William Nickols
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 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 2025-01-28 11:47 -0500 (Tue, 28 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" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 0.99.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_0.99.3.tar.gz |
| StartedAt: 2025-01-28 11:59:33 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 12:11:24 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 710.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_0.99.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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_from_output 53.948 0.358 54.422
maaslin_plot_results 52.765 0.323 53.205
maaslin3 33.017 0.775 33.871
maaslin_contrast_test 29.399 0.275 29.758
maaslin_write_results_lefse_format 25.330 0.175 25.570
maaslin_write_results 22.951 0.244 23.241
maaslin_fit 21.050 0.044 21.141
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘maaslin3’ ... ** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-01-28 12:07:57.135857 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:07:57.271217 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:07:57.408154 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:07:57.443304 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:07:57.509717 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:07:57.634227 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:07:57.642495 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:07:57.661429 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:07:57.827021 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:07:57.835335 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:07:57.915832 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:07:57.990461 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:07:58.009402 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:07:58.07386 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:07:58.187547 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:08:23.551688 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:08:23.675955 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:08:23.805391 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:08:23.843219 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:08:23.904306 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:08:24.050842 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:08:24.059303 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:08:24.078707 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:08:24.233304 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:08:24.24184 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:08:24.323014 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:08:24.388176 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:08:24.407111 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:08:24.471413 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:08:24.582229 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:08:49.453533 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:08:49.589742 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:08:49.746327 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:08:49.784967 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:08:49.845552 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:08:49.979576 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:08:49.988013 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:08:50.007111 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:08:50.161476 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:08:50.170035 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:08:50.250588 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:08:50.315976 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:08:50.33488 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:08:50.399127 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:08:50.513529 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:09:12.455992 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:09:12.589894 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:09:12.723998 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:09:12.762847 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:09:12.82421 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:09:12.961501 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:09:12.970754 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:09:12.992129 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:09:13.163258 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:09:13.172554 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:09:13.261145 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:09:13.364949 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:09:13.384018 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:09:13.448956 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:09:13.560889 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:09:13.857565 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_linear.rds
2025-01-28 12:09:13.923623 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_linear.rds
2025-01-28 12:09:13.992121 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_logistic.rds
2025-01-28 12:09:14.32501 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_logistic.rds
2025-01-28 12:09:35.836327 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:09:35.962418 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:09:36.083123 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:09:36.117152 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:09:36.170884 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:09:36.288655 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:09:36.296536 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:09:36.314571 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:09:36.465721 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:09:36.4741 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:09:36.553278 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:09:36.616216 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:09:36.635149 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:09:36.700024 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:09:36.809827 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:09:56.963726 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:09:57.091878 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:09:57.216381 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:09:57.253211 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:09:57.309633 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:09:57.433045 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:09:57.441289 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:09:57.459865 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:09:57.608919 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:09:57.616991 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:09:57.692671 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:09:57.754999 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:09:57.773358 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:09:57.837383 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:09:57.945601 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:09:58.280219 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_linear.rds
2025-01-28 12:09:58.349202 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_linear.rds
2025-01-28 12:09:58.420835 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_logistic.rds
2025-01-28 12:09:58.769101 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_logistic.rds
2025-01-28 12:10:20.514038 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:10:20.641863 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:10:20.770957 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:10:20.807837 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:10:20.867679 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:10:21.032193 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:10:21.041163 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:10:21.061364 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:10:21.229709 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:10:21.239032 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:10:21.323603 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:10:21.392154 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:10:21.412967 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:10:21.482466 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:10:21.603791 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:10:41.698452 WARNING::Fitting problem for feature 50 returning NA
2025-01-28 12:10:41.82479 WARNING::Fitting problem for feature 62 returning NA
2025-01-28 12:10:41.948687 WARNING::Fitting problem for feature 74 returning NA
2025-01-28 12:10:41.985275 WARNING::Fitting problem for feature 78 returning NA
2025-01-28 12:10:42.086196 WARNING::Fitting problem for feature 84 returning NA
2025-01-28 12:10:42.218242 WARNING::Fitting problem for feature 96 returning NA
2025-01-28 12:10:42.227011 WARNING::Fitting problem for feature 97 returning NA
2025-01-28 12:10:42.247254 WARNING::Fitting problem for feature 99 returning NA
2025-01-28 12:10:42.411555 WARNING::Fitting problem for feature 114 returning NA
2025-01-28 12:10:42.420598 WARNING::Fitting problem for feature 115 returning NA
2025-01-28 12:10:42.503374 WARNING::Fitting problem for feature 123 returning NA
2025-01-28 12:10:42.57053 WARNING::Fitting problem for feature 130 returning NA
2025-01-28 12:10:42.590238 WARNING::Fitting problem for feature 132 returning NA
2025-01-28 12:10:42.658064 WARNING::Fitting problem for feature 139 returning NA
2025-01-28 12:10:42.775442 WARNING::Fitting problem for feature 150 returning NA
2025-01-28 12:10:43.094382 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_linear.rds
2025-01-28 12:10:43.165439 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_linear.rds
2025-01-28 12:10:43.238052 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/residuals_logistic.rds
2025-01-28 12:10:43.58303 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpkZ8LEW/file301383c4d0702/fits/fitted_logistic.rds
2025-01-28 12:11:04.35079 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-28 12:11:04.367548 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-28 12:11:04.376461 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-28 12:11:04.44595 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-28 12:11:04.462487 ERROR::Effect name not found in metadata: d
2025-01-28 12:11:04.471186 ERROR::No user formula provided
2025-01-28 12:11:04.507462 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-28 12:11:04.516491 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-28 12:11:09.019331 INFO::Writing function arguments to log file
2025-01-28 12:11:09.039485 INFO::Verifying options selected are valid
2025-01-28 12:11:11.605901 INFO::Writing function arguments to log file
2025-01-28 12:11:11.624467 INFO::Verifying options selected are valid
2025-01-28 12:11:11.626066 INFO::Determining format of input files
2025-01-28 12:11:11.627595 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-28 12:11:11.631137 INFO::Running selected normalization method: TSS
2025-01-28 12:11:11.633392 INFO::Creating output feature tables folder
2025-01-28 12:11:11.634979 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/features/data_norm.tsv
2025-01-28 12:11:11.637339 INFO::Filter data based on min abundance and min prevalence
2025-01-28 12:11:11.638795 INFO::Total samples in data: 16
2025-01-28 12:11:11.640225 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-28 12:11:11.643212 INFO::Total filtered features: 0
2025-01-28 12:11:11.644767 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-28 12:11:11.646645 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-28 12:11:11.64814 INFO::Filtered feature names from variance filtering:
2025-01-28 12:11:11.649635 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/features/filtered_data.tsv
2025-01-28 12:11:11.652015 INFO::Running selected transform method: LOG
2025-01-28 12:11:11.653955 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/features/data_transformed.tsv
2025-01-28 12:11:11.656638 INFO::Applying z-score to standardize continuous metadata
2025-01-28 12:11:11.664385 INFO::Running the linear model component
2025-01-28 12:11:11.66889 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:11.676025 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:11.683108 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:11.69433 INFO::Counting total values for each feature
2025-01-28 12:11:11.697376 INFO::Running the logistic model component
2025-01-28 12:11:11.701865 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:11.712116 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:11.722346 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:11.737119 INFO::Counting total values for each feature
2025-01-28 12:11:11.740888 INFO::Re-running abundances for warn_prevalence
2025-01-28 12:11:11.742608 INFO::Running selected normalization method: TSS
2025-01-28 12:11:11.745293 INFO::Running selected transform method: LOG
2025-01-28 12:11:11.750381 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:11.757906 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:11.765397 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:11.899682 INFO::Creating fits folder
2025-01-28 12:11:11.901463 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/fits/residuals_linear.rds
2025-01-28 12:11:11.903045 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/fits/fitted_linear.rds
2025-01-28 12:11:11.904624 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/fits/residuals_logistic.rds
2025-01-28 12:11:11.906242 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/fits/fitted_logistic.rds
2025-01-28 12:11:11.909938 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/all_results.tsv
2025-01-28 12:11:11.912622 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): /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/significant_results.tsv
2025-01-28 12:11:11.914749 INFO::Creating output figures folder
2025-01-28 12:11:11.916961 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/figures/summary_plot.pdf
2025-01-28 12:11:13.645718 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/figures
2025-01-28 12:11:13.648031 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-28 12:11:13.655176 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-28 12:11:14.166999 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/figures/summary_plot.pdf
2025-01-28 12:11:15.916607 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpkZ8LEW/file3013834fa8a85b/figures
2025-01-28 12:11:15.91859 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-28 12:11:15.92551 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-28 12:11:16.437194 INFO::Running the linear model component
2025-01-28 12:11:16.441308 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:16.447579 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:16.453698 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:16.463922 INFO::Counting total values for each feature
2025-01-28 12:11:16.466537 INFO::Running the logistic model component
2025-01-28 12:11:16.470494 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:16.479466 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:16.488377 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:16.501466 INFO::Counting total values for each feature
2025-01-28 12:11:16.504541 INFO::Re-running abundances for warn_prevalence
2025-01-28 12:11:16.505722 INFO::Running selected normalization method: TSS
2025-01-28 12:11:16.507705 INFO::Running selected transform method: LOG
2025-01-28 12:11:16.512032 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:16.518306 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:16.524441 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:16.651791 INFO::Creating output folder
2025-01-28 12:11:16.653198 INFO::Creating output figures folder
2025-01-28 12:11:16.654911 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpkZ8LEW/file3013835372f4cb/figures/summary_plot.pdf
2025-01-28 12:11:18.422976 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpkZ8LEW/file3013835372f4cb/figures
2025-01-28 12:11:18.425064 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-28 12:11:18.431922 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-28 12:11:19.624213 INFO::Applying z-score to standardize continuous metadata
2025-01-28 12:11:19.635034 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-28 12:11:19.636212 INFO::Bypass z-score application to metadata
2025-01-28 12:11:19.63983 INFO::Bypass z-score application to metadata
2025-01-28 12:11:19.666209 INFO::Determining format of input files
2025-01-28 12:11:19.667537 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-28 12:11:19.668729 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-28 12:11:19.679128 INFO::Determining format of input files
2025-01-28 12:11:19.680681 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-28 12:11:19.682552 INFO::Input format is feature_specific_covariate samples as columns
2025-01-28 12:11:19.694071 INFO::Determining format of input files
2025-01-28 12:11:19.695515 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-28 12:11:19.696967 INFO::Input format is feature_specific_covariate samples as columns
2025-01-28 12:11:19.699377 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-01-28 12:11:19.700523 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-01-28 12:11:19.71601 INFO::Running selected transform method: LOG
2025-01-28 12:11:19.717612 INFO::Creating output feature tables folder
2025-01-28 12:11:19.718897 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383263886ac/features/data_transformed.tsv
2025-01-28 12:11:19.72449 INFO::Running selected transform method: LOG
2025-01-28 12:11:19.72613 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383263886ac/features/data_transformed.tsv
2025-01-28 12:11:19.731687 INFO::Running selected transform method: PLOG
2025-01-28 12:11:19.734206 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383263886ac/features/data_transformed.tsv
2025-01-28 12:11:19.738482 INFO::Running selected transform method: NONE
2025-01-28 12:11:19.73968 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383263886ac/features/data_transformed.tsv
2025-01-28 12:11:19.749744 INFO::Running the linear model component
2025-01-28 12:11:19.753747 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:19.759969 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:19.766281 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:19.776541 INFO::Counting total values for each feature
2025-01-28 12:11:19.779096 INFO::Running the logistic model component
2025-01-28 12:11:19.78305 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:19.792321 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:19.80132 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:19.814191 INFO::Counting total values for each feature
2025-01-28 12:11:19.817302 INFO::Re-running abundances for warn_prevalence
2025-01-28 12:11:19.818465 INFO::Running selected normalization method: TSS
2025-01-28 12:11:19.820452 INFO::Running selected transform method: LOG
2025-01-28 12:11:19.82478 INFO::Fitting model to feature number 1, a
2025-01-28 12:11:19.831059 INFO::Fitting model to feature number 2, b
2025-01-28 12:11:19.837397 INFO::Fitting model to feature number 3, c
2025-01-28 12:11:19.988267 INFO::Creating output folder
2025-01-28 12:11:19.989778 INFO::Creating fits folder
2025-01-28 12:11:19.991089 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/fits/residuals_linear.rds
2025-01-28 12:11:19.992489 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/fits/fitted_linear.rds
2025-01-28 12:11:19.994028 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/fits/residuals_logistic.rds
2025-01-28 12:11:19.995575 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/fits/fitted_logistic.rds
2025-01-28 12:11:19.999267 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/all_results.tsv
2025-01-28 12:11:20.001714 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): /home/biocbuild/tmp/RtmpkZ8LEW/file301383753b8ce/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
214.943 2.452 217.837
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 33.017 | 0.775 | 33.871 | |
| maaslin_check_arguments | 0.261 | 0.012 | 0.274 | |
| maaslin_check_formula | 0.253 | 0.016 | 0.270 | |
| maaslin_compute_formula | 0.302 | 0.008 | 0.311 | |
| maaslin_contrast_test | 29.399 | 0.275 | 29.758 | |
| maaslin_filter | 1.537 | 0.008 | 1.548 | |
| maaslin_fit | 21.050 | 0.044 | 21.141 | |
| maaslin_log_arguments | 0.245 | 0.000 | 0.245 | |
| maaslin_normalize | 0.437 | 0.004 | 0.442 | |
| maaslin_plot_results | 52.765 | 0.323 | 53.205 | |
| maaslin_plot_results_from_output | 53.948 | 0.358 | 54.422 | |
| maaslin_process_metadata | 0.724 | 0.021 | 0.747 | |
| maaslin_read_data | 0.236 | 0.008 | 0.245 | |
| maaslin_reorder_data | 0.255 | 0.000 | 0.256 | |
| maaslin_transform | 0.863 | 0.020 | 0.885 | |
| maaslin_write_results | 22.951 | 0.244 | 23.241 | |
| maaslin_write_results_lefse_format | 25.330 | 0.175 | 25.570 | |
| preprocess_dna_mtx | 0.006 | 0.000 | 0.005 | |