Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1155/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maaslin3 1.0.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: maaslin3 |
Version: 1.0.0 |
Command: /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_1.0.0.tar.gz |
StartedAt: 2025-08-20 23:52:28 -0400 (Wed, 20 Aug 2025) |
EndedAt: 2025-08-21 00:11:56 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 1167.5 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.0.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maaslin3’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 36.438 0.527 36.928 maaslin_plot_results_from_output 35.478 0.341 35.821 maaslin_contrast_test 19.193 0.632 19.827 maaslin3 19.035 0.626 19.666 maaslin_write_results_lefse_format 14.989 0.094 15.084 maaslin_write_results 13.440 0.282 13.722 maaslin_fit 13.434 0.089 13.524 * 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 ‘1.0.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" 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") 2025-08-20 23:58:23.606294 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:58:23.680576 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:58:23.763915 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:58:23.785074 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:58:23.826783 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:58:23.90354 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:58:23.90906 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:58:23.920978 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:58:24.020477 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:58:24.025657 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:58:24.073035 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:58:24.111965 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:58:24.123324 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:58:24.162439 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:58:24.238078 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:58:40.096171 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:58:40.170665 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:58:40.24563 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:58:40.269238 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:58:40.306641 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:58:40.390987 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:58:40.397278 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:58:40.411728 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:58:40.537276 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:58:40.542637 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:58:40.59148 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:58:40.63122 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:58:40.642786 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:58:40.682102 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:58:40.751952 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:58:59.225609 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:58:59.316391 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:58:59.391214 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:58:59.412899 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:58:59.447178 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:58:59.521933 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:58:59.527439 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:58:59.539408 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:58:59.636693 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:58:59.642576 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:58:59.722344 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:58:59.768061 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:58:59.780204 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:58:59.820195 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:58:59.887449 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:59:12.951433 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:59:13.028879 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:59:13.10154 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:59:13.122445 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:59:13.155724 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:59:13.228994 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:59:13.234331 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:59:13.245771 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:59:13.336204 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:59:13.34151 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:59:13.390324 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:59:13.430301 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:59:13.442074 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:59:13.48265 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:59:13.550964 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:59:13.783867 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds 2025-08-20 23:59:13.846273 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds 2025-08-20 23:59:13.910379 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds 2025-08-20 23:59:14.211494 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds 2025-08-20 23:59:30.82741 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:59:30.926561 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:59:31.004512 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:59:31.027686 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:59:31.064569 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:59:31.144409 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:59:31.150118 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:59:31.162783 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:59:31.261139 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:59:31.266773 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:59:31.316768 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:59:31.356505 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:59:31.368094 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:59:31.407008 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:59:31.475543 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:59:44.151783 WARNING::Fitting problem for feature 50 returning NA 2025-08-20 23:59:44.226765 WARNING::Fitting problem for feature 62 returning NA 2025-08-20 23:59:44.30115 WARNING::Fitting problem for feature 74 returning NA 2025-08-20 23:59:44.323188 WARNING::Fitting problem for feature 78 returning NA 2025-08-20 23:59:44.357823 WARNING::Fitting problem for feature 84 returning NA 2025-08-20 23:59:44.43394 WARNING::Fitting problem for feature 96 returning NA 2025-08-20 23:59:44.439843 WARNING::Fitting problem for feature 97 returning NA 2025-08-20 23:59:44.452338 WARNING::Fitting problem for feature 99 returning NA 2025-08-20 23:59:44.548516 WARNING::Fitting problem for feature 114 returning NA 2025-08-20 23:59:44.553979 WARNING::Fitting problem for feature 115 returning NA 2025-08-20 23:59:44.60408 WARNING::Fitting problem for feature 123 returning NA 2025-08-20 23:59:44.645165 WARNING::Fitting problem for feature 130 returning NA 2025-08-20 23:59:44.658923 WARNING::Fitting problem for feature 132 returning NA 2025-08-20 23:59:44.701982 WARNING::Fitting problem for feature 139 returning NA 2025-08-20 23:59:44.774384 WARNING::Fitting problem for feature 150 returning NA 2025-08-20 23:59:44.984754 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds 2025-08-20 23:59:45.045456 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds 2025-08-20 23:59:45.108271 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds 2025-08-20 23:59:45.409223 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds 2025-08-21 00:00:02.167132 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:00:02.243215 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:00:02.318333 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:00:02.340014 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:00:02.374471 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:00:02.452549 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:00:02.458198 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:00:02.470507 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:00:02.569526 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:00:02.575295 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:00:02.62837 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:00:02.671816 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:00:02.684543 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:00:02.726545 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:00:02.811038 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:00:14.869803 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:00:14.947856 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:00:15.025149 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:00:15.046834 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:00:15.080911 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:00:15.157269 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:00:15.162816 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:00:15.174966 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:00:15.27034 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:00:15.275722 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:00:15.325745 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:00:15.368392 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:00:15.381969 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:00:15.424185 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:00:15.496599 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:00:15.704002 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds 2025-08-21 00:00:15.765436 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds 2025-08-21 00:00:15.829647 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds 2025-08-21 00:00:16.132642 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds 2025-08-21 00:00:32.775272 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:00:32.850307 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:00:32.925143 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:00:32.94694 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:00:32.981642 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:00:33.057997 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:00:33.063529 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:00:33.075543 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:00:33.171884 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:00:33.177451 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:00:33.228448 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:00:33.269985 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:00:33.282526 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:00:33.323844 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:00:33.393555 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:00:45.200852 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:00:45.279269 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:00:45.354671 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:00:45.376484 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:00:45.41076 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:00:45.486995 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:00:45.492499 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:00:45.504451 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:00:45.600658 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:00:45.60603 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:00:45.655805 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:00:45.697776 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:00:45.710458 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:00:45.751664 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:00:45.82053 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:01:04.485921 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:01:14.289268 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:01:33.958329 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:01:43.336162 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:01:43.987976 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds 2025-08-21 00:01:44.049304 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds 2025-08-21 00:01:44.087703 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds 2025-08-21 00:01:44.155739 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds 2025-08-21 00:02:02.044698 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:02:07.374391 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:02:07.707165 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds 2025-08-21 00:02:07.769219 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds 2025-08-21 00:02:07.807769 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds 2025-08-21 00:02:07.876359 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds 2025-08-21 00:02:23.521142 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:02:28.588792 WARNING::Fitting problem for feature 124 returning NA 2025-08-21 00:02:28.899455 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds 2025-08-21 00:02:28.960909 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds 2025-08-21 00:02:29.000312 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds 2025-08-21 00:02:29.069989 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds 2025-08-21 00:02:44.416397 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:02:44.494793 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:02:44.570112 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:02:44.59284 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:02:44.636932 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:02:44.713373 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:02:44.718697 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:02:44.730484 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:02:44.827604 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:02:44.833278 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:02:44.885157 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:02:44.926008 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:02:44.9384 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:02:44.980234 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:02:45.049874 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:02:56.931822 WARNING::Fitting problem for feature 50 returning NA 2025-08-21 00:02:57.01224 WARNING::Fitting problem for feature 62 returning NA 2025-08-21 00:02:57.090774 WARNING::Fitting problem for feature 74 returning NA 2025-08-21 00:02:57.113954 WARNING::Fitting problem for feature 78 returning NA 2025-08-21 00:02:57.148656 WARNING::Fitting problem for feature 84 returning NA 2025-08-21 00:02:57.224502 WARNING::Fitting problem for feature 96 returning NA 2025-08-21 00:02:57.229879 WARNING::Fitting problem for feature 97 returning NA 2025-08-21 00:02:57.241662 WARNING::Fitting problem for feature 99 returning NA 2025-08-21 00:02:57.338153 WARNING::Fitting problem for feature 114 returning NA 2025-08-21 00:02:57.343687 WARNING::Fitting problem for feature 115 returning NA 2025-08-21 00:02:57.394006 WARNING::Fitting problem for feature 123 returning NA 2025-08-21 00:02:57.434854 WARNING::Fitting problem for feature 130 returning NA 2025-08-21 00:02:57.447407 WARNING::Fitting problem for feature 132 returning NA 2025-08-21 00:02:57.490029 WARNING::Fitting problem for feature 139 returning NA 2025-08-21 00:02:57.563994 WARNING::Fitting problem for feature 150 returning NA 2025-08-21 00:02:57.86167 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds 2025-08-21 00:02:57.922375 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds 2025-08-21 00:02:57.985532 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds 2025-08-21 00:02:58.284298 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds 2025-08-21 00:03:14.167752 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE 2025-08-21 00:03:14.185401 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE 2025-08-21 00:03:14.197734 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY 2025-08-21 00:03:14.251091 ERROR::No fixed, group, or ordered effects included in formula. 2025-08-21 00:03:14.267403 ERROR::Effect name not found in metadata: d 2025-08-21 00:03:14.279145 ERROR::No user formula provided 2025-08-21 00:03:14.308786 ERROR::Effect name not found in metadata so not applied to formula as random effect: d 2025-08-21 00:03:14.320694 ERROR::No fixed/group/ordered/ feature-specific effects provided. 2025-08-21 00:03:17.197488 INFO::Writing function arguments to log file 2025-08-21 00:03:17.212053 INFO::Verifying options selected are valid 2025-08-21 00:03:19.035642 INFO::Writing function arguments to log file 2025-08-21 00:03:19.047336 INFO::Verifying options selected are valid 2025-08-21 00:03:19.048517 INFO::Determining format of input files 2025-08-21 00:03:19.049541 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-21 00:03:19.051904 INFO::Running selected normalization method: TSS 2025-08-21 00:03:19.053443 INFO::Creating output feature tables folder 2025-08-21 00:03:19.054447 INFO::Writing normalized data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/data_norm.tsv 2025-08-21 00:03:19.055988 INFO::Filter data based on min abundance and min prevalence 2025-08-21 00:03:19.056932 INFO::Total samples in data: 16 2025-08-21 00:03:19.057813 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000 2025-08-21 00:03:19.059688 INFO::Total filtered features: 0 2025-08-21 00:03:19.060647 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-21 00:03:19.061806 INFO::Total features filtered by non-zero variance filtering: 0 2025-08-21 00:03:19.062753 INFO::Filtered feature names from variance filtering: 2025-08-21 00:03:19.063669 INFO::Writing filtered data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/filtered_data.tsv 2025-08-21 00:03:19.06517 INFO::Running selected transform method: LOG 2025-08-21 00:03:19.066403 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/data_transformed.tsv 2025-08-21 00:03:19.068046 INFO::Applying z-score to standardize continuous metadata 2025-08-21 00:03:19.073541 INFO::Running the linear model component 2025-08-21 00:03:19.087491 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:19.0921 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:19.096397 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:19.103715 INFO::Counting total values for each feature 2025-08-21 00:03:19.105529 INFO::Running the logistic model component 2025-08-21 00:03:19.119879 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:19.126719 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:19.132851 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:19.141821 INFO::Counting total values for each feature 2025-08-21 00:03:19.143962 INFO::Re-running abundances for warn_prevalence 2025-08-21 00:03:19.144912 INFO::Running selected normalization method: TSS 2025-08-21 00:03:19.146392 INFO::Running selected transform method: LOG 2025-08-21 00:03:19.160271 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:19.164683 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:19.168901 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:19.25456 INFO::Creating fits folder 2025-08-21 00:03:19.255836 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/residuals_linear.rds 2025-08-21 00:03:19.257004 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/fitted_linear.rds 2025-08-21 00:03:19.258263 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/residuals_logistic.rds 2025-08-21 00:03:19.259531 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/fitted_logistic.rds 2025-08-21 00:03:19.262262 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpkHO8LQ/file3f41833e3774a3/all_results.tsv 2025-08-21 00:03:19.263902 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/RtmpkHO8LQ/file3f41833e3774a3/significant_results.tsv 2025-08-21 00:03:19.265281 INFO::Creating output figures folder 2025-08-21 00:03:19.266679 INFO::Writing summary plot of significant results to file: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures/summary_plot.pdf 2025-08-21 00:03:20.522023 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures 2025-08-21 00:03:20.52404 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-21 00:03:20.529099 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-21 00:03:20.91683 INFO::Writing summary plot of significant results to file: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures/summary_plot.pdf 2025-08-21 00:03:22.185938 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures 2025-08-21 00:03:22.187543 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-21 00:03:22.192435 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-21 00:03:22.582797 INFO::Running the linear model component 2025-08-21 00:03:22.591504 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:22.595841 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:22.599928 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:22.606869 INFO::Counting total values for each feature 2025-08-21 00:03:22.608562 INFO::Running the logistic model component 2025-08-21 00:03:22.616975 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:22.623272 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:22.629353 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:22.638304 INFO::Counting total values for each feature 2025-08-21 00:03:22.640371 INFO::Re-running abundances for warn_prevalence 2025-08-21 00:03:22.641191 INFO::Running selected normalization method: TSS 2025-08-21 00:03:22.642548 INFO::Running selected transform method: LOG 2025-08-21 00:03:22.651158 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:22.655365 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:22.659344 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:22.749075 INFO::Creating output folder 2025-08-21 00:03:22.750175 INFO::Creating output figures folder 2025-08-21 00:03:22.751499 INFO::Writing summary plot of significant results to file: /tmp/RtmpkHO8LQ/file3f41833ef20514/figures/summary_plot.pdf 2025-08-21 00:03:24.046105 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833ef20514/figures 2025-08-21 00:03:24.048162 INFO::Plotting associations from most to least significant, grouped by metadata 2025-08-21 00:03:24.054169 INFO::Creating boxplot for continuous data (logistic), var1 vs a 2025-08-21 00:03:24.912592 INFO::Applying z-score to standardize continuous metadata 2025-08-21 00:03:24.920766 INFO::Factor detected for categorial metadata 'c'. Using as-is. 2025-08-21 00:03:24.921747 INFO::Bypass z-score application to metadata 2025-08-21 00:03:24.92437 INFO::Bypass z-score application to metadata 2025-08-21 00:03:24.943253 INFO::Determining format of input files 2025-08-21 00:03:24.944378 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-21 00:03:24.945313 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows 2025-08-21 00:03:24.952473 INFO::Determining format of input files 2025-08-21 00:03:24.953605 INFO::Input format is data samples as columns and metadata samples as rows 2025-08-21 00:03:24.954993 INFO::Input format is feature_specific_covariate samples as columns 2025-08-21 00:03:24.962923 INFO::Determining format of input files 2025-08-21 00:03:24.963925 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-21 00:03:24.964983 INFO::Input format is feature_specific_covariate samples as columns 2025-08-21 00:03:24.966656 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1 2025-08-21 00:03:24.967475 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1 2025-08-21 00:03:24.978252 INFO::Running selected transform method: LOG 2025-08-21 00:03:24.979325 INFO::Creating output feature tables folder 2025-08-21 00:03:24.980183 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv 2025-08-21 00:03:24.98372 INFO::Running selected transform method: LOG 2025-08-21 00:03:24.984688 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv 2025-08-21 00:03:24.987987 INFO::Running selected transform method: PLOG 2025-08-21 00:03:24.989446 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv 2025-08-21 00:03:24.992008 INFO::Running selected transform method: NONE 2025-08-21 00:03:24.992751 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv 2025-08-21 00:03:24.999424 INFO::Running the linear model component 2025-08-21 00:03:25.00782 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:25.011981 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:25.015814 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:25.022562 INFO::Counting total values for each feature 2025-08-21 00:03:25.024152 INFO::Running the logistic model component 2025-08-21 00:03:25.032341 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:25.038427 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:25.04413 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:25.052557 INFO::Counting total values for each feature 2025-08-21 00:03:25.054488 INFO::Re-running abundances for warn_prevalence 2025-08-21 00:03:25.055278 INFO::Running selected normalization method: TSS 2025-08-21 00:03:25.056617 INFO::Running selected transform method: LOG 2025-08-21 00:03:25.064958 INFO::Fitting model to feature number 1, a 2025-08-21 00:03:25.069044 INFO::Fitting model to feature number 2, b 2025-08-21 00:03:25.072941 INFO::Fitting model to feature number 3, c 2025-08-21 00:03:25.157548 INFO::Creating output folder 2025-08-21 00:03:25.15853 INFO::Creating fits folder 2025-08-21 00:03:25.159384 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/residuals_linear.rds 2025-08-21 00:03:25.160372 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/fitted_linear.rds 2025-08-21 00:03:25.16144 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/residuals_logistic.rds 2025-08-21 00:03:25.162476 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/fitted_logistic.rds 2025-08-21 00:03:25.164972 INFO::Writing all the results to file (ordered by increasing individual q-values): /tmp/RtmpkHO8LQ/file3f41837f0da59f/all_results.tsv 2025-08-21 00:03:25.166439 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/RtmpkHO8LQ/file3f41837f0da59f/significant_results.tsv [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ] > > > proc.time() user system elapsed 307.936 4.453 312.384
maaslin3.Rcheck/maaslin3-Ex.timings
name | user | system | elapsed | |
maaslin3 | 19.035 | 0.626 | 19.666 | |
maaslin_check_arguments | 0.138 | 0.002 | 0.139 | |
maaslin_check_formula | 0.130 | 0.005 | 0.137 | |
maaslin_compute_formula | 0.133 | 0.004 | 0.139 | |
maaslin_contrast_test | 19.193 | 0.632 | 19.827 | |
maaslin_filter | 0.439 | 0.023 | 0.462 | |
maaslin_fit | 13.434 | 0.089 | 13.524 | |
maaslin_log_arguments | 0.130 | 0.003 | 0.133 | |
maaslin_normalize | 0.287 | 0.010 | 0.297 | |
maaslin_plot_results | 36.438 | 0.527 | 36.928 | |
maaslin_plot_results_from_output | 35.478 | 0.341 | 35.821 | |
maaslin_process_metadata | 0.438 | 0.020 | 0.458 | |
maaslin_read_data | 0.132 | 0.005 | 0.137 | |
maaslin_reorder_data | 0.138 | 0.004 | 0.142 | |
maaslin_transform | 0.577 | 0.012 | 0.588 | |
maaslin_write_results | 13.440 | 0.282 | 13.722 | |
maaslin_write_results_lefse_format | 14.989 | 0.094 | 15.084 | |
preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |