William Nickols
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 1143/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.0.tar.gz |
| StartedAt: 2025-06-19 00:30:50 -0400 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 00:50:19 -0400 (Thu, 19 Jun 2025) |
| EllapsedTime: 1169.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 36.085 0.361 36.452
maaslin_plot_results 35.695 0.286 35.946
maaslin3 20.675 0.658 21.336
maaslin_contrast_test 16.704 0.436 17.141
maaslin_write_results_lefse_format 14.935 0.116 15.052
maaslin_write_results 12.715 0.174 12.889
maaslin_fit 12.519 0.116 12.635
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-06-19 00:36:43.14364 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:36:43.842938 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:36:43.934129 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:36:43.958828 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:36:43.998209 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:36:44.088025 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:36:44.09357 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:36:44.105568 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:36:44.202127 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:36:44.207475 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:36:44.263497 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:36:44.304969 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:36:44.317552 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:36:44.359979 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:36:44.430447 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:37:00.527524 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:37:00.600938 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:37:00.673433 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:37:00.694339 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:37:00.727404 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:37:00.799836 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:37:00.804931 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:37:00.816461 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:37:00.909782 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:37:00.915065 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:37:00.983826 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:37:01.02325 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:37:01.034697 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:37:01.073362 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:37:01.139729 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:37:20.190027 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:37:20.268393 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:37:20.344858 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:37:20.367122 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:37:20.401599 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:37:20.483746 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:37:20.489269 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:37:20.501342 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:37:20.596978 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:37:20.602325 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:37:20.651762 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:37:20.691747 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:37:20.704339 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:37:20.750048 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:37:20.828631 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:37:33.357907 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:37:33.4327 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:37:33.507392 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:37:33.529369 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:37:33.563678 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:37:33.640365 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:37:33.645786 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:37:33.658142 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:37:33.754219 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:37:33.759753 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:37:33.810566 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:37:33.853681 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:37:33.866426 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:37:33.909789 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:37:33.981101 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:37:34.215531 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_linear.rds
2025-06-19 00:37:34.27816 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_linear.rds
2025-06-19 00:37:34.342347 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_logistic.rds
2025-06-19 00:37:34.644098 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_logistic.rds
2025-06-19 00:37:51.5121 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:37:51.589059 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:37:51.664388 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:37:51.685817 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:37:51.719646 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:37:51.794337 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:37:51.799722 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:37:51.811484 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:37:51.90882 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:37:51.914438 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:37:51.965347 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:37:52.006601 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:37:52.018878 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:37:52.060217 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:37:52.129966 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:38:04.471562 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:38:04.556383 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:38:04.640326 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:38:04.665185 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:38:04.705688 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:38:04.823324 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:38:04.828964 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:38:04.840792 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:38:04.936088 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:38:04.941369 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:38:04.989885 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:38:05.028417 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:38:05.039748 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:38:05.079321 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:38:05.147955 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:38:05.348622 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_linear.rds
2025-06-19 00:38:05.409261 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_linear.rds
2025-06-19 00:38:05.471917 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_logistic.rds
2025-06-19 00:38:05.769851 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_logistic.rds
2025-06-19 00:38:22.333077 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:38:22.414004 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:38:22.489527 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:38:22.51202 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:38:22.548615 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:38:22.626526 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:38:22.632059 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:38:22.644139 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:38:22.740674 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:38:22.74628 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:38:22.796359 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:38:22.836197 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:38:22.847888 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:38:22.887475 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:38:22.956433 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:38:34.732231 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:38:34.837955 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:38:34.912457 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:38:34.934319 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:38:34.968902 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:38:35.044337 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:38:35.050024 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:38:35.062505 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:38:35.159719 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:38:35.165284 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:38:35.216961 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:38:35.25855 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:38:35.270708 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:38:35.313683 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:38:35.386894 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:38:35.610665 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_linear.rds
2025-06-19 00:38:35.671722 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_linear.rds
2025-06-19 00:38:35.735175 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/residuals_logistic.rds
2025-06-19 00:38:36.034298 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb113d298fa/fits/fitted_logistic.rds
2025-06-19 00:38:52.614562 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:38:52.691401 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:38:52.767538 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:38:52.790633 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:38:52.825995 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:38:52.902123 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:38:52.907531 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:38:52.919371 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:38:53.016486 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:38:53.022482 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:38:53.074462 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:38:53.116571 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:38:53.128832 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:38:53.170429 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:38:53.244222 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:39:05.091674 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:39:05.172715 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:39:05.249125 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:39:05.271719 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:39:05.338334 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:39:05.416776 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:39:05.422306 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:39:05.434322 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:39:05.53291 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:39:05.538661 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:39:05.588573 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:39:05.629853 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:39:05.641846 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:39:05.681594 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:39:05.751294 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:39:24.573565 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:39:34.680474 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:39:54.783137 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:04.508228 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:05.144613 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_linear.rds
2025-06-19 00:40:05.206399 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_linear.rds
2025-06-19 00:40:05.244958 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_logistic.rds
2025-06-19 00:40:05.31391 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_logistic.rds
2025-06-19 00:40:24.226318 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:29.251671 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:29.596924 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_linear.rds
2025-06-19 00:40:29.660038 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_linear.rds
2025-06-19 00:40:29.699598 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_logistic.rds
2025-06-19 00:40:29.770703 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_logistic.rds
2025-06-19 00:40:45.501864 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:50.790648 WARNING::Fitting problem for feature 124 returning NA
2025-06-19 00:40:51.133678 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_linear.rds
2025-06-19 00:40:51.195926 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_linear.rds
2025-06-19 00:40:51.234412 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_logistic.rds
2025-06-19 00:40:51.304037 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_logistic.rds
2025-06-19 00:41:06.440474 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:41:06.516844 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:41:06.593947 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:41:06.625162 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:41:06.66191 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:41:06.743116 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:41:06.748845 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:41:06.761789 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:41:06.865671 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:41:06.871406 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:41:06.924343 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:41:06.966449 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:41:06.978837 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:41:07.021615 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:41:07.094824 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:41:18.907103 WARNING::Fitting problem for feature 50 returning NA
2025-06-19 00:41:18.982844 WARNING::Fitting problem for feature 62 returning NA
2025-06-19 00:41:19.056701 WARNING::Fitting problem for feature 74 returning NA
2025-06-19 00:41:19.078234 WARNING::Fitting problem for feature 78 returning NA
2025-06-19 00:41:19.112822 WARNING::Fitting problem for feature 84 returning NA
2025-06-19 00:41:19.188701 WARNING::Fitting problem for feature 96 returning NA
2025-06-19 00:41:19.194062 WARNING::Fitting problem for feature 97 returning NA
2025-06-19 00:41:19.20584 WARNING::Fitting problem for feature 99 returning NA
2025-06-19 00:41:19.300861 WARNING::Fitting problem for feature 114 returning NA
2025-06-19 00:41:19.306471 WARNING::Fitting problem for feature 115 returning NA
2025-06-19 00:41:19.357548 WARNING::Fitting problem for feature 123 returning NA
2025-06-19 00:41:19.399358 WARNING::Fitting problem for feature 130 returning NA
2025-06-19 00:41:19.411602 WARNING::Fitting problem for feature 132 returning NA
2025-06-19 00:41:19.453002 WARNING::Fitting problem for feature 139 returning NA
2025-06-19 00:41:19.524206 WARNING::Fitting problem for feature 150 returning NA
2025-06-19 00:41:19.789296 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_linear.rds
2025-06-19 00:41:19.850317 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_linear.rds
2025-06-19 00:41:19.913821 WARNING::Deleting existing residuals file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/residuals_logistic.rds
2025-06-19 00:41:20.212186 WARNING::Deleting existing fitted file: /tmp/RtmptwAD5g/file27feb1f32dbc8/fits/fitted_logistic.rds
2025-06-19 00:41:35.964157 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-06-19 00:41:35.989835 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-06-19 00:41:36.007516 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-06-19 00:41:36.072442 ERROR::No fixed, group, or
ordered effects included in formula.
2025-06-19 00:41:36.088679 ERROR::Effect name not found in metadata: d
2025-06-19 00:41:36.099682 ERROR::No user formula provided
2025-06-19 00:41:36.128412 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-06-19 00:41:36.139981 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-06-19 00:41:39.0208 INFO::Writing function arguments to log file
2025-06-19 00:41:39.034941 INFO::Verifying options selected are valid
2025-06-19 00:41:40.865731 INFO::Writing function arguments to log file
2025-06-19 00:41:40.877502 INFO::Verifying options selected are valid
2025-06-19 00:41:40.878603 INFO::Determining format of input files
2025-06-19 00:41:40.879572 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-19 00:41:40.881878 INFO::Running selected normalization method: TSS
2025-06-19 00:41:40.883326 INFO::Creating output feature tables folder
2025-06-19 00:41:40.884277 INFO::Writing normalized data to file /tmp/RtmptwAD5g/file27feb159b64789/features/data_norm.tsv
2025-06-19 00:41:40.885728 INFO::Filter data based on min abundance and min prevalence
2025-06-19 00:41:40.88662 INFO::Total samples in data: 16
2025-06-19 00:41:40.887471 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-06-19 00:41:40.889277 INFO::Total filtered features: 0
2025-06-19 00:41:40.890218 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-19 00:41:40.891336 INFO::Total features filtered by non-zero variance filtering: 0
2025-06-19 00:41:40.892259 INFO::Filtered feature names from variance filtering:
2025-06-19 00:41:40.893114 INFO::Writing filtered data to file /tmp/RtmptwAD5g/file27feb159b64789/features/filtered_data.tsv
2025-06-19 00:41:40.894581 INFO::Running selected transform method: LOG
2025-06-19 00:41:40.895763 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmptwAD5g/file27feb159b64789/features/data_transformed.tsv
2025-06-19 00:41:40.897401 INFO::Applying z-score to standardize continuous metadata
2025-06-19 00:41:40.90253 INFO::Running the linear model component
2025-06-19 00:41:40.916509 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:40.921089 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:40.925583 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:40.933057 INFO::Counting total values for each feature
2025-06-19 00:41:40.935028 INFO::Running the logistic model component
2025-06-19 00:41:40.949088 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:40.955678 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:40.961885 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:40.97095 INFO::Counting total values for each feature
2025-06-19 00:41:40.973225 INFO::Re-running abundances for warn_prevalence
2025-06-19 00:41:40.974241 INFO::Running selected normalization method: TSS
2025-06-19 00:41:40.975775 INFO::Running selected transform method: LOG
2025-06-19 00:41:40.989683 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:40.994254 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:40.998527 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:41.086363 INFO::Creating fits folder
2025-06-19 00:41:41.087595 INFO::Writing residuals to file /tmp/RtmptwAD5g/file27feb159b64789/fits/residuals_linear.rds
2025-06-19 00:41:41.088793 INFO::Writing fitted values to file /tmp/RtmptwAD5g/file27feb159b64789/fits/fitted_linear.rds
2025-06-19 00:41:41.090055 INFO::Writing residuals to file /tmp/RtmptwAD5g/file27feb159b64789/fits/residuals_logistic.rds
2025-06-19 00:41:41.091279 INFO::Writing fitted values to file /tmp/RtmptwAD5g/file27feb159b64789/fits/fitted_logistic.rds
2025-06-19 00:41:41.093975 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmptwAD5g/file27feb159b64789/all_results.tsv
2025-06-19 00:41:41.095674 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/RtmptwAD5g/file27feb159b64789/significant_results.tsv
2025-06-19 00:41:41.097051 INFO::Creating output figures folder
2025-06-19 00:41:41.098417 INFO::Writing summary plot of significant
results to file: /tmp/RtmptwAD5g/file27feb159b64789/figures/summary_plot.pdf
2025-06-19 00:41:42.35529 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmptwAD5g/file27feb159b64789/figures
2025-06-19 00:41:42.357439 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-19 00:41:42.362694 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-19 00:41:42.750419 INFO::Writing summary plot of
significant results to file: /tmp/RtmptwAD5g/file27feb159b64789/figures/summary_plot.pdf
2025-06-19 00:41:43.998838 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmptwAD5g/file27feb159b64789/figures
2025-06-19 00:41:44.000353 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-19 00:41:44.005061 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-19 00:41:44.390167 INFO::Running the linear model component
2025-06-19 00:41:44.398737 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:44.403136 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:44.407163 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:44.414185 INFO::Counting total values for each feature
2025-06-19 00:41:44.415848 INFO::Running the logistic model component
2025-06-19 00:41:44.424124 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:44.430465 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:44.436213 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:44.444832 INFO::Counting total values for each feature
2025-06-19 00:41:44.446876 INFO::Re-running abundances for warn_prevalence
2025-06-19 00:41:44.44772 INFO::Running selected normalization method: TSS
2025-06-19 00:41:44.449121 INFO::Running selected transform method: LOG
2025-06-19 00:41:44.457438 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:44.461607 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:44.465556 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:44.550228 INFO::Creating output folder
2025-06-19 00:41:44.551191 INFO::Creating output figures folder
2025-06-19 00:41:44.552448 INFO::Writing summary plot of significant
results to file: /tmp/RtmptwAD5g/file27feb167e62ddf/figures/summary_plot.pdf
2025-06-19 00:41:45.790112 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmptwAD5g/file27feb167e62ddf/figures
2025-06-19 00:41:45.791849 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-19 00:41:45.79673 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-19 00:41:46.617306 INFO::Applying z-score to standardize continuous metadata
2025-06-19 00:41:46.624805 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-06-19 00:41:46.62566 INFO::Bypass z-score application to metadata
2025-06-19 00:41:46.628035 INFO::Bypass z-score application to metadata
2025-06-19 00:41:46.644632 INFO::Determining format of input files
2025-06-19 00:41:46.645554 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-19 00:41:46.646381 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-06-19 00:41:46.653025 INFO::Determining format of input files
2025-06-19 00:41:46.65397 INFO::Input format is data samples as columns and metadata samples as rows
2025-06-19 00:41:46.655245 INFO::Input format is feature_specific_covariate samples as columns
2025-06-19 00:41:46.66267 INFO::Determining format of input files
2025-06-19 00:41:46.663537 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-19 00:41:46.66451 INFO::Input format is feature_specific_covariate samples as columns
2025-06-19 00:41:46.666098 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-06-19 00:41:46.66684 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-06-19 00:41:46.676955 INFO::Running selected transform method: LOG
2025-06-19 00:41:46.677977 INFO::Creating output feature tables folder
2025-06-19 00:41:46.678798 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmptwAD5g/file27feb1120782d3/features/data_transformed.tsv
2025-06-19 00:41:46.682356 INFO::Running selected transform method: LOG
2025-06-19 00:41:46.683322 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmptwAD5g/file27feb1120782d3/features/data_transformed.tsv
2025-06-19 00:41:46.687006 INFO::Running selected transform method: PLOG
2025-06-19 00:41:46.688533 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmptwAD5g/file27feb1120782d3/features/data_transformed.tsv
2025-06-19 00:41:46.691126 INFO::Running selected transform method: NONE
2025-06-19 00:41:46.691842 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmptwAD5g/file27feb1120782d3/features/data_transformed.tsv
2025-06-19 00:41:46.698472 INFO::Running the linear model component
2025-06-19 00:41:46.706692 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:46.710823 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:46.714721 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:46.721532 INFO::Counting total values for each feature
2025-06-19 00:41:46.723102 INFO::Running the logistic model component
2025-06-19 00:41:46.731197 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:46.737095 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:46.742766 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:46.751238 INFO::Counting total values for each feature
2025-06-19 00:41:46.75313 INFO::Re-running abundances for warn_prevalence
2025-06-19 00:41:46.753864 INFO::Running selected normalization method: TSS
2025-06-19 00:41:46.755171 INFO::Running selected transform method: LOG
2025-06-19 00:41:46.763498 INFO::Fitting model to feature number 1, a
2025-06-19 00:41:46.767562 INFO::Fitting model to feature number 2, b
2025-06-19 00:41:46.771401 INFO::Fitting model to feature number 3, c
2025-06-19 00:41:46.856158 INFO::Creating output folder
2025-06-19 00:41:46.857167 INFO::Creating fits folder
2025-06-19 00:41:46.857991 INFO::Writing residuals to file /tmp/RtmptwAD5g/file27feb176923d81/fits/residuals_linear.rds
2025-06-19 00:41:46.858979 INFO::Writing fitted values to file /tmp/RtmptwAD5g/file27feb176923d81/fits/fitted_linear.rds
2025-06-19 00:41:46.860055 INFO::Writing residuals to file /tmp/RtmptwAD5g/file27feb176923d81/fits/residuals_logistic.rds
2025-06-19 00:41:46.861108 INFO::Writing fitted values to file /tmp/RtmptwAD5g/file27feb176923d81/fits/fitted_logistic.rds
2025-06-19 00:41:46.863614 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmptwAD5g/file27feb176923d81/all_results.tsv
2025-06-19 00:41:46.865126 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/RtmptwAD5g/file27feb176923d81/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
309.982 4.217 314.199
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.675 | 0.658 | 21.336 | |
| maaslin_check_arguments | 0.127 | 0.000 | 0.127 | |
| maaslin_check_formula | 0.137 | 0.001 | 0.138 | |
| maaslin_compute_formula | 0.140 | 0.001 | 0.141 | |
| maaslin_contrast_test | 16.704 | 0.436 | 17.141 | |
| maaslin_filter | 0.489 | 0.006 | 0.496 | |
| maaslin_fit | 12.519 | 0.116 | 12.635 | |
| maaslin_log_arguments | 0.126 | 0.001 | 0.128 | |
| maaslin_normalize | 0.262 | 0.002 | 0.264 | |
| maaslin_plot_results | 35.695 | 0.286 | 35.946 | |
| maaslin_plot_results_from_output | 36.085 | 0.361 | 36.452 | |
| maaslin_process_metadata | 0.460 | 0.011 | 0.472 | |
| maaslin_read_data | 0.129 | 0.002 | 0.131 | |
| maaslin_reorder_data | 0.131 | 0.003 | 0.133 | |
| maaslin_transform | 0.529 | 0.023 | 0.551 | |
| maaslin_write_results | 12.715 | 0.174 | 12.889 | |
| maaslin_write_results_lefse_format | 14.935 | 0.116 | 15.052 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.005 | |