William Nickols
| Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: e862fe9 |
| git_last_commit_date: 2025-03-17 23:20:44 -0400 (Mon, 17 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-19 11:41 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1142/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.13 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 0.99.13 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.13.tar.gz |
| StartedAt: 2025-03-18 23:33:23 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 23:52:49 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 1165.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.13.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘0.99.13’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 35.654 0.347 36.011
maaslin_plot_results 35.323 0.434 35.714
maaslin3 19.444 0.625 20.073
maaslin_contrast_test 18.263 0.439 18.703
maaslin_write_results 14.334 0.192 14.526
maaslin_write_results_lefse_format 13.764 0.113 13.879
maaslin_fit 12.839 0.263 13.102
* 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-3.21-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘0.99.13’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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")
2025-03-18 23:39:19.078923 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:39:19.154401 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:39:19.237921 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:39:19.259362 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:39:19.302513 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:39:19.38149 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:39:19.389094 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:39:19.40257 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:39:19.504026 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:39:19.509335 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:39:19.558231 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:39:19.598105 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:39:19.609771 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:39:19.649297 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:39:19.724541 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:39:35.289925 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:39:35.36744 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:39:35.443549 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:39:35.464973 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:39:35.50042 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:39:35.584399 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:39:35.59038 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:39:35.603756 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:39:35.723163 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:39:35.729809 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:39:35.800373 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:39:35.842833 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:39:35.855049 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:39:35.895926 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:39:35.965955 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:39:54.506876 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:39:54.640742 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:39:54.718454 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:39:54.741115 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:39:54.778574 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:39:54.853976 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:39:54.859577 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:39:54.871378 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:39:54.96669 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:39:54.972285 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:39:55.025523 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:39:55.924052 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:39:55.935719 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:39:55.975636 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:39:56.043736 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:40:08.499522 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:40:08.575746 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:40:08.649133 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:40:08.670825 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:40:08.70536 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:40:08.782883 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:40:08.788323 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:40:08.800455 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:40:08.927306 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:40:08.934172 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:40:08.988025 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:40:09.030207 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:40:09.043396 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:40:09.087342 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:40:09.161616 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:40:09.3752 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_linear.rds
2025-03-18 23:40:09.435525 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_linear.rds
2025-03-18 23:40:09.497989 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_logistic.rds
2025-03-18 23:40:09.805657 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_logistic.rds
2025-03-18 23:40:26.814433 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:40:26.892131 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:40:26.970007 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:40:26.992685 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:40:27.027953 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:40:27.106027 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:40:27.111751 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:40:27.123983 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:40:27.221693 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:40:27.227288 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:40:27.279363 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:40:27.32098 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:40:27.333386 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:40:27.37717 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:40:27.455107 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:40:40.495008 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:40:40.572769 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:40:40.651043 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:40:40.673889 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:40:40.709974 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:40:40.797963 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:40:40.803771 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:40:40.815788 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:40:40.912488 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:40:40.917934 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:40:40.967711 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:40:41.008224 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:40:41.020497 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:40:41.061954 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:40:41.134617 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:40:41.361198 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_linear.rds
2025-03-18 23:40:41.422608 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_linear.rds
2025-03-18 23:40:41.48629 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_logistic.rds
2025-03-18 23:40:41.785815 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_logistic.rds
2025-03-18 23:40:58.667638 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:40:58.749226 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:40:58.826108 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:40:58.848542 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:40:58.883615 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:40:58.959893 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:40:58.965277 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:40:58.977095 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:40:59.073811 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:40:59.0795 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:40:59.131222 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:40:59.173634 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:40:59.186034 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:40:59.227773 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:40:59.303609 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:41:11.351489 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:41:11.430444 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:41:11.511324 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:41:11.534383 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:41:11.569939 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:41:11.645923 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:41:11.65135 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:41:11.663296 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:41:11.760808 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:41:11.766779 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:41:11.820007 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:41:11.862079 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:41:11.874842 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:41:11.918985 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:41:11.992286 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:41:12.206147 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_linear.rds
2025-03-18 23:41:12.267732 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_linear.rds
2025-03-18 23:41:12.331947 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/residuals_logistic.rds
2025-03-18 23:41:12.634338 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file27171836a88a76/fits/fitted_logistic.rds
2025-03-18 23:41:29.15881 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:41:29.238846 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:41:29.321257 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:41:29.345286 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:41:29.382113 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:41:29.465275 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:41:29.471163 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:41:29.484836 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:41:29.58438 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:41:29.590001 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:41:29.64199 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:41:29.683784 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:41:29.696435 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:41:29.738589 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:41:29.811975 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:41:41.478434 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:41:41.554809 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:41:41.629851 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:41:41.651953 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:41:41.686424 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:41:41.763307 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:41:41.768906 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:41:41.78125 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:41:41.87781 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:41:41.883602 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:41:41.935223 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:41:41.979044 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:41:41.991529 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:41:42.033157 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:41:42.107038 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:42:01.029959 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:42:10.866943 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:42:30.920166 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:42:40.610964 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:42:41.242269 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_linear.rds
2025-03-18 23:42:41.303599 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_linear.rds
2025-03-18 23:42:41.342247 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_logistic.rds
2025-03-18 23:42:41.410937 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_logistic.rds
2025-03-18 23:43:00.335306 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:43:05.536759 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:43:05.8686 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_linear.rds
2025-03-18 23:43:05.930347 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_linear.rds
2025-03-18 23:43:05.969263 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_logistic.rds
2025-03-18 23:43:06.038505 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_logistic.rds
2025-03-18 23:43:20.986415 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:43:27.131243 WARNING::Fitting problem for feature 124 returning NA
2025-03-18 23:43:27.448512 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_linear.rds
2025-03-18 23:43:27.510036 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_linear.rds
2025-03-18 23:43:27.548841 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_logistic.rds
2025-03-18 23:43:27.617984 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_logistic.rds
2025-03-18 23:43:42.541234 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:43:42.622988 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:43:42.701195 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:43:42.723613 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:43:42.758605 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:43:42.860143 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:43:42.865579 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:43:42.877545 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:43:42.976175 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:43:42.981856 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:43:43.033203 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:43:43.07421 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:43:43.086939 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:43:43.128471 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:43:43.197671 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:43:55.034055 WARNING::Fitting problem for feature 50 returning NA
2025-03-18 23:43:55.112989 WARNING::Fitting problem for feature 62 returning NA
2025-03-18 23:43:55.189665 WARNING::Fitting problem for feature 74 returning NA
2025-03-18 23:43:55.212015 WARNING::Fitting problem for feature 78 returning NA
2025-03-18 23:43:55.284794 WARNING::Fitting problem for feature 84 returning NA
2025-03-18 23:43:55.367203 WARNING::Fitting problem for feature 96 returning NA
2025-03-18 23:43:55.372962 WARNING::Fitting problem for feature 97 returning NA
2025-03-18 23:43:55.385597 WARNING::Fitting problem for feature 99 returning NA
2025-03-18 23:43:55.48454 WARNING::Fitting problem for feature 114 returning NA
2025-03-18 23:43:55.490266 WARNING::Fitting problem for feature 115 returning NA
2025-03-18 23:43:55.541371 WARNING::Fitting problem for feature 123 returning NA
2025-03-18 23:43:55.583689 WARNING::Fitting problem for feature 130 returning NA
2025-03-18 23:43:55.596353 WARNING::Fitting problem for feature 132 returning NA
2025-03-18 23:43:55.638282 WARNING::Fitting problem for feature 139 returning NA
2025-03-18 23:43:55.709291 WARNING::Fitting problem for feature 150 returning NA
2025-03-18 23:43:55.960541 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_linear.rds
2025-03-18 23:43:56.021436 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_linear.rds
2025-03-18 23:43:56.084849 WARNING::Deleting existing residuals file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/residuals_logistic.rds
2025-03-18 23:43:56.38318 WARNING::Deleting existing fitted file: /tmp/RtmpV8rQ6c/file2717189a99e88/fits/fitted_logistic.rds
2025-03-18 23:44:13.008572 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-03-18 23:44:13.02506 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-03-18 23:44:13.03626 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-03-18 23:44:13.085936 ERROR::No fixed, group, or
ordered effects included in formula.
2025-03-18 23:44:13.102065 ERROR::Effect name not found in metadata: d
2025-03-18 23:44:13.1131 ERROR::No user formula provided
2025-03-18 23:44:13.141923 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-03-18 23:44:13.153321 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-03-18 23:44:16.092063 INFO::Writing function arguments to log file
2025-03-18 23:44:16.105448 INFO::Verifying options selected are valid
2025-03-18 23:44:17.935757 INFO::Writing function arguments to log file
2025-03-18 23:44:17.946768 INFO::Verifying options selected are valid
2025-03-18 23:44:17.947795 INFO::Determining format of input files
2025-03-18 23:44:17.948732 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 23:44:17.950934 INFO::Running selected normalization method: TSS
2025-03-18 23:44:17.952316 INFO::Creating output feature tables folder
2025-03-18 23:44:17.953249 INFO::Writing normalized data to file /tmp/RtmpV8rQ6c/file2717181440e429/features/data_norm.tsv
2025-03-18 23:44:17.954645 INFO::Filter data based on min abundance and min prevalence
2025-03-18 23:44:17.955536 INFO::Total samples in data: 16
2025-03-18 23:44:17.956371 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-03-18 23:44:17.958127 INFO::Total filtered features: 0
2025-03-18 23:44:17.95904 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 23:44:17.960133 INFO::Total features filtered by non-zero variance filtering: 0
2025-03-18 23:44:17.961032 INFO::Filtered feature names from variance filtering:
2025-03-18 23:44:17.961895 INFO::Writing filtered data to file /tmp/RtmpV8rQ6c/file2717181440e429/features/filtered_data.tsv
2025-03-18 23:44:17.963278 INFO::Running selected transform method: LOG
2025-03-18 23:44:17.964403 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpV8rQ6c/file2717181440e429/features/data_transformed.tsv
2025-03-18 23:44:17.96594 INFO::Applying z-score to standardize continuous metadata
2025-03-18 23:44:17.970893 INFO::Running the linear model component
2025-03-18 23:44:17.987251 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:17.991504 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:17.995532 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:18.00236 INFO::Counting total values for each feature
2025-03-18 23:44:18.004115 INFO::Running the logistic model component
2025-03-18 23:44:18.020651 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:18.02697 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:18.032898 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:18.041624 INFO::Counting total values for each feature
2025-03-18 23:44:18.043744 INFO::Re-running abundances for warn_prevalence
2025-03-18 23:44:18.044662 INFO::Running selected normalization method: TSS
2025-03-18 23:44:18.046139 INFO::Running selected transform method: LOG
2025-03-18 23:44:18.062827 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:18.067244 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:18.071439 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:18.153245 INFO::Creating fits folder
2025-03-18 23:44:18.154492 INFO::Writing residuals to file /tmp/RtmpV8rQ6c/file2717181440e429/fits/residuals_linear.rds
2025-03-18 23:44:18.155616 INFO::Writing fitted values to file /tmp/RtmpV8rQ6c/file2717181440e429/fits/fitted_linear.rds
2025-03-18 23:44:18.156792 INFO::Writing residuals to file /tmp/RtmpV8rQ6c/file2717181440e429/fits/residuals_logistic.rds
2025-03-18 23:44:18.157956 INFO::Writing fitted values to file /tmp/RtmpV8rQ6c/file2717181440e429/fits/fitted_logistic.rds
2025-03-18 23:44:18.160486 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpV8rQ6c/file2717181440e429/all_results.tsv
2025-03-18 23:44:18.162045 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/RtmpV8rQ6c/file2717181440e429/significant_results.tsv
2025-03-18 23:44:18.163327 INFO::Creating output figures folder
2025-03-18 23:44:18.164661 INFO::Writing summary plot of significant
results to file: /tmp/RtmpV8rQ6c/file2717181440e429/figures/summary_plot.pdf
2025-03-18 23:44:19.367473 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpV8rQ6c/file2717181440e429/figures
2025-03-18 23:44:19.369473 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 23:44:19.374714 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 23:44:19.769779 INFO::Writing summary plot of
significant results to file: /tmp/RtmpV8rQ6c/file2717181440e429/figures/summary_plot.pdf
2025-03-18 23:44:20.988081 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpV8rQ6c/file2717181440e429/figures
2025-03-18 23:44:20.989634 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 23:44:20.994598 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 23:44:21.386841 INFO::Running the linear model component
2025-03-18 23:44:21.398616 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:21.403131 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:21.407058 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:21.413837 INFO::Counting total values for each feature
2025-03-18 23:44:21.415526 INFO::Running the logistic model component
2025-03-18 23:44:21.426997 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:21.433393 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:21.439274 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:21.447936 INFO::Counting total values for each feature
2025-03-18 23:44:21.449975 INFO::Re-running abundances for warn_prevalence
2025-03-18 23:44:21.450768 INFO::Running selected normalization method: TSS
2025-03-18 23:44:21.452109 INFO::Running selected transform method: LOG
2025-03-18 23:44:21.463739 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:21.468246 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:21.472224 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:21.573626 INFO::Creating output folder
2025-03-18 23:44:21.574593 INFO::Creating output figures folder
2025-03-18 23:44:21.575783 INFO::Writing summary plot of significant
results to file: /tmp/RtmpV8rQ6c/file2717182c5ec284/figures/summary_plot.pdf
2025-03-18 23:44:22.786588 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpV8rQ6c/file2717182c5ec284/figures
2025-03-18 23:44:22.788313 INFO::Plotting associations from most to least significant, grouped by metadata
2025-03-18 23:44:22.793212 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-03-18 23:44:23.594099 INFO::Applying z-score to standardize continuous metadata
2025-03-18 23:44:23.601707 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-03-18 23:44:23.602605 INFO::Bypass z-score application to metadata
2025-03-18 23:44:23.605042 INFO::Bypass z-score application to metadata
2025-03-18 23:44:23.622129 INFO::Determining format of input files
2025-03-18 23:44:23.623092 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 23:44:23.623961 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-03-18 23:44:23.630661 INFO::Determining format of input files
2025-03-18 23:44:23.631682 INFO::Input format is data samples as columns and metadata samples as rows
2025-03-18 23:44:23.632984 INFO::Input format is feature_specific_covariate samples as columns
2025-03-18 23:44:23.640526 INFO::Determining format of input files
2025-03-18 23:44:23.641426 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 23:44:23.642412 INFO::Input format is feature_specific_covariate samples as columns
2025-03-18 23:44:23.644051 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-03-18 23:44:23.644802 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-03-18 23:44:23.655064 INFO::Running selected transform method: LOG
2025-03-18 23:44:23.656193 INFO::Creating output feature tables folder
2025-03-18 23:44:23.657073 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpV8rQ6c/file27171860c39d47/features/data_transformed.tsv
2025-03-18 23:44:23.660814 INFO::Running selected transform method: LOG
2025-03-18 23:44:23.661827 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpV8rQ6c/file27171860c39d47/features/data_transformed.tsv
2025-03-18 23:44:23.665348 INFO::Running selected transform method: PLOG
2025-03-18 23:44:23.666857 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpV8rQ6c/file27171860c39d47/features/data_transformed.tsv
2025-03-18 23:44:23.669559 INFO::Running selected transform method: NONE
2025-03-18 23:44:23.670287 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpV8rQ6c/file27171860c39d47/features/data_transformed.tsv
2025-03-18 23:44:23.67704 INFO::Running the linear model component
2025-03-18 23:44:23.688525 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:23.693102 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:23.697066 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:23.704258 INFO::Counting total values for each feature
2025-03-18 23:44:23.705968 INFO::Running the logistic model component
2025-03-18 23:44:23.717784 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:23.724339 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:23.730116 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:23.739047 INFO::Counting total values for each feature
2025-03-18 23:44:23.741101 INFO::Re-running abundances for warn_prevalence
2025-03-18 23:44:23.741968 INFO::Running selected normalization method: TSS
2025-03-18 23:44:23.743307 INFO::Running selected transform method: LOG
2025-03-18 23:44:23.755043 INFO::Fitting model to feature number 1, a
2025-03-18 23:44:23.759526 INFO::Fitting model to feature number 2, b
2025-03-18 23:44:23.763438 INFO::Fitting model to feature number 3, c
2025-03-18 23:44:23.848242 INFO::Creating output folder
2025-03-18 23:44:23.849206 INFO::Creating fits folder
2025-03-18 23:44:23.850042 INFO::Writing residuals to file /tmp/RtmpV8rQ6c/file27171828db2085/fits/residuals_linear.rds
2025-03-18 23:44:23.850971 INFO::Writing fitted values to file /tmp/RtmpV8rQ6c/file27171828db2085/fits/fitted_linear.rds
2025-03-18 23:44:23.852012 INFO::Writing residuals to file /tmp/RtmpV8rQ6c/file27171828db2085/fits/residuals_logistic.rds
2025-03-18 23:44:23.85302 INFO::Writing fitted values to file /tmp/RtmpV8rQ6c/file27171828db2085/fits/fitted_logistic.rds
2025-03-18 23:44:23.855531 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpV8rQ6c/file27171828db2085/all_results.tsv
2025-03-18 23:44:23.85704 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/RtmpV8rQ6c/file27171828db2085/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
311.088 5.584 316.671
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.444 | 0.625 | 20.073 | |
| maaslin_check_arguments | 0.134 | 0.007 | 0.142 | |
| maaslin_check_formula | 0.136 | 0.004 | 0.141 | |
| maaslin_compute_formula | 0.137 | 0.007 | 0.144 | |
| maaslin_contrast_test | 18.263 | 0.439 | 18.703 | |
| maaslin_filter | 0.414 | 0.010 | 0.424 | |
| maaslin_fit | 12.839 | 0.263 | 13.102 | |
| maaslin_log_arguments | 0.123 | 0.004 | 0.127 | |
| maaslin_normalize | 0.258 | 0.009 | 0.267 | |
| maaslin_plot_results | 35.323 | 0.434 | 35.714 | |
| maaslin_plot_results_from_output | 35.654 | 0.347 | 36.011 | |
| maaslin_process_metadata | 0.446 | 0.024 | 0.470 | |
| maaslin_read_data | 0.144 | 0.002 | 0.146 | |
| maaslin_reorder_data | 0.142 | 0.003 | 0.145 | |
| maaslin_transform | 0.568 | 0.017 | 0.585 | |
| maaslin_write_results | 14.334 | 0.192 | 14.526 | |
| maaslin_write_results_lefse_format | 13.764 | 0.113 | 13.879 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.001 | 0.004 | |