William Nickols
| Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: 05599a9 |
| git_last_commit_date: 2025-01-31 13:14:26 -0500 (Fri, 31 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:43 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 1133/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.4 (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 | | ||||||||
|
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: 0.99.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.4.tar.gz |
| StartedAt: 2025-02-05 19:59:21 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 20:02:35 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 194.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘0.99.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 13.626 0.806 14.550
maaslin_plot_results_from_output 13.573 0.655 14.302
maaslin3 8.139 0.428 8.602
maaslin_contrast_test 6.338 0.586 6.932
maaslin_write_results_lefse_format 5.673 0.476 6.160
maaslin_write_results 5.466 0.556 6.032
maaslin_fit 4.682 0.359 5.059
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘0.99.4’ ** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-02-05 20:01:37.71735 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:01:37.746762 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:01:37.776349 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:01:37.784263 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:01:37.802032 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:01:37.829523 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:01:37.831513 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:01:37.835733 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:01:37.869994 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:01:37.872076 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:01:37.893806 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:01:37.907572 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:01:37.911863 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:01:37.925708 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:01:37.954593 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:01:44.407085 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:01:44.433696 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:01:44.459368 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:01:44.466942 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:01:44.478705 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:01:44.504069 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:01:44.506024 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:01:44.510039 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:01:44.553792 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:01:44.555795 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:01:44.573271 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:01:44.587546 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:01:44.591832 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:01:44.604952 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:01:44.629169 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:01:45.842 R[14743:453219698] XType: Using static font registry.
2025-02-05 20:01:52.206195 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:01:52.233062 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:01:52.258194 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:01:52.265932 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:01:52.277873 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:01:52.304217 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:01:52.306198 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:01:52.310509 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:01:52.344697 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:01:52.346886 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:01:52.365953 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:01:52.385962 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:01:52.39017 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:01:52.404221 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:01:52.429051 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:01:57.275 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:01:57.299731 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:01:57.32423 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:01:57.332131 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:01:57.345555 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:01:57.383366 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:01:57.385313 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:01:57.389243 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:01:57.419897 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:01:57.421721 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:01:57.437079 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:01:57.449617 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:01:57.453447 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:01:57.465881 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:01:57.487134 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:01:57.54893 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_linear.rds
2025-02-05 20:01:57.579151 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_linear.rds
2025-02-05 20:01:57.61112 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_logistic.rds
2025-02-05 20:01:57.765789 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_logistic.rds
2025-02-05 20:02:04.001368 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:02:04.028366 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:02:04.05512 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:02:04.06323 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:02:04.075596 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:02:04.103951 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:02:04.106037 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:02:04.110203 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:02:04.143928 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:02:04.146052 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:02:04.163049 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:02:04.176815 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:02:04.181005 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:02:04.194955 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:02:04.218793 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:02:09.153616 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:02:09.1785 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:02:09.202806 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:02:09.210254 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:02:09.221924 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:02:09.247689 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:02:09.249738 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:02:09.253795 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:02:09.287626 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:02:09.289638 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:02:09.306519 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:02:09.320221 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:02:09.324374 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:02:09.338587 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:02:09.36337 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:02:09.444116 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_linear.rds
2025-02-05 20:02:09.476268 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_linear.rds
2025-02-05 20:02:09.509299 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_logistic.rds
2025-02-05 20:02:09.666365 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_logistic.rds
2025-02-05 20:02:16.036155 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:02:16.06282 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:02:16.088252 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:02:16.09575 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:02:16.107552 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:02:16.134244 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:02:16.136297 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:02:16.140467 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:02:16.188178 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:02:16.190151 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:02:16.206134 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:02:16.218922 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:02:16.222805 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:02:16.235665 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:02:16.257703 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:02:21.416334 WARNING::Fitting problem for feature 50 returning NA
2025-02-05 20:02:21.443516 WARNING::Fitting problem for feature 62 returning NA
2025-02-05 20:02:21.470299 WARNING::Fitting problem for feature 74 returning NA
2025-02-05 20:02:21.478685 WARNING::Fitting problem for feature 78 returning NA
2025-02-05 20:02:21.490699 WARNING::Fitting problem for feature 84 returning NA
2025-02-05 20:02:21.516576 WARNING::Fitting problem for feature 96 returning NA
2025-02-05 20:02:21.518617 WARNING::Fitting problem for feature 97 returning NA
2025-02-05 20:02:21.52278 WARNING::Fitting problem for feature 99 returning NA
2025-02-05 20:02:21.556528 WARNING::Fitting problem for feature 114 returning NA
2025-02-05 20:02:21.558644 WARNING::Fitting problem for feature 115 returning NA
2025-02-05 20:02:21.575959 WARNING::Fitting problem for feature 123 returning NA
2025-02-05 20:02:21.589941 WARNING::Fitting problem for feature 130 returning NA
2025-02-05 20:02:21.594263 WARNING::Fitting problem for feature 132 returning NA
2025-02-05 20:02:21.608419 WARNING::Fitting problem for feature 139 returning NA
2025-02-05 20:02:21.634226 WARNING::Fitting problem for feature 150 returning NA
2025-02-05 20:02:21.713824 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_linear.rds
2025-02-05 20:02:21.746699 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_linear.rds
2025-02-05 20:02:21.780834 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/residuals_logistic.rds
2025-02-05 20:02:21.948389 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399750c6b1a9/fits/fitted_logistic.rds
2025-02-05 20:02:28.100079 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-02-05 20:02:28.103907 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-02-05 20:02:28.106005 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-02-05 20:02:28.121187 ERROR::No fixed, group, or
ordered effects included in formula.
2025-02-05 20:02:28.124802 ERROR::Effect name not found in metadata: d
2025-02-05 20:02:28.126619 ERROR::No user formula provided
2025-02-05 20:02:28.134748 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-02-05 20:02:28.136826 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-02-05 20:02:29.075961 INFO::Writing function arguments to log file
2025-02-05 20:02:29.080919 INFO::Verifying options selected are valid
2025-02-05 20:02:29.754157 INFO::Writing function arguments to log file
2025-02-05 20:02:29.758893 INFO::Verifying options selected are valid
2025-02-05 20:02:29.759293 INFO::Determining format of input files
2025-02-05 20:02:29.759668 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 20:02:29.76059 INFO::Running selected normalization method: TSS
2025-02-05 20:02:29.761139 INFO::Creating output feature tables folder
2025-02-05 20:02:29.761527 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/features/data_norm.tsv
2025-02-05 20:02:29.762128 INFO::Filter data based on min abundance and min prevalence
2025-02-05 20:02:29.762421 INFO::Total samples in data: 16
2025-02-05 20:02:29.762722 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-02-05 20:02:29.763371 INFO::Total filtered features: 0
2025-02-05 20:02:29.763705 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 20:02:29.764082 INFO::Total features filtered by non-zero variance filtering: 0
2025-02-05 20:02:29.764392 INFO::Filtered feature names from variance filtering:
2025-02-05 20:02:29.764694 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/features/filtered_data.tsv
2025-02-05 20:02:29.765258 INFO::Running selected transform method: LOG
2025-02-05 20:02:29.765657 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/features/data_transformed.tsv
2025-02-05 20:02:29.766263 INFO::Applying z-score to standardize continuous metadata
2025-02-05 20:02:29.768421 INFO::Running the linear model component
2025-02-05 20:02:29.769525 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:29.771116 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:29.772489 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:29.774927 INFO::Counting total values for each feature
2025-02-05 20:02:29.775596 INFO::Running the logistic model component
2025-02-05 20:02:29.776634 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:29.77879 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:29.780892 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:29.784128 INFO::Counting total values for each feature
2025-02-05 20:02:29.785062 INFO::Re-running abundances for warn_prevalence
2025-02-05 20:02:29.785426 INFO::Running selected normalization method: TSS
2025-02-05 20:02:29.786006 INFO::Running selected transform method: LOG
2025-02-05 20:02:29.787182 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:29.7888 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:29.790141 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:29.816452 INFO::Creating fits folder
2025-02-05 20:02:29.817041 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/fits/residuals_linear.rds
2025-02-05 20:02:29.817662 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/fits/fitted_linear.rds
2025-02-05 20:02:29.818133 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/fits/residuals_logistic.rds
2025-02-05 20:02:29.818608 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/fits/fitted_logistic.rds
2025-02-05 20:02:29.819565 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/all_results.tsv
2025-02-05 20:02:29.820276 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/significant_results.tsv
2025-02-05 20:02:29.820844 INFO::Creating output figures folder
2025-02-05 20:02:29.821363 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/figures/summary_plot.pdf
2025-02-05 20:02:30.291293 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/figures
2025-02-05 20:02:30.292085 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-05 20:02:30.293969 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-05 20:02:30.446755 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/figures/summary_plot.pdf
2025-02-05 20:02:30.915427 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997114e4e4b/figures
2025-02-05 20:02:30.915969 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-05 20:02:30.917789 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-05 20:02:31.072731 INFO::Running the linear model component
2025-02-05 20:02:31.073878 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.075366 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.076636 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:31.079118 INFO::Counting total values for each feature
2025-02-05 20:02:31.079705 INFO::Running the logistic model component
2025-02-05 20:02:31.080689 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.082773 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.08463 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:31.087353 INFO::Counting total values for each feature
2025-02-05 20:02:31.088003 INFO::Re-running abundances for warn_prevalence
2025-02-05 20:02:31.08823 INFO::Running selected normalization method: TSS
2025-02-05 20:02:31.088633 INFO::Running selected transform method: LOG
2025-02-05 20:02:31.089601 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.09082 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.091961 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:31.117425 INFO::Creating output folder
2025-02-05 20:02:31.117875 INFO::Creating output figures folder
2025-02-05 20:02:31.118301 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file39976cab519d/figures/summary_plot.pdf
2025-02-05 20:02:31.594802 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file39976cab519d/figures
2025-02-05 20:02:31.595399 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-05 20:02:31.597288 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-05 20:02:31.936019 INFO::Applying z-score to standardize continuous metadata
2025-02-05 20:02:31.938454 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-02-05 20:02:31.938696 INFO::Bypass z-score application to metadata
2025-02-05 20:02:31.939396 INFO::Bypass z-score application to metadata
2025-02-05 20:02:31.946042 INFO::Determining format of input files
2025-02-05 20:02:31.946418 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 20:02:31.946682 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-02-05 20:02:31.954477 INFO::Determining format of input files
2025-02-05 20:02:31.954921 INFO::Input format is data samples as columns and metadata samples as rows
2025-02-05 20:02:31.955372 INFO::Input format is feature_specific_covariate samples as columns
2025-02-05 20:02:31.958002 INFO::Determining format of input files
2025-02-05 20:02:31.958323 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 20:02:31.958638 INFO::Input format is feature_specific_covariate samples as columns
2025-02-05 20:02:31.959135 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-02-05 20:02:31.959373 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-02-05 20:02:31.963153 INFO::Running selected transform method: LOG
2025-02-05 20:02:31.963494 INFO::Creating output feature tables folder
2025-02-05 20:02:31.963851 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997416516f8/features/data_transformed.tsv
2025-02-05 20:02:31.965161 INFO::Running selected transform method: LOG
2025-02-05 20:02:31.965484 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997416516f8/features/data_transformed.tsv
2025-02-05 20:02:31.966665 INFO::Running selected transform method: PLOG
2025-02-05 20:02:31.967155 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997416516f8/features/data_transformed.tsv
2025-02-05 20:02:31.968054 INFO::Running selected transform method: NONE
2025-02-05 20:02:31.968291 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file3997416516f8/features/data_transformed.tsv
2025-02-05 20:02:31.970924 INFO::Running the linear model component
2025-02-05 20:02:31.971908 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.973317 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.974517 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:31.976872 INFO::Counting total values for each feature
2025-02-05 20:02:31.977459 INFO::Running the logistic model component
2025-02-05 20:02:31.978419 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.980467 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.982363 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:31.985506 INFO::Counting total values for each feature
2025-02-05 20:02:31.986206 INFO::Re-running abundances for warn_prevalence
2025-02-05 20:02:31.986442 INFO::Running selected normalization method: TSS
2025-02-05 20:02:31.986847 INFO::Running selected transform method: LOG
2025-02-05 20:02:31.987839 INFO::Fitting model to feature number 1, a
2025-02-05 20:02:31.989087 INFO::Fitting model to feature number 2, b
2025-02-05 20:02:31.990264 INFO::Fitting model to feature number 3, c
2025-02-05 20:02:32.015718 INFO::Creating output folder
2025-02-05 20:02:32.016122 INFO::Creating fits folder
2025-02-05 20:02:32.016419 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/fits/residuals_linear.rds
2025-02-05 20:02:32.016886 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/fits/fitted_linear.rds
2025-02-05 20:02:32.017248 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/fits/residuals_logistic.rds
2025-02-05 20:02:32.017605 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/fits/fitted_logistic.rds
2025-02-05 20:02:32.018478 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/all_results.tsv
2025-02-05 20:02:32.01904 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwHbFgS/file399753c71552/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
56.488 2.161 58.775
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.139 | 0.428 | 8.602 | |
| maaslin_check_arguments | 0.060 | 0.002 | 0.062 | |
| maaslin_check_formula | 0.060 | 0.004 | 0.064 | |
| maaslin_compute_formula | 0.063 | 0.003 | 0.067 | |
| maaslin_contrast_test | 6.338 | 0.586 | 6.932 | |
| maaslin_filter | 0.219 | 0.014 | 0.233 | |
| maaslin_fit | 4.682 | 0.359 | 5.059 | |
| maaslin_log_arguments | 0.059 | 0.003 | 0.062 | |
| maaslin_normalize | 0.130 | 0.009 | 0.139 | |
| maaslin_plot_results | 13.626 | 0.806 | 14.550 | |
| maaslin_plot_results_from_output | 13.573 | 0.655 | 14.302 | |
| maaslin_process_metadata | 0.235 | 0.019 | 0.255 | |
| maaslin_read_data | 0.066 | 0.003 | 0.068 | |
| maaslin_reorder_data | 0.070 | 0.003 | 0.073 | |
| maaslin_transform | 0.285 | 0.020 | 0.306 | |
| maaslin_write_results | 5.466 | 0.556 | 6.032 | |
| maaslin_write_results_lefse_format | 5.673 | 0.476 | 6.160 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.002 | |