William Nickols
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 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 2025-01-25 15:37 -0500 (Sat, 25 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" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| 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 | | ||||||||
| 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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.3.tar.gz |
| StartedAt: 2025-01-24 23:39:01 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 23:55:44 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 1002.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_0.99.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 35.892 0.392 36.252
maaslin_plot_results_from_output 35.383 0.359 35.744
maaslin3 19.300 0.811 20.114
maaslin_contrast_test 16.730 0.330 17.060
maaslin_write_results_lefse_format 14.631 0.172 14.805
maaslin_write_results 13.383 0.197 13.582
maaslin_fit 12.344 0.166 12.510
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘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-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-01-24 23:44:50.311444 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:44:51.035964 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:44:51.128342 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:44:51.15382 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:44:51.193154 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:44:51.28424 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:44:51.28978 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:44:51.302171 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:44:51.40286 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:44:51.408434 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:44:51.466294 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:44:51.505616 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:44:51.517019 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:44:51.556211 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:44:51.624531 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:45:07.670049 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:45:07.75103 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:45:07.832781 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:45:07.856529 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:45:07.893358 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:45:07.988371 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:45:07.994078 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:45:08.006924 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:45:08.105216 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:45:08.11066 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:45:08.160968 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:45:08.201641 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:45:08.213562 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:45:08.254807 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:45:08.334576 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:45:27.045142 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:45:27.138405 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:45:27.222232 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:45:27.245393 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:45:27.280512 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:45:27.358641 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:45:27.364583 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:45:27.376899 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:45:27.480692 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:45:28.337696 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:45:28.388582 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:45:28.429754 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:45:28.441575 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:45:28.482536 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:45:28.552695 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:45:41.229847 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:45:41.30934 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:45:41.387568 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:45:41.410625 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:45:41.445962 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:45:41.542068 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:45:41.547645 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:45:41.559932 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:45:41.657102 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:45:41.662674 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:45:41.714142 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:45:41.756311 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:45:41.768576 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:45:41.810418 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:45:41.880913 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:45:42.079736 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_linear.rds
2025-01-24 23:45:42.140414 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_linear.rds
2025-01-24 23:45:42.203258 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_logistic.rds
2025-01-24 23:45:42.502451 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_logistic.rds
2025-01-24 23:45:59.139685 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:45:59.217692 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:45:59.295501 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:45:59.317773 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:45:59.352763 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:45:59.434591 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:45:59.440314 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:45:59.453182 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:45:59.550575 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:45:59.556144 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:45:59.608182 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:45:59.651246 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:45:59.664026 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:45:59.706705 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:45:59.779296 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:46:12.328407 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:46:12.40576 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:46:12.480497 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:46:12.502137 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:46:12.536009 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:46:12.612133 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:46:12.617585 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:46:12.629549 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:46:12.726318 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:46:12.731877 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:46:12.782256 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:46:12.822522 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:46:12.834679 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:46:12.875349 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:46:12.945109 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:46:13.151177 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_linear.rds
2025-01-24 23:46:13.211649 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_linear.rds
2025-01-24 23:46:13.274333 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_logistic.rds
2025-01-24 23:46:13.572442 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_logistic.rds
2025-01-24 23:46:31.108824 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:46:31.186825 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:46:31.265868 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:46:31.287516 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:46:31.321584 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:46:31.396501 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:46:31.401809 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:46:31.414718 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:46:31.512152 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:46:31.517645 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:46:31.568196 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:46:31.610004 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:46:31.622438 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:46:31.664408 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:46:31.735873 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:46:42.453444 WARNING::Fitting problem for feature 50 returning NA
2025-01-24 23:46:42.530105 WARNING::Fitting problem for feature 62 returning NA
2025-01-24 23:46:42.609747 WARNING::Fitting problem for feature 74 returning NA
2025-01-24 23:46:42.633083 WARNING::Fitting problem for feature 78 returning NA
2025-01-24 23:46:42.670049 WARNING::Fitting problem for feature 84 returning NA
2025-01-24 23:46:42.754106 WARNING::Fitting problem for feature 96 returning NA
2025-01-24 23:46:42.759977 WARNING::Fitting problem for feature 97 returning NA
2025-01-24 23:46:42.773496 WARNING::Fitting problem for feature 99 returning NA
2025-01-24 23:46:42.881254 WARNING::Fitting problem for feature 114 returning NA
2025-01-24 23:46:42.887442 WARNING::Fitting problem for feature 115 returning NA
2025-01-24 23:46:42.942685 WARNING::Fitting problem for feature 123 returning NA
2025-01-24 23:46:43.025083 WARNING::Fitting problem for feature 130 returning NA
2025-01-24 23:46:43.039134 WARNING::Fitting problem for feature 132 returning NA
2025-01-24 23:46:43.084738 WARNING::Fitting problem for feature 139 returning NA
2025-01-24 23:46:43.157314 WARNING::Fitting problem for feature 150 returning NA
2025-01-24 23:46:43.36474 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_linear.rds
2025-01-24 23:46:43.426579 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_linear.rds
2025-01-24 23:46:43.490208 WARNING::Deleting existing residuals file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/residuals_logistic.rds
2025-01-24 23:46:43.79057 WARNING::Deleting existing fitted file: /tmp/RtmpbKZQ7K/file435b647da1c82/fits/fitted_logistic.rds
2025-01-24 23:47:00.578383 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-24 23:47:00.590703 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-24 23:47:00.597512 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-24 23:47:00.646539 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-24 23:47:00.658828 ERROR::Effect name not found in metadata: d
2025-01-24 23:47:00.665131 ERROR::No user formula provided
2025-01-24 23:47:00.691354 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-24 23:47:00.697982 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-24 23:47:03.412576 INFO::Writing function arguments to log file
2025-01-24 23:47:03.426289 INFO::Verifying options selected are valid
2025-01-24 23:47:05.289854 INFO::Writing function arguments to log file
2025-01-24 23:47:05.301027 INFO::Verifying options selected are valid
2025-01-24 23:47:05.302044 INFO::Determining format of input files
2025-01-24 23:47:05.303051 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 23:47:05.305416 INFO::Running selected normalization method: TSS
2025-01-24 23:47:05.306854 INFO::Creating output feature tables folder
2025-01-24 23:47:05.307859 INFO::Writing normalized data to file /tmp/RtmpbKZQ7K/file435b6179a8c08/features/data_norm.tsv
2025-01-24 23:47:05.309439 INFO::Filter data based on min abundance and min prevalence
2025-01-24 23:47:05.31035 INFO::Total samples in data: 16
2025-01-24 23:47:05.311228 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-24 23:47:05.313155 INFO::Total filtered features: 0
2025-01-24 23:47:05.314148 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-24 23:47:05.315375 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-24 23:47:05.316339 INFO::Filtered feature names from variance filtering:
2025-01-24 23:47:05.317231 INFO::Writing filtered data to file /tmp/RtmpbKZQ7K/file435b6179a8c08/features/filtered_data.tsv
2025-01-24 23:47:05.318812 INFO::Running selected transform method: LOG
2025-01-24 23:47:05.32004 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbKZQ7K/file435b6179a8c08/features/data_transformed.tsv
2025-01-24 23:47:05.321791 INFO::Applying z-score to standardize continuous metadata
2025-01-24 23:47:05.327476 INFO::Running the linear model component
2025-01-24 23:47:05.330309 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:05.335004 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:05.339553 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:05.347148 INFO::Counting total values for each feature
2025-01-24 23:47:05.349091 INFO::Running the logistic model component
2025-01-24 23:47:05.352028 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:05.358597 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:05.364866 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:05.373992 INFO::Counting total values for each feature
2025-01-24 23:47:05.376278 INFO::Re-running abundances for warn_prevalence
2025-01-24 23:47:05.377242 INFO::Running selected normalization method: TSS
2025-01-24 23:47:05.378745 INFO::Running selected transform method: LOG
2025-01-24 23:47:05.381748 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:05.386162 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:05.39044 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:05.477114 INFO::Creating fits folder
2025-01-24 23:47:05.478488 INFO::Writing residuals to file /tmp/RtmpbKZQ7K/file435b6179a8c08/fits/residuals_linear.rds
2025-01-24 23:47:05.479775 INFO::Writing fitted values to file /tmp/RtmpbKZQ7K/file435b6179a8c08/fits/fitted_linear.rds
2025-01-24 23:47:05.481135 INFO::Writing residuals to file /tmp/RtmpbKZQ7K/file435b6179a8c08/fits/residuals_logistic.rds
2025-01-24 23:47:05.494858 INFO::Writing fitted values to file /tmp/RtmpbKZQ7K/file435b6179a8c08/fits/fitted_logistic.rds
2025-01-24 23:47:05.497782 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpbKZQ7K/file435b6179a8c08/all_results.tsv
2025-01-24 23:47:05.499581 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/RtmpbKZQ7K/file435b6179a8c08/significant_results.tsv
2025-01-24 23:47:05.500985 INFO::Creating output figures folder
2025-01-24 23:47:05.502376 INFO::Writing summary plot of significant
results to file: /tmp/RtmpbKZQ7K/file435b6179a8c08/figures/summary_plot.pdf
2025-01-24 23:47:06.70566 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbKZQ7K/file435b6179a8c08/figures
2025-01-24 23:47:06.707638 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-24 23:47:06.712935 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-24 23:47:07.113725 INFO::Writing summary plot of
significant results to file: /tmp/RtmpbKZQ7K/file435b6179a8c08/figures/summary_plot.pdf
2025-01-24 23:47:08.364783 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbKZQ7K/file435b6179a8c08/figures
2025-01-24 23:47:08.366677 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-24 23:47:08.372487 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-24 23:47:08.786426 INFO::Running the linear model component
2025-01-24 23:47:08.789758 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:08.794729 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:08.798999 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:08.806474 INFO::Counting total values for each feature
2025-01-24 23:47:08.808238 INFO::Running the logistic model component
2025-01-24 23:47:08.810942 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:08.817543 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:08.823481 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:08.832279 INFO::Counting total values for each feature
2025-01-24 23:47:08.834369 INFO::Re-running abundances for warn_prevalence
2025-01-24 23:47:08.835179 INFO::Running selected normalization method: TSS
2025-01-24 23:47:08.836564 INFO::Running selected transform method: LOG
2025-01-24 23:47:08.839414 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:08.84362 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:08.84764 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:08.937937 INFO::Creating output folder
2025-01-24 23:47:08.939296 INFO::Creating output figures folder
2025-01-24 23:47:08.94092 INFO::Writing summary plot of significant
results to file: /tmp/RtmpbKZQ7K/file435b6412519d2/figures/summary_plot.pdf
2025-01-24 23:47:10.250556 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbKZQ7K/file435b6412519d2/figures
2025-01-24 23:47:10.25227 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-24 23:47:10.257515 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-24 23:47:11.096298 INFO::Applying z-score to standardize continuous metadata
2025-01-24 23:47:11.104345 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-24 23:47:11.10523 INFO::Bypass z-score application to metadata
2025-01-24 23:47:11.107892 INFO::Bypass z-score application to metadata
2025-01-24 23:47:11.126194 INFO::Determining format of input files
2025-01-24 23:47:11.127237 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 23:47:11.12816 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-24 23:47:11.135147 INFO::Determining format of input files
2025-01-24 23:47:11.136131 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-24 23:47:11.137399 INFO::Input format is feature_specific_covariate samples as columns
2025-01-24 23:47:11.14532 INFO::Determining format of input files
2025-01-24 23:47:11.14628 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 23:47:11.147348 INFO::Input format is feature_specific_covariate samples as columns
2025-01-24 23:47:11.14902 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-01-24 23:47:11.149798 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-01-24 23:47:11.160689 INFO::Running selected transform method: LOG
2025-01-24 23:47:11.162 INFO::Creating output feature tables folder
2025-01-24 23:47:11.162953 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbKZQ7K/file435b618bbbfbf/features/data_transformed.tsv
2025-01-24 23:47:11.167103 INFO::Running selected transform method: LOG
2025-01-24 23:47:11.168186 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbKZQ7K/file435b618bbbfbf/features/data_transformed.tsv
2025-01-24 23:47:11.171874 INFO::Running selected transform method: PLOG
2025-01-24 23:47:11.173432 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbKZQ7K/file435b618bbbfbf/features/data_transformed.tsv
2025-01-24 23:47:11.176302 INFO::Running selected transform method: NONE
2025-01-24 23:47:11.177047 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbKZQ7K/file435b618bbbfbf/features/data_transformed.tsv
2025-01-24 23:47:11.184397 INFO::Running the linear model component
2025-01-24 23:47:11.187181 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:11.191728 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:11.196277 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:11.203599 INFO::Counting total values for each feature
2025-01-24 23:47:11.205481 INFO::Running the logistic model component
2025-01-24 23:47:11.208301 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:11.214768 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:11.220867 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:11.229914 INFO::Counting total values for each feature
2025-01-24 23:47:11.232027 INFO::Re-running abundances for warn_prevalence
2025-01-24 23:47:11.232871 INFO::Running selected normalization method: TSS
2025-01-24 23:47:11.23423 INFO::Running selected transform method: LOG
2025-01-24 23:47:11.23704 INFO::Fitting model to feature number 1, a
2025-01-24 23:47:11.24122 INFO::Fitting model to feature number 2, b
2025-01-24 23:47:11.245235 INFO::Fitting model to feature number 3, c
2025-01-24 23:47:11.333538 INFO::Creating output folder
2025-01-24 23:47:11.334696 INFO::Creating fits folder
2025-01-24 23:47:11.335604 INFO::Writing residuals to file /tmp/RtmpbKZQ7K/file435b62a9d6784/fits/residuals_linear.rds
2025-01-24 23:47:11.336581 INFO::Writing fitted values to file /tmp/RtmpbKZQ7K/file435b62a9d6784/fits/fitted_linear.rds
2025-01-24 23:47:11.337649 INFO::Writing residuals to file /tmp/RtmpbKZQ7K/file435b62a9d6784/fits/residuals_logistic.rds
2025-01-24 23:47:11.338674 INFO::Writing fitted values to file /tmp/RtmpbKZQ7K/file435b62a9d6784/fits/fitted_logistic.rds
2025-01-24 23:47:11.341294 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpbKZQ7K/file435b62a9d6784/all_results.tsv
2025-01-24 23:47:11.342798 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/RtmpbKZQ7K/file435b62a9d6784/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
148.850 2.590 151.428
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.300 | 0.811 | 20.114 | |
| maaslin_check_arguments | 0.172 | 0.004 | 0.176 | |
| maaslin_check_formula | 0.169 | 0.005 | 0.173 | |
| maaslin_compute_formula | 0.168 | 0.004 | 0.172 | |
| maaslin_contrast_test | 16.73 | 0.33 | 17.06 | |
| maaslin_filter | 0.441 | 0.024 | 0.464 | |
| maaslin_fit | 12.344 | 0.166 | 12.510 | |
| maaslin_log_arguments | 0.166 | 0.005 | 0.171 | |
| maaslin_normalize | 0.292 | 0.006 | 0.299 | |
| maaslin_plot_results | 35.892 | 0.392 | 36.252 | |
| maaslin_plot_results_from_output | 35.383 | 0.359 | 35.744 | |
| maaslin_process_metadata | 0.479 | 0.014 | 0.493 | |
| maaslin_read_data | 0.156 | 0.002 | 0.157 | |
| maaslin_reorder_data | 0.161 | 0.003 | 0.165 | |
| maaslin_transform | 0.567 | 0.011 | 0.579 | |
| maaslin_write_results | 13.383 | 0.197 | 13.582 | |
| maaslin_write_results_lefse_format | 14.631 | 0.172 | 14.805 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |