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 11:41 -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 19:20:30 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 19:30:13 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 583.7 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_0.99.3.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: x86_64-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 Monterey 12.7.6
* 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 41.084 1.158 42.630
maaslin_plot_results_from_output 40.530 0.975 41.866
maaslin3 23.590 1.147 25.109
maaslin_contrast_test 20.285 1.124 21.737
maaslin_write_results 16.635 0.854 17.615
maaslin_write_results_lefse_format 16.227 0.534 16.899
maaslin_fit 14.531 0.802 15.508
* 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-x86_64/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: x86_64-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 19:27:23.927559 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:27:24.732828 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:27:24.854872 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:27:24.884177 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:27:24.933735 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:27:25.055063 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:27:25.063077 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:27:25.080611 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:27:25.226328 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:27:25.2345 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:27:25.318421 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:27:25.377988 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:27:25.395323 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:27:25.458166 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:27:25.559545 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:27:44.05327 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:27:44.18023 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:27:44.274506 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:27:44.298693 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:27:44.338539 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:27:44.433594 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:27:44.441444 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:27:44.455218 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:27:44.58431 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:27:44.591303 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:27:44.651426 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:27:44.708165 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:27:44.725097 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:27:44.776706 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:27:44.889675 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:27:48.406 R[4742:984232007] XType: com.apple.fonts is not accessible.
2025-01-23 19:27:48.406 R[4742:984232007] XType: XTFontStaticRegistry is enabled.
2025-01-23 19:28:06.306994 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:28:06.459695 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:28:06.559466 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:28:06.589215 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:28:06.635345 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:28:06.738754 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:28:06.746194 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:28:06.761403 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:28:06.89512 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:28:06.903753 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:28:06.96854 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:28:07.028383 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:28:07.047481 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:28:07.106118 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:28:07.200103 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:28:22.015751 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:28:22.10194 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:28:22.202443 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:28:22.230882 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:28:22.276543 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:28:22.379367 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:28:22.386382 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:28:22.428109 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:28:22.529568 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:28:22.535397 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:28:22.592709 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:28:22.639063 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:28:22.652272 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:28:22.696889 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:28:22.773013 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:28:23.012205 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_linear.rds
2025-01-23 19:28:23.082364 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_linear.rds
2025-01-23 19:28:23.151668 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_logistic.rds
2025-01-23 19:28:23.487 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_logistic.rds
2025-01-23 19:28:42.562617 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:28:42.663607 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:28:42.765219 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:28:42.799386 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:28:42.845933 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:28:42.954238 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:28:42.96316 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:28:42.982992 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:28:43.123121 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:28:43.1317 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:28:43.190542 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:28:43.244145 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:28:43.262926 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:28:43.315699 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:28:43.415761 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:28:58.049821 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:28:58.13413 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:28:58.229961 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:28:58.259656 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:28:58.308169 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:28:58.399113 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:28:58.405866 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:28:58.421096 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:28:58.548425 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:28:58.555043 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:28:58.621739 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:28:58.671046 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:28:58.684804 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:28:58.746862 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:28:58.837487 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:28:59.118698 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_linear.rds
2025-01-23 19:28:59.18408 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_linear.rds
2025-01-23 19:28:59.250806 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_logistic.rds
2025-01-23 19:28:59.606737 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_logistic.rds
2025-01-23 19:29:18.966254 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:29:19.064578 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:29:19.161096 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:29:19.19446 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:29:19.248786 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:29:19.359714 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:29:19.36592 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:29:19.382213 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:29:19.495798 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:29:19.504525 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:29:19.571529 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:29:19.621353 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:29:19.63745 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:29:19.739329 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:29:19.82713 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:29:31.653408 WARNING::Fitting problem for feature 50 returning NA
2025-01-23 19:29:31.755499 WARNING::Fitting problem for feature 62 returning NA
2025-01-23 19:29:31.854587 WARNING::Fitting problem for feature 74 returning NA
2025-01-23 19:29:31.92481 WARNING::Fitting problem for feature 78 returning NA
2025-01-23 19:29:31.973694 WARNING::Fitting problem for feature 84 returning NA
2025-01-23 19:29:32.074197 WARNING::Fitting problem for feature 96 returning NA
2025-01-23 19:29:32.081553 WARNING::Fitting problem for feature 97 returning NA
2025-01-23 19:29:32.096765 WARNING::Fitting problem for feature 99 returning NA
2025-01-23 19:29:32.205713 WARNING::Fitting problem for feature 114 returning NA
2025-01-23 19:29:32.21186 WARNING::Fitting problem for feature 115 returning NA
2025-01-23 19:29:32.278842 WARNING::Fitting problem for feature 123 returning NA
2025-01-23 19:29:32.330837 WARNING::Fitting problem for feature 130 returning NA
2025-01-23 19:29:32.348332 WARNING::Fitting problem for feature 132 returning NA
2025-01-23 19:29:32.398323 WARNING::Fitting problem for feature 139 returning NA
2025-01-23 19:29:32.490919 WARNING::Fitting problem for feature 150 returning NA
2025-01-23 19:29:32.732425 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_linear.rds
2025-01-23 19:29:32.799023 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_linear.rds
2025-01-23 19:29:32.869681 WARNING::Deleting existing residuals file: /tmp/RtmpziJ4FU/file12862ea02334/fits/residuals_logistic.rds
2025-01-23 19:29:33.214856 WARNING::Deleting existing fitted file: /tmp/RtmpziJ4FU/file12862ea02334/fits/fitted_logistic.rds
2025-01-23 19:29:51.455566 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-23 19:29:51.471517 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-23 19:29:51.478798 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-23 19:29:51.54032 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-23 19:29:51.556274 ERROR::Effect name not found in metadata: d
2025-01-23 19:29:51.563578 ERROR::No user formula provided
2025-01-23 19:29:51.592003 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-23 19:29:51.599042 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-23 19:29:54.55739 INFO::Writing function arguments to log file
2025-01-23 19:29:54.579705 INFO::Verifying options selected are valid
2025-01-23 19:29:56.700002 INFO::Writing function arguments to log file
2025-01-23 19:29:56.717496 INFO::Verifying options selected are valid
2025-01-23 19:29:56.719162 INFO::Determining format of input files
2025-01-23 19:29:56.721055 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 19:29:56.725362 INFO::Running selected normalization method: TSS
2025-01-23 19:29:56.727489 INFO::Creating output feature tables folder
2025-01-23 19:29:56.72887 INFO::Writing normalized data to file /tmp/RtmpziJ4FU/file12866b9c061c/features/data_norm.tsv
2025-01-23 19:29:56.73093 INFO::Filter data based on min abundance and min prevalence
2025-01-23 19:29:56.732529 INFO::Total samples in data: 16
2025-01-23 19:29:56.733814 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-23 19:29:56.735799 INFO::Total filtered features: 0
2025-01-23 19:29:56.737194 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-23 19:29:56.738503 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-23 19:29:56.740004 INFO::Filtered feature names from variance filtering:
2025-01-23 19:29:56.741151 INFO::Writing filtered data to file /tmp/RtmpziJ4FU/file12866b9c061c/features/filtered_data.tsv
2025-01-23 19:29:56.743197 INFO::Running selected transform method: LOG
2025-01-23 19:29:56.744893 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpziJ4FU/file12866b9c061c/features/data_transformed.tsv
2025-01-23 19:29:56.747774 INFO::Applying z-score to standardize continuous metadata
2025-01-23 19:29:56.754489 INFO::Running the linear model component
2025-01-23 19:29:56.759395 INFO::Fitting model to feature number 1, a
2025-01-23 19:29:56.76589 INFO::Fitting model to feature number 2, b
2025-01-23 19:29:56.772271 INFO::Fitting model to feature number 3, c
2025-01-23 19:29:56.779892 INFO::Counting total values for each feature
2025-01-23 19:29:56.782412 INFO::Running the logistic model component
2025-01-23 19:29:56.786452 INFO::Fitting model to feature number 1, a
2025-01-23 19:29:56.794358 INFO::Fitting model to feature number 2, b
2025-01-23 19:29:56.801882 INFO::Fitting model to feature number 3, c
2025-01-23 19:29:56.813968 INFO::Counting total values for each feature
2025-01-23 19:29:56.816995 INFO::Re-running abundances for warn_prevalence
2025-01-23 19:29:56.818617 INFO::Running selected normalization method: TSS
2025-01-23 19:29:56.820238 INFO::Running selected transform method: LOG
2025-01-23 19:29:56.824953 INFO::Fitting model to feature number 1, a
2025-01-23 19:29:56.831902 INFO::Fitting model to feature number 2, b
2025-01-23 19:29:56.838464 INFO::Fitting model to feature number 3, c
2025-01-23 19:29:56.947245 INFO::Creating fits folder
2025-01-23 19:29:56.94886 INFO::Writing residuals to file /tmp/RtmpziJ4FU/file12866b9c061c/fits/residuals_linear.rds
2025-01-23 19:29:56.950376 INFO::Writing fitted values to file /tmp/RtmpziJ4FU/file12866b9c061c/fits/fitted_linear.rds
2025-01-23 19:29:56.951982 INFO::Writing residuals to file /tmp/RtmpziJ4FU/file12866b9c061c/fits/residuals_logistic.rds
2025-01-23 19:29:56.953759 INFO::Writing fitted values to file /tmp/RtmpziJ4FU/file12866b9c061c/fits/fitted_logistic.rds
2025-01-23 19:29:56.957089 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpziJ4FU/file12866b9c061c/all_results.tsv
2025-01-23 19:29:56.959378 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/RtmpziJ4FU/file12866b9c061c/significant_results.tsv
2025-01-23 19:29:56.961246 INFO::Creating output figures folder
2025-01-23 19:29:56.963032 INFO::Writing summary plot of significant
results to file: /tmp/RtmpziJ4FU/file12866b9c061c/figures/summary_plot.pdf
2025-01-23 19:29:58.412841 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpziJ4FU/file12866b9c061c/figures
2025-01-23 19:29:58.415251 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 19:29:58.42249 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 19:29:58.810432 INFO::Writing summary plot of
significant results to file: /tmp/RtmpziJ4FU/file12866b9c061c/figures/summary_plot.pdf
2025-01-23 19:30:00.239433 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpziJ4FU/file12866b9c061c/figures
2025-01-23 19:30:00.24198 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 19:30:00.25019 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 19:30:00.678288 INFO::Running the linear model component
2025-01-23 19:30:00.681798 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:00.687277 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:00.693235 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:00.703155 INFO::Counting total values for each feature
2025-01-23 19:30:00.704683 INFO::Running the logistic model component
2025-01-23 19:30:00.70859 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:00.717121 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:00.725124 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:00.736399 INFO::Counting total values for each feature
2025-01-23 19:30:00.738383 INFO::Re-running abundances for warn_prevalence
2025-01-23 19:30:00.739592 INFO::Running selected normalization method: TSS
2025-01-23 19:30:00.741142 INFO::Running selected transform method: LOG
2025-01-23 19:30:00.745427 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:00.750962 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:00.756596 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:00.872835 INFO::Creating output folder
2025-01-23 19:30:00.873907 INFO::Creating output figures folder
2025-01-23 19:30:00.875492 INFO::Writing summary plot of significant
results to file: /tmp/RtmpziJ4FU/file12863aaf6cb2/figures/summary_plot.pdf
2025-01-23 19:30:02.403972 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpziJ4FU/file12863aaf6cb2/figures
2025-01-23 19:30:02.405522 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-23 19:30:02.411847 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-23 19:30:03.388693 INFO::Applying z-score to standardize continuous metadata
2025-01-23 19:30:03.399163 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-23 19:30:03.400196 INFO::Bypass z-score application to metadata
2025-01-23 19:30:03.402561 INFO::Bypass z-score application to metadata
2025-01-23 19:30:03.426022 INFO::Determining format of input files
2025-01-23 19:30:03.426924 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 19:30:03.427643 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-23 19:30:03.43604 INFO::Determining format of input files
2025-01-23 19:30:03.437384 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-23 19:30:03.438903 INFO::Input format is feature_specific_covariate samples as columns
2025-01-23 19:30:03.446028 INFO::Determining format of input files
2025-01-23 19:30:03.447391 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-23 19:30:03.4488 INFO::Input format is feature_specific_covariate samples as columns
2025-01-23 19:30:03.451073 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 19:30:03.452131 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 19:30:03.465111 INFO::Running selected transform method: LOG
2025-01-23 19:30:03.46637 INFO::Creating output feature tables folder
2025-01-23 19:30:03.467408 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpziJ4FU/file12863b508274/features/data_transformed.tsv
2025-01-23 19:30:03.472049 INFO::Running selected transform method: LOG
2025-01-23 19:30:03.47353 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpziJ4FU/file12863b508274/features/data_transformed.tsv
2025-01-23 19:30:03.477149 INFO::Running selected transform method: PLOG
2025-01-23 19:30:03.478487 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpziJ4FU/file12863b508274/features/data_transformed.tsv
2025-01-23 19:30:03.482428 INFO::Running selected transform method: NONE
2025-01-23 19:30:03.483474 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpziJ4FU/file12863b508274/features/data_transformed.tsv
2025-01-23 19:30:03.495274 INFO::Running the linear model component
2025-01-23 19:30:03.499624 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:03.504476 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:03.508259 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:03.517003 INFO::Counting total values for each feature
2025-01-23 19:30:03.519515 INFO::Running the logistic model component
2025-01-23 19:30:03.522323 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:03.53094 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:03.536696 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:03.546463 INFO::Counting total values for each feature
2025-01-23 19:30:03.549384 INFO::Re-running abundances for warn_prevalence
2025-01-23 19:30:03.550556 INFO::Running selected normalization method: TSS
2025-01-23 19:30:03.55242 INFO::Running selected transform method: LOG
2025-01-23 19:30:03.555546 INFO::Fitting model to feature number 1, a
2025-01-23 19:30:03.559885 INFO::Fitting model to feature number 2, b
2025-01-23 19:30:03.564934 INFO::Fitting model to feature number 3, c
2025-01-23 19:30:03.666528 INFO::Creating output folder
2025-01-23 19:30:03.667539 INFO::Creating fits folder
2025-01-23 19:30:03.668387 INFO::Writing residuals to file /tmp/RtmpziJ4FU/file128622a4ac18/fits/residuals_linear.rds
2025-01-23 19:30:03.669455 INFO::Writing fitted values to file /tmp/RtmpziJ4FU/file128622a4ac18/fits/fitted_linear.rds
2025-01-23 19:30:03.670484 INFO::Writing residuals to file /tmp/RtmpziJ4FU/file128622a4ac18/fits/residuals_logistic.rds
2025-01-23 19:30:03.671495 INFO::Writing fitted values to file /tmp/RtmpziJ4FU/file128622a4ac18/fits/fitted_logistic.rds
2025-01-23 19:30:03.673757 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpziJ4FU/file128622a4ac18/all_results.tsv
2025-01-23 19:30:03.676198 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/RtmpziJ4FU/file128622a4ac18/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
166.679 4.564 172.641
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 23.590 | 1.147 | 25.109 | |
| maaslin_check_arguments | 0.219 | 0.007 | 0.228 | |
| maaslin_check_formula | 0.209 | 0.015 | 0.232 | |
| maaslin_compute_formula | 0.218 | 0.017 | 0.248 | |
| maaslin_contrast_test | 20.285 | 1.124 | 21.737 | |
| maaslin_filter | 0.613 | 0.042 | 0.664 | |
| maaslin_fit | 14.531 | 0.802 | 15.508 | |
| maaslin_log_arguments | 0.174 | 0.010 | 0.187 | |
| maaslin_normalize | 0.416 | 0.048 | 0.474 | |
| maaslin_plot_results | 41.084 | 1.158 | 42.630 | |
| maaslin_plot_results_from_output | 40.530 | 0.975 | 41.866 | |
| maaslin_process_metadata | 0.657 | 0.044 | 0.714 | |
| maaslin_read_data | 0.215 | 0.012 | 0.229 | |
| maaslin_reorder_data | 0.214 | 0.012 | 0.229 | |
| maaslin_transform | 0.796 | 0.062 | 0.867 | |
| maaslin_write_results | 16.635 | 0.854 | 17.615 | |
| maaslin_write_results_lefse_format | 16.227 | 0.534 | 16.899 | |
| preprocess_dna_mtx | 0.004 | 0.001 | 0.005 | |