William Nickols
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: cc4bab0 |
| git_last_commit_date: 2025-01-06 15:46:01 -0500 (Mon, 06 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-24 11:42 -0500 (Fri, 24 Jan 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" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1129/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.3 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 0.99.3 |
| 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_0.99.3.tar.gz |
| StartedAt: 2025-01-23 18:31:36 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 18:34:48 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 192.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_0.99.3.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 ‘0.99.3’
* 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_from_output 13.630 0.644 14.322
maaslin_plot_results 13.386 0.654 14.106
maaslin3 7.915 0.469 8.390
maaslin_contrast_test 6.672 0.459 7.144
maaslin_write_results_lefse_format 5.363 0.410 5.797
maaslin_write_results 4.902 0.431 5.346
maaslin_fit 4.607 0.432 5.068
* 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 ‘0.99.3’ ** 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")
2025-01-23 18:33:49.175732 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:33:49.492459 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:33:49.522189 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:33:49.530079 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:33:49.542305 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:33:49.57555 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:33:49.577565 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:33:49.581702 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:33:49.621028 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:33:49.623192 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:33:49.651988 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:33:49.666439 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:33:49.670772 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:33:49.686708 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:33:49.711478 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:33:56.240555 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:33:56.266579 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:33:56.291191 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:33:56.298611 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:33:56.310509 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:33:56.337211 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:33:56.339195 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:33:56.34331 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:33:56.380177 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:33:56.382284 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:33:56.399335 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:33:56.413301 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:33:56.420362 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:33:56.438637 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:33:56.4715 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:33:57.657 R[37633:368659249] XType: Using static font registry.
2025-01-23 18:34:03.729439 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:04.119848 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:04.145807 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:04.153345 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:04.16535 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:04.191473 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:04.193449 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:04.197492 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:04.229956 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:04.231922 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:04.24853 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:04.262016 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:04.266221 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:04.28027 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:04.303336 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:09.224945 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:09.25079 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:09.275922 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:09.283325 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:09.295078 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:09.320549 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:09.322475 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:09.326497 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:09.373719 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:09.375668 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:09.391722 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:09.404772 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:09.408718 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:09.421599 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:09.44464 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:09.511547 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_linear.rds
2025-01-23 18:34:09.543591 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_linear.rds
2025-01-23 18:34:09.576861 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_logistic.rds
2025-01-23 18:34:09.74229 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_logistic.rds
2025-01-23 18:34:16.35478 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:16.379978 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:16.404359 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:16.412012 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:16.423629 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:16.449749 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:16.451753 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:16.455869 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:16.489429 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:16.491398 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:16.508739 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:16.522745 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:16.526585 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:16.540424 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:16.564527 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:21.655785 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:21.683188 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:21.709308 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:21.717102 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:21.729247 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:21.757669 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:21.759754 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:21.764271 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:21.802393 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:21.80455 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:21.825768 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:21.842805 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:21.847765 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:21.864547 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:21.934184 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:22.000384 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_linear.rds
2025-01-23 18:34:22.032303 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_linear.rds
2025-01-23 18:34:22.065735 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_logistic.rds
2025-01-23 18:34:22.23482 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_logistic.rds
2025-01-23 18:34:28.678894 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:28.70475 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:28.73005 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:28.752417 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:28.763473 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:28.788924 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:28.790927 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:28.794923 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:28.826905 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:28.828919 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:28.845022 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:28.858211 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:28.862353 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:28.875719 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:28.898695 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:33.682436 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 18:34:33.706061 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 18:34:33.728801 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 18:34:33.73555 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 18:34:33.746339 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 18:34:33.770616 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 18:34:33.772646 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 18:34:33.776441 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 18:34:33.807327 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 18:34:33.809286 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 18:34:33.824907 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 18:34:33.838927 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 18:34:33.843347 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 18:34:33.857618 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 18:34:33.882326 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 18:34:33.970596 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_linear.rds
2025-01-23 18:34:34.003006 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_linear.rds
2025-01-23 18:34:34.036035 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/residuals_logistic.rds
2025-01-23 18:34:34.200914 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93011f7e1303/fits/fitted_logistic.rds
2025-01-23 18:34:40.748661 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-23 18:34:40.752212 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-23 18:34:40.754138 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-23 18:34:40.768934 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-23 18:34:40.772485 ERROR::Effect name not found in metadata: d
2025-01-23 18:34:40.774296 ERROR::No user formula provided
2025-01-23 18:34:40.782236 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-23 18:34:40.784314 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-23 18:34:41.707588 INFO::Writing function arguments to log file
2025-01-23 18:34:41.712424 INFO::Verifying options selected are valid
2025-01-23 18:34:42.382728 INFO::Writing function arguments to log file
2025-01-23 18:34:42.387052 INFO::Verifying options selected are valid
2025-01-23 18:34:42.387395 INFO::Determining format of input files
2025-01-23 18:34:42.387715 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 18:34:42.388501 INFO::Running selected normalization method: TSS
2025-01-23 18:34:42.388994 INFO::Creating output feature tables folder
2025-01-23 18:34:42.389387 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/features/data_norm.tsv
2025-01-23 18:34:42.389999 INFO::Filter data based on min abundance and min prevalence
2025-01-23 18:34:42.390307 INFO::Total samples in data: 16
2025-01-23 18:34:42.390583 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-23 18:34:42.391172 INFO::Total filtered features: 0
2025-01-23 18:34:42.391505 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-23 18:34:42.391885 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-23 18:34:42.392196 INFO::Filtered feature names from variance filtering:
2025-01-23 18:34:42.392487 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/features/filtered_data.tsv
2025-01-23 18:34:42.393047 INFO::Running selected transform method: LOG
2025-01-23 18:34:42.393427 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/features/data_transformed.tsv
2025-01-23 18:34:42.394026 INFO::Applying z-score to standardize continuous metadata
2025-01-23 18:34:42.395938 INFO::Running the linear model component
2025-01-23 18:34:42.397013 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:42.398502 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:42.399801 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:42.402074 INFO::Counting total values for each feature
2025-01-23 18:34:42.402701 INFO::Running the logistic model component
2025-01-23 18:34:42.403678 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:42.405626 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:42.4075 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:42.410189 INFO::Counting total values for each feature
2025-01-23 18:34:42.410939 INFO::Re-running abundances for warn_prevalence
2025-01-23 18:34:42.411252 INFO::Running selected normalization method: TSS
2025-01-23 18:34:42.411734 INFO::Running selected transform method: LOG
2025-01-23 18:34:42.412795 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:42.414124 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:42.415364 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:42.441229 INFO::Creating fits folder
2025-01-23 18:34:42.441774 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/fits/residuals_linear.rds
2025-01-23 18:34:42.442351 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/fits/fitted_linear.rds
2025-01-23 18:34:42.442796 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/fits/residuals_logistic.rds
2025-01-23 18:34:42.443308 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/fits/fitted_logistic.rds
2025-01-23 18:34:42.444293 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/all_results.tsv
2025-01-23 18:34:42.444946 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//RtmpwrMpky/file93012193542b/significant_results.tsv
2025-01-23 18:34:42.445471 INFO::Creating output figures folder
2025-01-23 18:34:42.445922 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/figures/summary_plot.pdf
2025-01-23 18:34:42.920668 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/figures
2025-01-23 18:34:42.921453 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 18:34:42.92336 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 18:34:43.071534 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/figures/summary_plot.pdf
2025-01-23 18:34:43.548857 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93012193542b/figures
2025-01-23 18:34:43.549421 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 18:34:43.551245 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 18:34:43.702246 INFO::Running the linear model component
2025-01-23 18:34:43.703421 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:43.704888 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:43.706114 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:43.708415 INFO::Counting total values for each feature
2025-01-23 18:34:43.708943 INFO::Running the logistic model component
2025-01-23 18:34:43.709864 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:43.711739 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:43.715583 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:43.718355 INFO::Counting total values for each feature
2025-01-23 18:34:43.719009 INFO::Re-running abundances for warn_prevalence
2025-01-23 18:34:43.719247 INFO::Running selected normalization method: TSS
2025-01-23 18:34:43.719667 INFO::Running selected transform method: LOG
2025-01-23 18:34:43.720657 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:43.721927 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:43.723122 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:43.753329 INFO::Creating output folder
2025-01-23 18:34:43.753738 INFO::Creating output figures folder
2025-01-23 18:34:43.754141 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301568ae98c/figures/summary_plot.pdf
2025-01-23 18:34:44.213529 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301568ae98c/figures
2025-01-23 18:34:44.214172 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 18:34:44.216126 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 18:34:44.569348 INFO::Applying z-score to standardize continuous metadata
2025-01-23 18:34:44.572033 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-23 18:34:44.572301 INFO::Bypass z-score application to metadata
2025-01-23 18:34:44.573024 INFO::Bypass z-score application to metadata
2025-01-23 18:34:44.579373 INFO::Determining format of input files
2025-01-23 18:34:44.579674 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 18:34:44.579921 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-23 18:34:44.582039 INFO::Determining format of input files
2025-01-23 18:34:44.582357 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-23 18:34:44.582726 INFO::Input format is feature_specific_covariate samples as columns
2025-01-23 18:34:44.585045 INFO::Determining format of input files
2025-01-23 18:34:44.585319 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 18:34:44.585607 INFO::Input format is feature_specific_covariate samples as columns
2025-01-23 18:34:44.586066 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-01-23 18:34:44.586279 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-01-23 18:34:44.589762 INFO::Running selected transform method: LOG
2025-01-23 18:34:44.590104 INFO::Creating output feature tables folder
2025-01-23 18:34:44.590497 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93016522664c/features/data_transformed.tsv
2025-01-23 18:34:44.591791 INFO::Running selected transform method: LOG
2025-01-23 18:34:44.592098 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93016522664c/features/data_transformed.tsv
2025-01-23 18:34:44.593251 INFO::Running selected transform method: PLOG
2025-01-23 18:34:44.593742 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93016522664c/features/data_transformed.tsv
2025-01-23 18:34:44.594633 INFO::Running selected transform method: NONE
2025-01-23 18:34:44.594865 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file93016522664c/features/data_transformed.tsv
2025-01-23 18:34:44.597567 INFO::Running the linear model component
2025-01-23 18:34:44.598537 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:44.599926 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:44.601117 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:44.603362 INFO::Counting total values for each feature
2025-01-23 18:34:44.6039 INFO::Running the logistic model component
2025-01-23 18:34:44.604822 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:44.606683 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:44.608412 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:44.611113 INFO::Counting total values for each feature
2025-01-23 18:34:44.611779 INFO::Re-running abundances for warn_prevalence
2025-01-23 18:34:44.612017 INFO::Running selected normalization method: TSS
2025-01-23 18:34:44.612428 INFO::Running selected transform method: LOG
2025-01-23 18:34:44.613439 INFO::Fitting model to feature number 1, a
2025-01-23 18:34:44.614743 INFO::Fitting model to feature number 2, b
2025-01-23 18:34:44.615921 INFO::Fitting model to feature number 3, c
2025-01-23 18:34:44.643607 INFO::Creating output folder
2025-01-23 18:34:44.644056 INFO::Creating fits folder
2025-01-23 18:34:44.644373 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301356a3b73/fits/residuals_linear.rds
2025-01-23 18:34:44.644815 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301356a3b73/fits/fitted_linear.rds
2025-01-23 18:34:44.645189 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301356a3b73/fits/residuals_logistic.rds
2025-01-23 18:34:44.645556 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301356a3b73/fits/fitted_logistic.rds
2025-01-23 18:34:44.646389 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwrMpky/file9301356a3b73/all_results.tsv
2025-01-23 18:34:44.646956 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//RtmpwrMpky/file9301356a3b73/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
57.073 2.147 59.562
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 7.915 | 0.469 | 8.390 | |
| maaslin_check_arguments | 0.074 | 0.004 | 0.078 | |
| maaslin_check_formula | 0.062 | 0.004 | 0.065 | |
| maaslin_compute_formula | 0.068 | 0.003 | 0.072 | |
| maaslin_contrast_test | 6.672 | 0.459 | 7.144 | |
| maaslin_filter | 0.196 | 0.018 | 0.215 | |
| maaslin_fit | 4.607 | 0.432 | 5.068 | |
| maaslin_log_arguments | 0.061 | 0.003 | 0.064 | |
| maaslin_normalize | 0.131 | 0.008 | 0.139 | |
| maaslin_plot_results | 13.386 | 0.654 | 14.106 | |
| maaslin_plot_results_from_output | 13.630 | 0.644 | 14.322 | |
| maaslin_process_metadata | 0.225 | 0.020 | 0.246 | |
| maaslin_read_data | 0.057 | 0.002 | 0.060 | |
| maaslin_reorder_data | 0.057 | 0.003 | 0.059 | |
| maaslin_transform | 0.271 | 0.023 | 0.297 | |
| maaslin_write_results | 4.902 | 0.431 | 5.346 | |
| maaslin_write_results_lefse_format | 5.363 | 0.410 | 5.797 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.002 | |