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 15:39 -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. - 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: 2025-01-25 08:24:35 -0000 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 08:36:27 -0000 (Sat, 25 Jan 2025) |
| EllapsedTime: 711.8 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 54.027 0.351 54.491
maaslin_plot_results_from_output 52.630 0.291 53.027
maaslin3 32.742 1.035 33.845
maaslin_contrast_test 28.825 0.391 29.284
maaslin_write_results_lefse_format 25.079 0.112 25.258
maaslin_write_results 22.646 0.116 22.811
maaslin_fit 21.310 0.068 21.422
* 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")
2025-01-25 08:33:01.345474 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:33:01.486377 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:33:01.624753 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:33:01.659125 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:33:01.726253 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:33:01.849271 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:33:01.858112 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:33:01.876889 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:33:02.043823 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:33:02.052387 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:33:02.132452 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:33:02.208129 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:33:02.228667 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:33:02.298134 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:33:02.416115 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:33:27.43149 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:33:27.560323 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:33:27.698658 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:33:27.736266 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:33:27.795202 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:33:27.936984 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:33:27.945212 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:33:27.96345 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:33:28.115177 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:33:28.123428 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:33:28.201401 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:33:28.265446 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:33:28.283971 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:33:28.347285 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:33:28.456259 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:33:53.166665 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:33:53.292612 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:33:53.435824 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:33:53.469939 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:33:53.523255 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:33:53.640849 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:33:53.64893 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:33:53.666859 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:33:53.812931 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:33:53.821017 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:33:53.897745 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:33:53.959383 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:33:53.977424 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:33:54.03871 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:33:54.144441 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:34:15.684605 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:34:15.817036 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:34:15.949308 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:34:15.988426 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:34:16.051991 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:34:16.188045 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:34:16.197321 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:34:16.219149 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:34:16.40153 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:34:16.411295 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:34:16.504448 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:34:16.61017 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:34:16.629857 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:34:16.697101 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:34:16.811246 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:34:17.111803 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_linear.rds
2025-01-25 08:34:17.180453 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_linear.rds
2025-01-25 08:34:17.251641 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_logistic.rds
2025-01-25 08:34:17.59849 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_logistic.rds
2025-01-25 08:34:39.035385 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:34:39.156723 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:34:39.275759 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:34:39.310199 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:34:39.364828 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:34:39.487127 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:34:39.495372 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:34:39.513942 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:34:39.667056 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:34:39.675488 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:34:39.754157 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:34:39.8183 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:34:39.837313 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:34:39.90213 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:34:40.014174 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:35:00.065638 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:35:00.19004 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:35:00.313607 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:35:00.349399 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:35:00.405991 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:35:00.533481 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:35:00.542319 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:35:00.562265 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:35:00.714753 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:35:00.72278 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:35:00.798591 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:35:00.859597 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:35:00.877543 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:35:00.939962 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:35:01.046781 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:35:01.382684 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_linear.rds
2025-01-25 08:35:01.443622 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_linear.rds
2025-01-25 08:35:01.507058 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_logistic.rds
2025-01-25 08:35:01.79975 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_logistic.rds
2025-01-25 08:35:23.052801 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:35:23.177029 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:35:23.299562 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:35:23.335398 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:35:23.392612 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:35:23.549062 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:35:23.557546 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:35:23.576849 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:35:23.735842 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:35:23.744581 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:35:23.829066 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:35:23.896098 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:35:23.915941 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:35:23.983773 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:35:24.095893 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:35:43.912673 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 08:35:44.031162 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 08:35:44.147558 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 08:35:44.181528 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 08:35:44.269966 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 08:35:44.392049 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 08:35:44.4004 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 08:35:44.419145 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 08:35:44.575928 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 08:35:44.584432 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 08:35:44.665231 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 08:35:44.730268 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 08:35:44.749279 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 08:35:44.815795 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 08:35:44.928929 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 08:35:45.23313 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_linear.rds
2025-01-25 08:35:45.301856 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_linear.rds
2025-01-25 08:35:45.372837 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/residuals_logistic.rds
2025-01-25 08:35:45.719346 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e9a5241c/fits/fitted_logistic.rds
2025-01-25 08:36:06.31127 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-25 08:36:06.327956 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-25 08:36:06.336899 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-25 08:36:06.404949 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-25 08:36:06.421679 ERROR::Effect name not found in metadata: d
2025-01-25 08:36:06.430163 ERROR::No user formula provided
2025-01-25 08:36:06.464919 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-25 08:36:06.474042 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-25 08:36:10.995244 INFO::Writing function arguments to log file
2025-01-25 08:36:11.014601 INFO::Verifying options selected are valid
2025-01-25 08:36:13.558415 INFO::Writing function arguments to log file
2025-01-25 08:36:13.576023 INFO::Verifying options selected are valid
2025-01-25 08:36:13.57752 INFO::Determining format of input files
2025-01-25 08:36:13.5789 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 08:36:13.582287 INFO::Running selected normalization method: TSS
2025-01-25 08:36:13.584431 INFO::Creating output feature tables folder
2025-01-25 08:36:13.58595 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/features/data_norm.tsv
2025-01-25 08:36:13.58818 INFO::Filter data based on min abundance and min prevalence
2025-01-25 08:36:13.589588 INFO::Total samples in data: 16
2025-01-25 08:36:13.590898 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-25 08:36:13.593803 INFO::Total filtered features: 0
2025-01-25 08:36:13.595257 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-25 08:36:13.597044 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-25 08:36:13.598449 INFO::Filtered feature names from variance filtering:
2025-01-25 08:36:13.599821 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/features/filtered_data.tsv
2025-01-25 08:36:13.602247 INFO::Running selected transform method: LOG
2025-01-25 08:36:13.604169 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/features/data_transformed.tsv
2025-01-25 08:36:13.60693 INFO::Applying z-score to standardize continuous metadata
2025-01-25 08:36:13.61474 INFO::Running the linear model component
2025-01-25 08:36:13.619379 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:13.626403 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:13.633297 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:13.644264 INFO::Counting total values for each feature
2025-01-25 08:36:13.647191 INFO::Running the logistic model component
2025-01-25 08:36:13.65141 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:13.661196 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:13.670778 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:13.684452 INFO::Counting total values for each feature
2025-01-25 08:36:13.687815 INFO::Re-running abundances for warn_prevalence
2025-01-25 08:36:13.689254 INFO::Running selected normalization method: TSS
2025-01-25 08:36:13.691437 INFO::Running selected transform method: LOG
2025-01-25 08:36:13.695837 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:13.702511 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:13.709157 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:13.840103 INFO::Creating fits folder
2025-01-25 08:36:13.841784 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/fits/residuals_linear.rds
2025-01-25 08:36:13.843342 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/fits/fitted_linear.rds
2025-01-25 08:36:13.844964 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/fits/residuals_logistic.rds
2025-01-25 08:36:13.846586 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/fits/fitted_logistic.rds
2025-01-25 08:36:13.850405 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/all_results.tsv
2025-01-25 08:36:13.852925 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/RtmpfoOOdD/file30da3e74497102/significant_results.tsv
2025-01-25 08:36:13.854876 INFO::Creating output figures folder
2025-01-25 08:36:13.856931 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/figures/summary_plot.pdf
2025-01-25 08:36:15.577708 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/figures
2025-01-25 08:36:15.58014 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 08:36:15.587506 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 08:36:16.104801 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/figures/summary_plot.pdf
2025-01-25 08:36:17.83088 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e74497102/figures
2025-01-25 08:36:17.832937 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 08:36:17.840148 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 08:36:18.360315 INFO::Running the linear model component
2025-01-25 08:36:18.365017 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:18.372547 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:18.379936 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:18.392025 INFO::Counting total values for each feature
2025-01-25 08:36:18.395133 INFO::Running the logistic model component
2025-01-25 08:36:18.399934 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:18.411263 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:18.421693 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:18.436462 INFO::Counting total values for each feature
2025-01-25 08:36:18.439757 INFO::Re-running abundances for warn_prevalence
2025-01-25 08:36:18.440975 INFO::Running selected normalization method: TSS
2025-01-25 08:36:18.443 INFO::Running selected transform method: LOG
2025-01-25 08:36:18.447392 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:18.453921 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:18.460348 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:18.590905 INFO::Creating output folder
2025-01-25 08:36:18.592227 INFO::Creating output figures folder
2025-01-25 08:36:18.602301 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e7e991bf4/figures/summary_plot.pdf
2025-01-25 08:36:20.36949 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfoOOdD/file30da3e7e991bf4/figures
2025-01-25 08:36:20.371644 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 08:36:20.378845 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 08:36:21.587143 INFO::Applying z-score to standardize continuous metadata
2025-01-25 08:36:21.598422 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-25 08:36:21.59966 INFO::Bypass z-score application to metadata
2025-01-25 08:36:21.603471 INFO::Bypass z-score application to metadata
2025-01-25 08:36:21.630602 INFO::Determining format of input files
2025-01-25 08:36:21.63193 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 08:36:21.633221 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-25 08:36:21.644068 INFO::Determining format of input files
2025-01-25 08:36:21.645673 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-25 08:36:21.647608 INFO::Input format is feature_specific_covariate samples as columns
2025-01-25 08:36:21.660089 INFO::Determining format of input files
2025-01-25 08:36:21.661649 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 08:36:21.663229 INFO::Input format is feature_specific_covariate samples as columns
2025-01-25 08:36:21.665967 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-01-25 08:36:21.667232 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-01-25 08:36:21.683681 INFO::Running selected transform method: LOG
2025-01-25 08:36:21.685382 INFO::Creating output feature tables folder
2025-01-25 08:36:21.686712 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e43a9d46f/features/data_transformed.tsv
2025-01-25 08:36:21.692613 INFO::Running selected transform method: LOG
2025-01-25 08:36:21.694301 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e43a9d46f/features/data_transformed.tsv
2025-01-25 08:36:21.700036 INFO::Running selected transform method: PLOG
2025-01-25 08:36:21.702647 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e43a9d46f/features/data_transformed.tsv
2025-01-25 08:36:21.707136 INFO::Running selected transform method: NONE
2025-01-25 08:36:21.708387 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e43a9d46f/features/data_transformed.tsv
2025-01-25 08:36:21.719655 INFO::Running the linear model component
2025-01-25 08:36:21.724235 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:21.731331 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:21.738141 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:21.749202 INFO::Counting total values for each feature
2025-01-25 08:36:21.751889 INFO::Running the logistic model component
2025-01-25 08:36:21.756169 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:21.765808 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:21.775231 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:21.788833 INFO::Counting total values for each feature
2025-01-25 08:36:21.792032 INFO::Re-running abundances for warn_prevalence
2025-01-25 08:36:21.793361 INFO::Running selected normalization method: TSS
2025-01-25 08:36:21.795488 INFO::Running selected transform method: LOG
2025-01-25 08:36:21.800113 INFO::Fitting model to feature number 1, a
2025-01-25 08:36:21.806875 INFO::Fitting model to feature number 2, b
2025-01-25 08:36:21.813568 INFO::Fitting model to feature number 3, c
2025-01-25 08:36:21.969327 INFO::Creating output folder
2025-01-25 08:36:21.970757 INFO::Creating fits folder
2025-01-25 08:36:21.972042 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e29c5e3a9/fits/residuals_linear.rds
2025-01-25 08:36:21.973525 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e29c5e3a9/fits/fitted_linear.rds
2025-01-25 08:36:21.975054 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e29c5e3a9/fits/residuals_logistic.rds
2025-01-25 08:36:21.976622 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfoOOdD/file30da3e29c5e3a9/fits/fitted_logistic.rds
2025-01-25 08:36:21.980294 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpfoOOdD/file30da3e29c5e3a9/all_results.tsv
2025-01-25 08:36:21.982754 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/RtmpfoOOdD/file30da3e29c5e3a9/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
212.356 2.397 215.138
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 32.742 | 1.035 | 33.845 | |
| maaslin_check_arguments | 0.253 | 0.008 | 0.262 | |
| maaslin_check_formula | 0.261 | 0.008 | 0.269 | |
| maaslin_compute_formula | 0.283 | 0.020 | 0.304 | |
| maaslin_contrast_test | 28.825 | 0.391 | 29.284 | |
| maaslin_filter | 1.542 | 0.008 | 1.553 | |
| maaslin_fit | 21.310 | 0.068 | 21.422 | |
| maaslin_log_arguments | 0.243 | 0.012 | 0.256 | |
| maaslin_normalize | 0.439 | 0.008 | 0.448 | |
| maaslin_plot_results | 54.027 | 0.351 | 54.491 | |
| maaslin_plot_results_from_output | 52.630 | 0.291 | 53.027 | |
| maaslin_process_metadata | 0.744 | 0.020 | 0.766 | |
| maaslin_read_data | 0.250 | 0.004 | 0.254 | |
| maaslin_reorder_data | 0.260 | 0.008 | 0.268 | |
| maaslin_transform | 0.850 | 0.004 | 0.855 | |
| maaslin_write_results | 22.646 | 0.116 | 22.811 | |
| maaslin_write_results_lefse_format | 25.079 | 0.112 | 25.258 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |