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 13:18 -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 20:05:30 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:10:05 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 274.3 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: aarch64-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 Ventura 13.7.1
* 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 13.843 0.866 14.767
maaslin_plot_results_from_output 13.823 0.689 14.604
maaslin3 8.050 0.554 8.645
maaslin_contrast_test 7.165 0.705 7.906
maaslin_write_results_lefse_format 5.862 0.557 6.670
maaslin_write_results 5.594 0.636 6.241
maaslin_fit 5.105 0.541 5.689
* 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-arm64/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: aarch64-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 20:07:55.471378 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:07:55.499296 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:07:55.536383 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:07:55.54445 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:07:55.55706 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:07:55.585568 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:07:55.587883 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:07:55.592567 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:07:55.633275 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:07:55.635415 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:07:55.653305 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:07:55.668925 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:07:55.673933 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:07:55.693907 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:07:55.71805 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:02.633532 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:02.671802 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:02.698184 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:02.706053 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:02.717891 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:02.744319 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:02.746306 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:02.750527 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:02.78323 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:02.785211 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:02.801905 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:02.815302 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:02.819444 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:02.83337 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:02.857133 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:04.044 R[66392:1004285209] XType: Using static font registry.
2025-04-21 20:08:10.961608 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:11.005515 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:11.032501 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:11.04 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:11.052098 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:11.078845 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:11.080955 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:11.085153 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:11.118653 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:11.120764 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:11.137727 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:11.155041 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:11.160162 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:11.17484 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:11.201723 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:16.610182 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:16.636933 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:16.663008 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:16.670879 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:16.683336 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:16.710906 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:16.712866 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:16.717318 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:16.760157 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:16.762228 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:16.781056 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:16.796281 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:16.801496 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:16.819268 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:16.851146 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:16.931066 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_linear.rds
2025-04-21 20:08:16.963782 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_linear.rds
2025-04-21 20:08:16.997534 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_logistic.rds
2025-04-21 20:08:17.165982 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_logistic.rds
2025-04-21 20:08:24.193238 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:24.219125 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:24.244568 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:24.252084 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:24.263908 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:24.290224 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:24.292228 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:24.29636 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:24.328873 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:24.330881 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:24.347581 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:24.361522 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:24.365842 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:24.379613 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:24.403247 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:29.457837 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:29.48577 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:29.512309 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:29.52016 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:29.531872 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:29.558021 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:29.56004 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:29.564133 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:29.600529 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:29.602821 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:29.621679 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:29.666919 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:29.671186 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:29.685064 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:29.708427 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:29.779422 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_linear.rds
2025-04-21 20:08:29.811548 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_linear.rds
2025-04-21 20:08:29.84475 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_logistic.rds
2025-04-21 20:08:30.010974 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_logistic.rds
2025-04-21 20:08:36.53076 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:36.55807 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:36.584746 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:36.592236 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:36.603959 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:36.62984 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:36.631848 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:36.635936 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:36.683352 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:36.685333 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:36.702027 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:36.715628 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:36.719872 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:36.733478 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:36.75686 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:41.851882 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:41.878141 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:41.903422 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:41.911186 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:41.922964 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:41.948904 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:41.950964 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:41.955017 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:41.988128 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:41.990253 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:42.007295 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:42.021308 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:42.025546 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:42.039483 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:42.06446 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:42.134803 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_linear.rds
2025-04-21 20:08:42.167023 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_linear.rds
2025-04-21 20:08:42.201787 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/residuals_logistic.rds
2025-04-21 20:08:42.370268 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103584d691cca/fits/fitted_logistic.rds
2025-04-21 20:08:48.868217 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:48.89359 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:48.91804 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:48.925389 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:48.936759 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:48.961526 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:48.963472 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:48.967422 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:48.999358 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:49.001344 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:49.017775 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:49.031806 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:49.035924 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:49.049025 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:49.071445 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:08:54.367972 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:08:54.396459 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:08:54.422935 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:08:54.430768 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:08:54.442823 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:08:54.469735 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:08:54.471898 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:08:54.476191 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:08:54.510181 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:08:54.512333 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:08:54.530074 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:08:54.544455 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:08:54.548965 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:08:54.563733 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:08:54.58906 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:09:02.036166 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:06.365976 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:14.228379 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:17.986931 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:18.175611 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_linear.rds
2025-04-21 20:09:18.207878 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_linear.rds
2025-04-21 20:09:18.229693 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_logistic.rds
2025-04-21 20:09:18.269561 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_logistic.rds
2025-04-21 20:09:25.602255 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:28.312616 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:28.440263 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_linear.rds
2025-04-21 20:09:28.476254 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_linear.rds
2025-04-21 20:09:28.501508 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_logistic.rds
2025-04-21 20:09:28.542961 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_logistic.rds
2025-04-21 20:09:34.5589 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:37.357019 WARNING::Fitting problem for feature 124 returning NA
2025-04-21 20:09:37.485061 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_linear.rds
2025-04-21 20:09:37.517935 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_linear.rds
2025-04-21 20:09:37.540457 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_logistic.rds
2025-04-21 20:09:37.580652 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_logistic.rds
2025-04-21 20:09:43.390727 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:09:43.417594 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:09:43.444433 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:09:43.452444 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:09:43.46506 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:09:43.491673 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:09:43.493684 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:09:43.497776 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:09:43.530409 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:09:43.53241 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:09:43.549747 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:09:43.563808 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:09:43.568187 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:09:43.582172 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:09:43.61452 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:09:48.776008 WARNING::Fitting problem for feature 50 returning NA
2025-04-21 20:09:48.802515 WARNING::Fitting problem for feature 62 returning NA
2025-04-21 20:09:48.828333 WARNING::Fitting problem for feature 74 returning NA
2025-04-21 20:09:48.83629 WARNING::Fitting problem for feature 78 returning NA
2025-04-21 20:09:48.848478 WARNING::Fitting problem for feature 84 returning NA
2025-04-21 20:09:48.874831 WARNING::Fitting problem for feature 96 returning NA
2025-04-21 20:09:48.87691 WARNING::Fitting problem for feature 97 returning NA
2025-04-21 20:09:48.881045 WARNING::Fitting problem for feature 99 returning NA
2025-04-21 20:09:48.914074 WARNING::Fitting problem for feature 114 returning NA
2025-04-21 20:09:48.916064 WARNING::Fitting problem for feature 115 returning NA
2025-04-21 20:09:48.933068 WARNING::Fitting problem for feature 123 returning NA
2025-04-21 20:09:48.946229 WARNING::Fitting problem for feature 130 returning NA
2025-04-21 20:09:48.950478 WARNING::Fitting problem for feature 132 returning NA
2025-04-21 20:09:48.964105 WARNING::Fitting problem for feature 139 returning NA
2025-04-21 20:09:48.988061 WARNING::Fitting problem for feature 150 returning NA
2025-04-21 20:09:49.072954 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_linear.rds
2025-04-21 20:09:49.105048 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_linear.rds
2025-04-21 20:09:49.138319 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/residuals_logistic.rds
2025-04-21 20:09:49.304076 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103586e3ea047/fits/fitted_logistic.rds
2025-04-21 20:09:55.600832 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-04-21 20:09:55.606307 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-04-21 20:09:55.615913 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-04-21 20:09:55.632644 ERROR::No fixed, group, or
ordered effects included in formula.
2025-04-21 20:09:55.637958 ERROR::Effect name not found in metadata: d
2025-04-21 20:09:55.641472 ERROR::No user formula provided
2025-04-21 20:09:55.65082 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-04-21 20:09:55.654568 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-04-21 20:09:56.663085 INFO::Writing function arguments to log file
2025-04-21 20:09:56.668027 INFO::Verifying options selected are valid
2025-04-21 20:09:57.350413 INFO::Writing function arguments to log file
2025-04-21 20:09:57.354519 INFO::Verifying options selected are valid
2025-04-21 20:09:57.354882 INFO::Determining format of input files
2025-04-21 20:09:57.355177 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 20:09:57.355915 INFO::Running selected normalization method: TSS
2025-04-21 20:09:57.356416 INFO::Creating output feature tables folder
2025-04-21 20:09:57.356785 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/features/data_norm.tsv
2025-04-21 20:09:57.35733 INFO::Filter data based on min abundance and min prevalence
2025-04-21 20:09:57.357617 INFO::Total samples in data: 16
2025-04-21 20:09:57.357885 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-04-21 20:09:57.358474 INFO::Total filtered features: 0
2025-04-21 20:09:57.358803 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 20:09:57.359169 INFO::Total features filtered by non-zero variance filtering: 0
2025-04-21 20:09:57.359467 INFO::Filtered feature names from variance filtering:
2025-04-21 20:09:57.359739 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/features/filtered_data.tsv
2025-04-21 20:09:57.360249 INFO::Running selected transform method: LOG
2025-04-21 20:09:57.360631 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/features/data_transformed.tsv
2025-04-21 20:09:57.361202 INFO::Applying z-score to standardize continuous metadata
2025-04-21 20:09:57.363015 INFO::Running the linear model component
2025-04-21 20:09:57.373406 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:57.374947 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:57.376248 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:57.378626 INFO::Counting total values for each feature
2025-04-21 20:09:57.379293 INFO::Running the logistic model component
2025-04-21 20:09:57.384067 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:57.38617 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:57.388137 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:57.392466 INFO::Counting total values for each feature
2025-04-21 20:09:57.393287 INFO::Re-running abundances for warn_prevalence
2025-04-21 20:09:57.393627 INFO::Running selected normalization method: TSS
2025-04-21 20:09:57.394156 INFO::Running selected transform method: LOG
2025-04-21 20:09:57.400189 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:57.401725 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:57.403078 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:57.429957 INFO::Creating fits folder
2025-04-21 20:09:57.430586 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/fits/residuals_linear.rds
2025-04-21 20:09:57.431183 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/fits/fitted_linear.rds
2025-04-21 20:09:57.431671 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/fits/residuals_logistic.rds
2025-04-21 20:09:57.432166 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/fits/fitted_logistic.rds
2025-04-21 20:09:57.433179 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/all_results.tsv
2025-04-21 20:09:57.433885 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/significant_results.tsv
2025-04-21 20:09:57.434432 INFO::Creating output figures folder
2025-04-21 20:09:57.434936 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/figures/summary_plot.pdf
2025-04-21 20:09:57.899629 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/figures
2025-04-21 20:09:57.900436 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 20:09:57.90249 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 20:09:58.05961 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/figures/summary_plot.pdf
2025-04-21 20:09:58.543621 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358221982de/figures
2025-04-21 20:09:58.544292 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 20:09:58.546287 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 20:09:58.705946 INFO::Running the linear model component
2025-04-21 20:09:58.708766 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:58.710248 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:58.71145 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:58.713802 INFO::Counting total values for each feature
2025-04-21 20:09:58.714338 INFO::Running the logistic model component
2025-04-21 20:09:58.716832 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:58.718749 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:58.720476 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:58.72314 INFO::Counting total values for each feature
2025-04-21 20:09:58.72378 INFO::Re-running abundances for warn_prevalence
2025-04-21 20:09:58.724006 INFO::Running selected normalization method: TSS
2025-04-21 20:09:58.724421 INFO::Running selected transform method: LOG
2025-04-21 20:09:58.726959 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:58.728243 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:58.729384 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:58.755114 INFO::Creating output folder
2025-04-21 20:09:58.755591 INFO::Creating output figures folder
2025-04-21 20:09:58.756023 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358720326d9/figures/summary_plot.pdf
2025-04-21 20:09:59.240733 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358720326d9/figures
2025-04-21 20:09:59.241418 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-21 20:09:59.24338 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-21 20:09:59.585099 INFO::Applying z-score to standardize continuous metadata
2025-04-21 20:09:59.587928 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-04-21 20:09:59.588235 INFO::Bypass z-score application to metadata
2025-04-21 20:09:59.589024 INFO::Bypass z-score application to metadata
2025-04-21 20:09:59.59556 INFO::Determining format of input files
2025-04-21 20:09:59.595901 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 20:09:59.596165 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-04-21 20:09:59.59836 INFO::Determining format of input files
2025-04-21 20:09:59.598702 INFO::Input format is data samples as columns and metadata samples as rows
2025-04-21 20:09:59.599087 INFO::Input format is feature_specific_covariate samples as columns
2025-04-21 20:09:59.601504 INFO::Determining format of input files
2025-04-21 20:09:59.601808 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 20:09:59.602136 INFO::Input format is feature_specific_covariate samples as columns
2025-04-21 20:09:59.602596 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 20:09:59.602816 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 20:09:59.606415 INFO::Running selected transform method: LOG
2025-04-21 20:09:59.606779 INFO::Creating output feature tables folder
2025-04-21 20:09:59.607137 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103583e0ab18b/features/data_transformed.tsv
2025-04-21 20:09:59.608458 INFO::Running selected transform method: LOG
2025-04-21 20:09:59.608786 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103583e0ab18b/features/data_transformed.tsv
2025-04-21 20:09:59.610036 INFO::Running selected transform method: PLOG
2025-04-21 20:09:59.610522 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103583e0ab18b/features/data_transformed.tsv
2025-04-21 20:09:59.61143 INFO::Running selected transform method: NONE
2025-04-21 20:09:59.611661 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file103583e0ab18b/features/data_transformed.tsv
2025-04-21 20:09:59.614318 INFO::Running the linear model component
2025-04-21 20:09:59.617042 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:59.6185 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:59.619707 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:59.622019 INFO::Counting total values for each feature
2025-04-21 20:09:59.622556 INFO::Running the logistic model component
2025-04-21 20:09:59.625083 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:59.627021 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:59.628801 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:59.631637 INFO::Counting total values for each feature
2025-04-21 20:09:59.632303 INFO::Re-running abundances for warn_prevalence
2025-04-21 20:09:59.632537 INFO::Running selected normalization method: TSS
2025-04-21 20:09:59.632948 INFO::Running selected transform method: LOG
2025-04-21 20:09:59.63555 INFO::Fitting model to feature number 1, a
2025-04-21 20:09:59.636863 INFO::Fitting model to feature number 2, b
2025-04-21 20:09:59.638061 INFO::Fitting model to feature number 3, c
2025-04-21 20:09:59.665819 INFO::Creating output folder
2025-04-21 20:09:59.66628 INFO::Creating fits folder
2025-04-21 20:09:59.666605 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/fits/residuals_linear.rds
2025-04-21 20:09:59.667088 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/fits/fitted_linear.rds
2025-04-21 20:09:59.667484 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/fits/residuals_logistic.rds
2025-04-21 20:09:59.667892 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/fits/fitted_logistic.rds
2025-04-21 20:09:59.668836 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/all_results.tsv
2025-04-21 20:09:59.669438 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdHLtEj/file10358300e3c7f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
121.879 5.749 128.985
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.050 | 0.554 | 8.645 | |
| maaslin_check_arguments | 0.067 | 0.003 | 0.070 | |
| maaslin_check_formula | 0.070 | 0.006 | 0.075 | |
| maaslin_compute_formula | 0.057 | 0.003 | 0.060 | |
| maaslin_contrast_test | 7.165 | 0.705 | 7.906 | |
| maaslin_filter | 0.209 | 0.018 | 0.230 | |
| maaslin_fit | 5.105 | 0.541 | 5.689 | |
| maaslin_log_arguments | 0.055 | 0.003 | 0.058 | |
| maaslin_normalize | 0.136 | 0.017 | 0.158 | |
| maaslin_plot_results | 13.843 | 0.866 | 14.767 | |
| maaslin_plot_results_from_output | 13.823 | 0.689 | 14.604 | |
| maaslin_process_metadata | 0.229 | 0.022 | 0.252 | |
| maaslin_read_data | 0.053 | 0.003 | 0.056 | |
| maaslin_reorder_data | 0.055 | 0.003 | 0.059 | |
| maaslin_transform | 0.285 | 0.026 | 0.312 | |
| maaslin_write_results | 5.594 | 0.636 | 6.241 | |
| maaslin_write_results_lefse_format | 5.862 | 0.557 | 6.670 | |
| preprocess_dna_mtx | 0.001 | 0.001 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |