221 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:45:54.85961 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:45:54.950214 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:45:54.956203 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:45:54.97309 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:45:55.104839 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:45:55.11044 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:45:55.178242 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:45:55.221282 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:45:55.233199 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:45:55.284327 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:45:55.365084 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:46:16.324524 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:46:26.916843 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:46:48.986887 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:46:59.57342 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:47:00.300109 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_linear.rds
2025-04-21 21:47:00.368167 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_linear.rds
2025-04-21 21:47:00.412089 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_logistic.rds
2025-04-21 21:47:00.480551 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_logistic.rds
2025-04-21 21:47:20.20867 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:47:26.002083 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:47:26.517704 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_linear.rds
2025-04-21 21:47:26.579158 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_linear.rds
2025-04-21 21:47:26.617539 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_logistic.rds
2025-04-21 21:47:26.698501 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_logistic.rds
2025-04-21 21:47:43.425553 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:47:49.450132 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 21:47:49.805599 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_linear.rds
2025-04-21 21:47:49.869989 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_linear.rds
2025-04-21 21:47:49.914987 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_logistic.rds
2025-04-21 21:47:49.993381 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_logistic.rds
2025-04-21 21:48:06.86501 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:48:06.965486 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:48:07.056084 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:48:07.085044 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:48:07.13336 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:48:07.234608 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:48:07.241243 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:48:07.257224 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:48:07.379111 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:48:07.387205 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:48:07.450444 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:48:07.504519 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:48:07.522181 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:48:07.572251 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:48:07.665329 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:48:21.006335 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 21:48:21.115457 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 21:48:21.230733 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 21:48:21.261873 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 21:48:21.307033 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 21:48:21.404612 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 21:48:21.411907 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 21:48:21.427464 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 21:48:21.620317 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 21:48:21.628472 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 21:48:21.689302 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 21:48:21.73665 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 21:48:21.754581 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 21:48:21.814449 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 21:48:21.906073 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 21:48:22.185425 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_linear.rds
2025-04-21 21:48:22.255949 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_linear.rds
2025-04-21 21:48:22.318412 WARNING::Deleting existing residuals file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/residuals_logistic.rds
2025-04-21 21:48:22.65913 WARNING::Deleting existing fitted file: /tmp/RtmpuhYLQJ/file82ff15bbf79b/fits/fitted_logistic.rds
2025-04-21 21:48:39.486786 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-04-21 21:48:39.508965 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-04-21 21:48:39.525161 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-04-21 21:48:39.595956 ERROR::No fixed, group, or
ordered effects included in formula.
2025-04-21 21:48:39.611989 ERROR::Effect name not found in metadata: d
2025-04-21 21:48:39.626667 ERROR::No user formula provided
2025-04-21 21:48:39.665174 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-04-21 21:48:39.679059 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-04-21 21:48:42.745454 INFO::Writing function arguments to log file
2025-04-21 21:48:42.77096 INFO::Verifying options selected are valid
2025-04-21 21:48:44.861542 INFO::Writing function arguments to log file
2025-04-21 21:48:44.879339 INFO::Verifying options selected are valid
2025-04-21 21:48:44.880495 INFO::Determining format of input files
2025-04-21 21:48:44.881545 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 21:48:44.884098 INFO::Running selected normalization method: TSS
2025-04-21 21:48:44.886035 INFO::Creating output feature tables folder
2025-04-21 21:48:44.887774 INFO::Writing normalized data to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/features/data_norm.tsv
2025-04-21 21:48:44.890459 INFO::Filter data based on min abundance and min prevalence
2025-04-21 21:48:44.892015 INFO::Total samples in data: 16
2025-04-21 21:48:44.893462 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-04-21 21:48:44.895738 INFO::Total filtered features: 0
2025-04-21 21:48:44.896747 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 21:48:44.897933 INFO::Total features filtered by non-zero variance filtering: 0
2025-04-21 21:48:44.899201 INFO::Filtered feature names from variance filtering:
2025-04-21 21:48:44.900716 INFO::Writing filtered data to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/features/filtered_data.tsv
2025-04-21 21:48:44.903159 INFO::Running selected transform method: LOG
2025-04-21 21:48:44.904857 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/features/data_transformed.tsv
2025-04-21 21:48:44.907453 INFO::Applying z-score to standardize continuous metadata
2025-04-21 21:48:44.91583 INFO::Running the linear model component
2025-04-21 21:48:44.942647 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:44.949822 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:44.956796 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:44.966756 INFO::Counting total values for each feature
2025-04-21 21:48:44.969589 INFO::Running the logistic model component
2025-04-21 21:48:44.996741 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:45.006908 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:45.017033 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:45.031716 INFO::Counting total values for each feature
2025-04-21 21:48:45.035693 INFO::Re-running abundances for warn_prevalence
2025-04-21 21:48:45.037503 INFO::Running selected normalization method: TSS
2025-04-21 21:48:45.039818 INFO::Running selected transform method: LOG
2025-04-21 21:48:45.065929 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:45.07278 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:45.080079 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:45.224785 INFO::Creating fits folder
2025-04-21 21:48:45.227204 INFO::Writing residuals to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/fits/residuals_linear.rds
2025-04-21 21:48:45.229194 INFO::Writing fitted values to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/fits/fitted_linear.rds
2025-04-21 21:48:45.231118 INFO::Writing residuals to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/fits/residuals_logistic.rds
2025-04-21 21:48:45.233043 INFO::Writing fitted values to file /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/fits/fitted_logistic.rds
2025-04-21 21:48:45.23675 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/all_results.tsv
2025-04-21 21:48:45.239305 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/RtmpuhYLQJ/file82ff5b8bd7cb/significant_results.tsv
2025-04-21 21:48:45.241985 INFO::Creating output figures folder
2025-04-21 21:48:45.244431 INFO::Writing summary plot of significant
results to file: /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/figures/summary_plot.pdf
2025-04-21 21:48:46.596866 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/figures
2025-04-21 21:48:46.598849 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 21:48:46.603839 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 21:48:47.031654 INFO::Writing summary plot of
significant results to file: /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/figures/summary_plot.pdf
2025-04-21 21:48:48.326526 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuhYLQJ/file82ff5b8bd7cb/figures
2025-04-21 21:48:48.328063 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 21:48:48.332618 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 21:48:48.757007 INFO::Running the linear model component
2025-04-21 21:48:48.766055 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:48.770783 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:48.775601 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:48.783115 INFO::Counting total values for each feature
2025-04-21 21:48:48.785593 INFO::Running the logistic model component
2025-04-21 21:48:48.794821 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:48.801518 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:48.807175 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:48.815638 INFO::Counting total values for each feature
2025-04-21 21:48:48.817463 INFO::Re-running abundances for warn_prevalence
2025-04-21 21:48:48.818202 INFO::Running selected normalization method: TSS
2025-04-21 21:48:48.819392 INFO::Running selected transform method: LOG
2025-04-21 21:48:48.826867 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:48.830816 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:48.834935 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:48.942512 INFO::Creating output folder
2025-04-21 21:48:48.944016 INFO::Creating output figures folder
2025-04-21 21:48:48.946049 INFO::Writing summary plot of significant
results to file: /tmp/RtmpuhYLQJ/file82ff35cf8e79/figures/summary_plot.pdf
2025-04-21 21:48:50.353339 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpuhYLQJ/file82ff35cf8e79/figures
2025-04-21 21:48:50.354731 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 21:48:50.36093 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 21:48:51.371591 INFO::Applying z-score to standardize continuous metadata
2025-04-21 21:48:51.381096 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-04-21 21:48:51.382499 INFO::Bypass z-score application to metadata
2025-04-21 21:48:51.3863 INFO::Bypass z-score application to metadata
2025-04-21 21:48:51.410339 INFO::Determining format of input files
2025-04-21 21:48:51.411827 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 21:48:51.413155 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-04-21 21:48:51.424192 INFO::Determining format of input files
2025-04-21 21:48:51.425629 INFO::Input format is data samples as columns and metadata samples as rows
2025-04-21 21:48:51.427687 INFO::Input format is feature_specific_covariate samples as columns
2025-04-21 21:48:51.43798 INFO::Determining format of input files
2025-04-21 21:48:51.439159 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 21:48:51.440755 INFO::Input format is feature_specific_covariate samples as columns
2025-04-21 21:48:51.443235 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-04-21 21:48:51.444426 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-04-21 21:48:51.462494 INFO::Running selected transform method: LOG
2025-04-21 21:48:51.464268 INFO::Creating output feature tables folder
2025-04-21 21:48:51.465457 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuhYLQJ/file82ff71d0f2d3/features/data_transformed.tsv
2025-04-21 21:48:51.470102 INFO::Running selected transform method: LOG
2025-04-21 21:48:51.471421 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuhYLQJ/file82ff71d0f2d3/features/data_transformed.tsv
2025-04-21 21:48:51.477062 INFO::Running selected transform method: PLOG
2025-04-21 21:48:51.478747 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuhYLQJ/file82ff71d0f2d3/features/data_transformed.tsv
2025-04-21 21:48:51.482289 INFO::Running selected transform method: NONE
2025-04-21 21:48:51.483141 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpuhYLQJ/file82ff71d0f2d3/features/data_transformed.tsv
2025-04-21 21:48:51.494034 INFO::Running the linear model component
2025-04-21 21:48:51.505105 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:51.51175 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:51.518102 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:51.528513 INFO::Counting total values for each feature
2025-04-21 21:48:51.531038 INFO::Running the logistic model component
2025-04-21 21:48:51.54148 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:51.547858 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:51.55331 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:51.562841 INFO::Counting total values for each feature
2025-04-21 21:48:51.565779 INFO::Re-running abundances for warn_prevalence
2025-04-21 21:48:51.567002 INFO::Running selected normalization method: TSS
2025-04-21 21:48:51.569166 INFO::Running selected transform method: LOG
2025-04-21 21:48:51.58305 INFO::Fitting model to feature number 1, a
2025-04-21 21:48:51.589214 INFO::Fitting model to feature number 2, b
2025-04-21 21:48:51.595594 INFO::Fitting model to feature number 3, c
2025-04-21 21:48:51.715722 INFO::Creating output folder
2025-04-21 21:48:51.717265 INFO::Creating fits folder
2025-04-21 21:48:51.718242 INFO::Writing residuals to file /tmp/RtmpuhYLQJ/file82ff4cf63505/fits/residuals_linear.rds
2025-04-21 21:48:51.719482 INFO::Writing fitted values to file /tmp/RtmpuhYLQJ/file82ff4cf63505/fits/fitted_linear.rds
2025-04-21 21:48:51.72134 INFO::Writing residuals to file /tmp/RtmpuhYLQJ/file82ff4cf63505/fits/residuals_logistic.rds
2025-04-21 21:48:51.723195 INFO::Writing fitted values to file /tmp/RtmpuhYLQJ/file82ff4cf63505/fits/fitted_logistic.rds
2025-04-21 21:48:51.726798 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpuhYLQJ/file82ff4cf63505/all_results.tsv
2025-04-21 21:48:51.728803 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/RtmpuhYLQJ/file82ff4cf63505/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
338.185 7.646 347.946
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 22.157 | 1.081 | 23.607 | |
| maaslin_check_arguments | 0.185 | 0.006 | 0.192 | |
| maaslin_check_formula | 0.212 | 0.012 | 0.227 | |
| maaslin_compute_formula | 0.167 | 0.011 | 0.180 | |
| maaslin_contrast_test | 20.514 | 1.100 | 21.837 | |
| maaslin_filter | 0.606 | 0.045 | 0.657 | |
| maaslin_fit | 14.486 | 0.591 | 15.159 | |
| maaslin_log_arguments | 0.168 | 0.009 | 0.178 | |
| maaslin_normalize | 0.372 | 0.043 | 0.419 | |
| maaslin_plot_results | 39.759 | 1.045 | 41.089 | |
| maaslin_plot_results_from_output | 40.710 | 1.020 | 42.282 | |
| maaslin_process_metadata | 0.643 | 0.043 | 0.692 | |
| maaslin_read_data | 0.178 | 0.010 | 0.189 | |
| maaslin_reorder_data | 0.173 | 0.010 | 0.185 | |
| maaslin_transform | 0.839 | 0.067 | 0.913 | |
| maaslin_write_results | 15.880 | 0.870 | 16.872 | |
| maaslin_write_results_lefse_format | 16.388 | 0.770 | 17.234 | |
| preprocess_dna_mtx | 0.004 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.001 | 0.004 | |