William Nickols
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 1149/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-01 00:41:16 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 01:02:58 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 1301.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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 42.944 0.471 43.416
maaslin_plot_results 42.819 0.381 43.158
maaslin3 20.885 0.803 21.693
maaslin_contrast_test 18.574 0.488 19.066
maaslin_write_results_lefse_format 14.819 0.100 14.919
maaslin_write_results 13.377 0.142 13.519
maaslin_fit 12.489 0.211 12.701
* 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-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "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")
2025-11-01 00:47:27.162283 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:47:27.236064 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:47:28.017894 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:47:28.039259 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:47:28.074394 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:47:28.162311 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:47:28.168148 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:47:28.181146 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:47:28.289381 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:47:28.294757 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:47:28.343019 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:47:28.382959 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:47:28.395298 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:47:28.43486 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:47:28.513151 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:47:43.980709 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:47:44.0581 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:47:44.131939 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:47:44.153504 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:47:44.188379 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:47:44.263229 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:47:44.268495 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:47:44.280204 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:47:44.373422 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:47:44.378642 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:47:44.427598 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:47:44.467243 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:47:44.479129 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:47:44.519337 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:47:44.590625 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:48:07.861217 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:48:07.939301 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:48:08.017174 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:48:08.040036 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:48:08.075608 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:48:08.152631 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:48:08.158309 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:48:08.170724 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:48:09.255584 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:48:09.261305 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:48:09.313123 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:48:09.353243 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:48:09.364725 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:48:09.404053 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:48:09.472738 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:48:22.35835 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:48:22.455544 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:48:22.531152 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:48:22.552711 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:48:22.587347 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:48:22.665512 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:48:22.671594 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:48:22.684035 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:48:22.777397 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:48:22.782728 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:48:22.831465 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:48:22.871177 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:48:22.883214 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:48:22.924154 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:48:22.991949 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:48:23.20525 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_linear.rds
2025-11-01 00:48:23.266102 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_linear.rds
2025-11-01 00:48:23.328867 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_logistic.rds
2025-11-01 00:48:23.628577 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_logistic.rds
2025-11-01 00:48:45.190014 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:48:45.265738 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:48:45.340339 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:48:45.362132 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:48:45.395969 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:48:45.471329 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:48:45.476859 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:48:45.488992 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:48:45.585852 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:48:45.591527 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:48:45.641351 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:48:45.681646 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:48:45.693729 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:48:45.73565 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:48:45.827763 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:48:58.61512 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:48:58.690405 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:48:58.765856 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:48:58.787537 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:48:58.821744 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:48:58.925266 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:48:58.930775 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:48:58.942702 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:48:59.039452 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:48:59.04495 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:48:59.095673 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:48:59.13652 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:48:59.148592 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:48:59.188961 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:48:59.259238 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:48:59.467832 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_linear.rds
2025-11-01 00:48:59.528884 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_linear.rds
2025-11-01 00:48:59.591922 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_logistic.rds
2025-11-01 00:48:59.892369 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_logistic.rds
2025-11-01 00:49:21.156035 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:49:21.231324 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:49:21.308884 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:49:21.331342 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:49:21.366917 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:49:21.443837 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:49:21.449077 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:49:21.460689 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:49:21.557749 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:49:21.563191 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:49:21.612989 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:49:21.654036 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:49:21.666223 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:49:21.707973 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:49:21.785774 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:49:34.005007 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:49:34.091519 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:49:34.177179 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:49:34.201275 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:49:34.239911 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:49:34.325952 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:49:34.332462 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:49:34.346066 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:49:34.453835 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:49:34.459817 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:49:34.510035 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:49:34.550501 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:49:34.562959 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:49:34.604366 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:49:34.673145 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:49:34.877669 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_linear.rds
2025-11-01 00:49:34.938816 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_linear.rds
2025-11-01 00:49:35.001666 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/residuals_logistic.rds
2025-11-01 00:49:35.301212 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a307c03e199/fits/fitted_logistic.rds
2025-11-01 00:49:56.829832 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:49:56.911514 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:49:56.994541 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:49:57.018375 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:49:57.059475 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:49:57.146148 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:49:57.152569 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:49:57.167162 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:49:57.273243 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:49:57.279283 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:49:57.333759 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:49:57.377874 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:49:57.390223 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:49:57.433211 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:49:57.507963 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:50:09.727337 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:50:09.807469 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:50:09.886107 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:50:09.910578 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:50:09.94886 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:50:10.030775 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:50:10.036487 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:50:10.048702 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:50:10.184038 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:50:10.190332 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:50:10.247683 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:50:10.294942 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:50:10.308659 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:50:10.352402 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:50:10.425706 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:50:35.229728 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:50:45.07741 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:51:10.819333 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:51:20.513007 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:51:21.126062 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_linear.rds
2025-11-01 00:51:21.191414 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_linear.rds
2025-11-01 00:51:21.23414 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_logistic.rds
2025-11-01 00:51:21.30332 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_logistic.rds
2025-11-01 00:51:43.620936 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:51:50.007806 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:51:50.309988 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_linear.rds
2025-11-01 00:51:50.371535 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_linear.rds
2025-11-01 00:51:50.410011 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_logistic.rds
2025-11-01 00:51:50.480992 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_logistic.rds
2025-11-01 00:52:09.052037 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:52:15.167379 WARNING::Fitting problem for feature 124 returning NA
2025-11-01 00:52:15.463723 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_linear.rds
2025-11-01 00:52:15.525206 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_linear.rds
2025-11-01 00:52:15.56412 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_logistic.rds
2025-11-01 00:52:15.63439 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_logistic.rds
2025-11-01 00:52:33.691496 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:52:33.769947 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:52:33.849656 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:52:33.873507 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:52:33.910565 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:52:33.99611 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:52:34.001918 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:52:34.042815 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:52:34.143971 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:52:34.150277 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:52:34.20399 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:52:34.24832 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:52:34.261887 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:52:34.309033 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:52:34.383507 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:52:46.443873 WARNING::Fitting problem for feature 50 returning NA
2025-11-01 00:52:46.523115 WARNING::Fitting problem for feature 62 returning NA
2025-11-01 00:52:46.633579 WARNING::Fitting problem for feature 74 returning NA
2025-11-01 00:52:46.656648 WARNING::Fitting problem for feature 78 returning NA
2025-11-01 00:52:46.691977 WARNING::Fitting problem for feature 84 returning NA
2025-11-01 00:52:46.770722 WARNING::Fitting problem for feature 96 returning NA
2025-11-01 00:52:46.77623 WARNING::Fitting problem for feature 97 returning NA
2025-11-01 00:52:46.788382 WARNING::Fitting problem for feature 99 returning NA
2025-11-01 00:52:46.886997 WARNING::Fitting problem for feature 114 returning NA
2025-11-01 00:52:46.892627 WARNING::Fitting problem for feature 115 returning NA
2025-11-01 00:52:46.942388 WARNING::Fitting problem for feature 123 returning NA
2025-11-01 00:52:46.982395 WARNING::Fitting problem for feature 130 returning NA
2025-11-01 00:52:46.993856 WARNING::Fitting problem for feature 132 returning NA
2025-11-01 00:52:47.032559 WARNING::Fitting problem for feature 139 returning NA
2025-11-01 00:52:47.098827 WARNING::Fitting problem for feature 150 returning NA
2025-11-01 00:52:47.371733 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_linear.rds
2025-11-01 00:52:47.438477 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_linear.rds
2025-11-01 00:52:47.513608 WARNING::Deleting existing residuals file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/residuals_logistic.rds
2025-11-01 00:52:47.812004 WARNING::Deleting existing fitted file: /tmp/Rtmp3VvdSr/file159a304998ba9/fits/fitted_logistic.rds
2025-11-01 00:53:08.024702 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-01 00:53:08.041251 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-01 00:53:08.052486 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-01 00:53:08.101084 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-01 00:53:08.116558 ERROR::Effect name not found in metadata: d
2025-11-01 00:53:08.127127 ERROR::No user formula provided
2025-11-01 00:53:08.155368 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-01 00:53:08.166604 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-01 00:53:11.246271 INFO::Writing function arguments to log file
2025-11-01 00:53:11.260448 INFO::Verifying options selected are valid
2025-11-01 00:53:13.702684 INFO::Writing function arguments to log file
2025-11-01 00:53:13.714996 INFO::Verifying options selected are valid
2025-11-01 00:53:13.716114 INFO::Determining format of input files
2025-11-01 00:53:13.717132 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-01 00:53:13.719736 INFO::Running selected normalization method: TSS
2025-11-01 00:53:13.72143 INFO::Creating output feature tables folder
2025-11-01 00:53:13.722509 INFO::Writing normalized data to file /tmp/Rtmp3VvdSr/file159a309df1539/features/data_norm.tsv
2025-11-01 00:53:13.724288 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-01 00:53:13.725291 INFO::Total samples in data: 16
2025-11-01 00:53:13.726313 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-01 00:53:13.727308 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-01 00:53:13.729784 INFO::Total filtered features: 0
2025-11-01 00:53:13.730872 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-01 00:53:13.732241 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-01 00:53:13.733289 INFO::Filtered feature names from variance filtering:
2025-11-01 00:53:13.734302 INFO::Writing filtered data to file /tmp/Rtmp3VvdSr/file159a309df1539/features/filtered_data.tsv
2025-11-01 00:53:13.736065 INFO::Running selected transform method: LOG
2025-11-01 00:53:13.737386 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3VvdSr/file159a309df1539/features/data_transformed.tsv
2025-11-01 00:53:13.739319 INFO::Applying z-score to standardize continuous metadata
2025-11-01 00:53:13.745966 INFO::Running the linear model component
2025-11-01 00:53:13.76106 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:13.766421 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:13.771215 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:13.779146 INFO::Counting total values for each feature
2025-11-01 00:53:13.78107 INFO::Running the logistic model component
2025-11-01 00:53:13.79527 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:13.802719 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:13.809688 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:13.819711 INFO::Counting total values for each feature
2025-11-01 00:53:13.822223 INFO::Re-running abundances for warn_prevalence
2025-11-01 00:53:13.823321 INFO::Running selected normalization method: TSS
2025-11-01 00:53:13.825144 INFO::Running selected transform method: LOG
2025-11-01 00:53:13.840196 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:13.845001 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:13.849517 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:13.938905 INFO::Creating fits folder
2025-11-01 00:53:13.94023 INFO::Writing residuals to file /tmp/Rtmp3VvdSr/file159a309df1539/fits/residuals_linear.rds
2025-11-01 00:53:13.941418 INFO::Writing fitted values to file /tmp/Rtmp3VvdSr/file159a309df1539/fits/fitted_linear.rds
2025-11-01 00:53:13.942727 INFO::Writing residuals to file /tmp/Rtmp3VvdSr/file159a309df1539/fits/residuals_logistic.rds
2025-11-01 00:53:13.944006 INFO::Writing fitted values to file /tmp/Rtmp3VvdSr/file159a309df1539/fits/fitted_logistic.rds
2025-11-01 00:53:13.946769 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp3VvdSr/file159a309df1539/all_results.tsv
2025-11-01 00:53:13.948451 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/Rtmp3VvdSr/file159a309df1539/significant_results.tsv
2025-11-01 00:53:13.949855 INFO::Creating output figures folder
2025-11-01 00:53:13.951267 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp3VvdSr/file159a309df1539/figures/summary_plot.pdf
2025-11-01 00:53:15.537487 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3VvdSr/file159a309df1539/figures
2025-11-01 00:53:15.539771 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-01 00:53:15.545217 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-01 00:53:16.074348 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp3VvdSr/file159a309df1539/figures/summary_plot.pdf
2025-11-01 00:53:17.687362 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3VvdSr/file159a309df1539/figures
2025-11-01 00:53:17.688934 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-01 00:53:17.693629 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-01 00:53:18.215476 INFO::Running the linear model component
2025-11-01 00:53:18.237393 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:18.243799 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:18.248952 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:18.256528 INFO::Counting total values for each feature
2025-11-01 00:53:18.258301 INFO::Running the logistic model component
2025-11-01 00:53:18.267065 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:18.273399 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:18.279095 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:18.287626 INFO::Counting total values for each feature
2025-11-01 00:53:18.289666 INFO::Re-running abundances for warn_prevalence
2025-11-01 00:53:18.2905 INFO::Running selected normalization method: TSS
2025-11-01 00:53:18.291932 INFO::Running selected transform method: LOG
2025-11-01 00:53:18.300504 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:18.30467 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:18.308577 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:18.394954 INFO::Creating output folder
2025-11-01 00:53:18.39598 INFO::Creating output figures folder
2025-11-01 00:53:18.397265 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp3VvdSr/file159a305bb91a1b/figures/summary_plot.pdf
2025-11-01 00:53:19.967033 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3VvdSr/file159a305bb91a1b/figures
2025-11-01 00:53:19.969014 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-01 00:53:19.974183 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-01 00:53:20.943698 INFO::Applying z-score to standardize continuous metadata
2025-11-01 00:53:20.95193 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-01 00:53:20.952837 INFO::Bypass z-score application to metadata
2025-11-01 00:53:20.955405 INFO::Bypass z-score application to metadata
2025-11-01 00:53:20.973407 INFO::Determining format of input files
2025-11-01 00:53:20.974428 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-01 00:53:20.975358 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-01 00:53:20.982506 INFO::Determining format of input files
2025-11-01 00:53:20.983591 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-01 00:53:20.984927 INFO::Input format is feature_specific_covariate samples as columns
2025-11-01 00:53:20.99266 INFO::Determining format of input files
2025-11-01 00:53:20.993596 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-01 00:53:20.994643 INFO::Input format is feature_specific_covariate samples as columns
2025-11-01 00:53:20.996296 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-01 00:53:20.997061 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-01 00:53:21.00761 INFO::Running selected transform method: LOG
2025-11-01 00:53:21.008803 INFO::Creating output feature tables folder
2025-11-01 00:53:21.009695 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3VvdSr/file159a3020fe38c7/features/data_transformed.tsv
2025-11-01 00:53:21.01354 INFO::Running selected transform method: LOG
2025-11-01 00:53:21.014627 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3VvdSr/file159a3020fe38c7/features/data_transformed.tsv
2025-11-01 00:53:21.018268 INFO::Running selected transform method: PLOG
2025-11-01 00:53:21.019891 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3VvdSr/file159a3020fe38c7/features/data_transformed.tsv
2025-11-01 00:53:21.022662 INFO::Running selected transform method: NONE
2025-11-01 00:53:21.023429 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3VvdSr/file159a3020fe38c7/features/data_transformed.tsv
2025-11-01 00:53:21.030787 INFO::Running the linear model component
2025-11-01 00:53:21.039543 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:21.043835 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:21.047831 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:21.054858 INFO::Counting total values for each feature
2025-11-01 00:53:21.056535 INFO::Running the logistic model component
2025-11-01 00:53:21.079197 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:21.087691 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:21.094248 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:21.102921 INFO::Counting total values for each feature
2025-11-01 00:53:21.105027 INFO::Re-running abundances for warn_prevalence
2025-11-01 00:53:21.105812 INFO::Running selected normalization method: TSS
2025-11-01 00:53:21.107183 INFO::Running selected transform method: LOG
2025-11-01 00:53:21.115981 INFO::Fitting model to feature number 1, a
2025-11-01 00:53:21.120249 INFO::Fitting model to feature number 2, b
2025-11-01 00:53:21.124247 INFO::Fitting model to feature number 3, c
2025-11-01 00:53:21.211115 INFO::Creating output folder
2025-11-01 00:53:21.21207 INFO::Creating fits folder
2025-11-01 00:53:21.2129 INFO::Writing residuals to file /tmp/Rtmp3VvdSr/file159a308354bd6/fits/residuals_linear.rds
2025-11-01 00:53:21.213826 INFO::Writing fitted values to file /tmp/Rtmp3VvdSr/file159a308354bd6/fits/fitted_linear.rds
2025-11-01 00:53:21.214912 INFO::Writing residuals to file /tmp/Rtmp3VvdSr/file159a308354bd6/fits/residuals_logistic.rds
2025-11-01 00:53:21.215954 INFO::Writing fitted values to file /tmp/Rtmp3VvdSr/file159a308354bd6/fits/fitted_logistic.rds
2025-11-01 00:53:21.218518 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp3VvdSr/file159a308354bd6/all_results.tsv
2025-11-01 00:53:21.22001 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/Rtmp3VvdSr/file159a308354bd6/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
359.307 5.055 364.339
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.885 | 0.803 | 21.693 | |
| maaslin_check_arguments | 0.162 | 0.001 | 0.163 | |
| maaslin_check_formula | 0.150 | 0.004 | 0.154 | |
| maaslin_compute_formula | 0.171 | 0.005 | 0.176 | |
| maaslin_contrast_test | 18.574 | 0.488 | 19.066 | |
| maaslin_filter | 0.440 | 0.011 | 0.451 | |
| maaslin_fit | 12.489 | 0.211 | 12.701 | |
| maaslin_log_arguments | 0.128 | 0.001 | 0.129 | |
| maaslin_normalize | 0.275 | 0.006 | 0.281 | |
| maaslin_plot_results | 42.819 | 0.381 | 43.158 | |
| maaslin_plot_results_from_output | 42.944 | 0.471 | 43.416 | |
| maaslin_process_metadata | 0.455 | 0.025 | 0.480 | |
| maaslin_read_data | 0.130 | 0.004 | 0.134 | |
| maaslin_reorder_data | 0.135 | 0.004 | 0.140 | |
| maaslin_transform | 0.540 | 0.034 | 0.574 | |
| maaslin_write_results | 13.377 | 0.142 | 13.519 | |
| maaslin_write_results_lefse_format | 14.819 | 0.100 | 14.919 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.005 | |