William Nickols
| Snapshot Date: 2025-01-28 13:40 -0500 (Tue, 28 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 2025-01-29 11:42 -0500 (Wed, 29 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" | 4661 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4457 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4468 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4421 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4411 |
| 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 | NA | ||||||||||
|
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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_0.99.3.tar.gz |
| StartedAt: 2025-01-29 02:08:48 -0500 (Wed, 29 Jan 2025) |
| EndedAt: 2025-01-29 02:19:53 -0500 (Wed, 29 Jan 2025) |
| EllapsedTime: 664.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_0.99.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'maaslin3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 47.54 1.97 49.50
maaslin_plot_results_from_output 46.99 1.95 49.39
maaslin3 28.34 1.14 29.70
maaslin_contrast_test 24.86 2.06 26.94
maaslin_write_results_lefse_format 21.89 1.51 23.41
maaslin_write_results 20.56 1.28 21.87
maaslin_fit 19.36 1.92 21.28
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-01-29 02:16:30.486208 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:16:31.31244 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:16:31.474189 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:16:31.522171 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:16:31.592933 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:16:31.717536 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:16:31.727613 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:16:31.749554 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:16:31.926135 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:16:31.941183 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:16:32.031561 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:16:32.080269 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:16:32.095129 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:16:32.144224 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:16:32.268555 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:16:52.419849 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:16:52.572004 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:16:52.721649 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:16:52.767299 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:16:52.839698 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:16:52.992202 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:16:53.003874 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:16:53.029984 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:16:53.17407 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:16:53.181675 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:16:53.259065 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:16:53.311871 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:16:53.327768 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:16:53.380744 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:16:53.481022 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:17:17.182988 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:17:17.358752 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:17:17.499161 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:17:17.539213 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:17:17.602283 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:17:17.690005 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:17:17.697393 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:17:17.71313 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:17:17.83542 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:17:18.818255 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:17:18.908019 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:17:18.984601 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:17:19.008784 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:17:19.071968 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:17:19.200467 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:17:37.087178 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:17:37.233949 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:17:37.380367 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:17:37.413608 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:17:37.483591 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:17:37.641299 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:17:37.652118 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:17:37.675404 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:17:37.855675 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:17:37.867907 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:17:37.965327 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:17:38.044072 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:17:38.063087 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:17:38.114354 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:17:38.210485 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:17:38.455798 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_linear.rds
2025-01-29 02:17:38.529231 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_linear.rds
2025-01-29 02:17:38.604355 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_logistic.rds
2025-01-29 02:17:38.885031 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_logistic.rds
2025-01-29 02:18:01.402618 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:18:01.537848 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:18:01.669456 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:18:01.70888 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:18:01.770306 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:18:01.904521 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:18:01.916132 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:18:01.944283 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:18:02.121866 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:18:02.135027 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:18:02.235867 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:18:02.315372 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:18:02.339127 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:18:02.418818 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:18:02.533721 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:18:20.846632 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:18:20.942121 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:18:21.124709 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:18:21.165307 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:18:21.226217 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:18:21.328189 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:18:21.335266 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:18:21.352821 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:18:21.533947 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:18:21.544852 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:18:21.644464 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:18:21.724985 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:18:21.750098 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:18:21.831922 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:18:21.91786 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:18:22.117738 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_linear.rds
2025-01-29 02:18:22.186742 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_linear.rds
2025-01-29 02:18:22.266147 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_logistic.rds
2025-01-29 02:18:22.577842 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_logistic.rds
2025-01-29 02:18:43.461934 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:18:43.554688 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:18:43.645673 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:18:43.674405 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:18:43.718578 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:18:43.814257 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:18:43.82203 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:18:43.837891 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:18:43.96809 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:18:43.977566 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:18:44.041636 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:18:44.095751 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:18:44.1132 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:18:44.188348 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:18:44.310125 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:19:03.720523 WARNING::Fitting problem for feature 50 returning NA
2025-01-29 02:19:03.873881 WARNING::Fitting problem for feature 62 returning NA
2025-01-29 02:19:04.02096 WARNING::Fitting problem for feature 74 returning NA
2025-01-29 02:19:04.057529 WARNING::Fitting problem for feature 78 returning NA
2025-01-29 02:19:04.10332 WARNING::Fitting problem for feature 84 returning NA
2025-01-29 02:19:04.206422 WARNING::Fitting problem for feature 96 returning NA
2025-01-29 02:19:04.218441 WARNING::Fitting problem for feature 97 returning NA
2025-01-29 02:19:04.2439 WARNING::Fitting problem for feature 99 returning NA
2025-01-29 02:19:04.436874 WARNING::Fitting problem for feature 114 returning NA
2025-01-29 02:19:04.449395 WARNING::Fitting problem for feature 115 returning NA
2025-01-29 02:19:04.530031 WARNING::Fitting problem for feature 123 returning NA
2025-01-29 02:19:04.589877 WARNING::Fitting problem for feature 130 returning NA
2025-01-29 02:19:04.614349 WARNING::Fitting problem for feature 132 returning NA
2025-01-29 02:19:04.741396 WARNING::Fitting problem for feature 139 returning NA
2025-01-29 02:19:04.870417 WARNING::Fitting problem for feature 150 returning NA
2025-01-29 02:19:05.173421 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_linear.rds
2025-01-29 02:19:05.246743 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_linear.rds
2025-01-29 02:19:05.308995 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/residuals_logistic.rds
2025-01-29 02:19:05.613295 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175546cfd14b1/fits/fitted_logistic.rds
2025-01-29 02:19:25.161033 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-29 02:19:25.179582 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-29 02:19:25.190105 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-29 02:19:25.256208 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-29 02:19:25.275112 ERROR::Effect name not found in metadata: d
2025-01-29 02:19:25.28557 ERROR::No user formula provided
2025-01-29 02:19:25.322077 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-29 02:19:25.328771 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-29 02:19:29.147044 INFO::Writing function arguments to log file
2025-01-29 02:19:29.180731 INFO::Verifying options selected are valid
2025-01-29 02:19:31.720985 INFO::Writing function arguments to log file
2025-01-29 02:19:31.761514 INFO::Verifying options selected are valid
2025-01-29 02:19:31.763311 INFO::Determining format of input files
2025-01-29 02:19:31.765071 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-29 02:19:31.76907 INFO::Running selected normalization method: TSS
2025-01-29 02:19:31.771369 INFO::Creating output feature tables folder
2025-01-29 02:19:31.773516 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/features/data_norm.tsv
2025-01-29 02:19:31.776332 INFO::Filter data based on min abundance and min prevalence
2025-01-29 02:19:31.778057 INFO::Total samples in data: 16
2025-01-29 02:19:31.779757 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-29 02:19:31.782458 INFO::Total filtered features: 0
2025-01-29 02:19:31.784123 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-29 02:19:31.786024 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-29 02:19:31.787686 INFO::Filtered feature names from variance filtering:
2025-01-29 02:19:31.789383 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/features/filtered_data.tsv
2025-01-29 02:19:31.792231 INFO::Running selected transform method: LOG
2025-01-29 02:19:31.794226 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/features/data_transformed.tsv
2025-01-29 02:19:31.797174 INFO::Applying z-score to standardize continuous metadata
2025-01-29 02:19:31.803402 INFO::Running the linear model component
2025-01-29 02:19:31.81038 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:31.816457 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:31.822251 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:31.830793 INFO::Counting total values for each feature
2025-01-29 02:19:31.833473 INFO::Running the logistic model component
2025-01-29 02:19:31.840531 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:31.848556 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:31.85666 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:31.867989 INFO::Counting total values for each feature
2025-01-29 02:19:31.872029 INFO::Re-running abundances for warn_prevalence
2025-01-29 02:19:31.875015 INFO::Running selected normalization method: TSS
2025-01-29 02:19:31.878962 INFO::Running selected transform method: LOG
2025-01-29 02:19:31.89245 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:31.899597 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:31.905653 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:31.993321 INFO::Creating fits folder
2025-01-29 02:19:31.995563 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/fits/residuals_linear.rds
2025-01-29 02:19:31.997966 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/fits/fitted_linear.rds
2025-01-29 02:19:32.000209 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/fits/residuals_logistic.rds
2025-01-29 02:19:32.002496 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/fits/fitted_logistic.rds
2025-01-29 02:19:32.006022 INFO::Writing all the results to file (ordered
by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/all_results.tsv
2025-01-29 02:19:32.008978 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/significant_results.tsv
2025-01-29 02:19:32.011573 INFO::Creating output figures folder
2025-01-29 02:19:32.013863 INFO::Writing summary plot of significant
results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/figures/summary_plot.pdf
2025-01-29 02:19:33.144001 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/figures
2025-01-29 02:19:33.146504 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-29 02:19:33.152466 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-29 02:19:33.629675 INFO::Writing summary plot of
significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/figures/summary_plot.pdf
2025-01-29 02:19:35.194118 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file1755448cd5885/figures
2025-01-29 02:19:35.196927 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-29 02:19:35.205426 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-29 02:19:35.633201 INFO::Running the linear model component
2025-01-29 02:19:35.640016 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:35.645588 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:35.650928 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:35.658914 INFO::Counting total values for each feature
2025-01-29 02:19:35.661045 INFO::Running the logistic model component
2025-01-29 02:19:35.667873 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:35.675563 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:35.682868 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:35.692875 INFO::Counting total values for each feature
2025-01-29 02:19:35.69534 INFO::Re-running abundances for warn_prevalence
2025-01-29 02:19:35.696608 INFO::Running selected normalization method: TSS
2025-01-29 02:19:35.698405 INFO::Running selected transform method: LOG
2025-01-29 02:19:35.705285 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:35.712162 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:35.721137 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:35.874478 INFO::Creating output folder
2025-01-29 02:19:35.877065 INFO::Creating output figures folder
2025-01-29 02:19:35.880069 INFO::Writing summary plot of significant
results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554300832f1/figures/summary_plot.pdf
2025-01-29 02:19:37.366483 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554300832f1/figures
2025-01-29 02:19:37.369541 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-29 02:19:37.37822 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-29 02:19:38.442285 INFO::Applying z-score to standardize continuous metadata
2025-01-29 02:19:38.460577 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-29 02:19:38.463185 INFO::Bypass z-score application to metadata
2025-01-29 02:19:38.469819 INFO::Bypass z-score application to metadata
2025-01-29 02:19:38.570983 INFO::Determining format of input files
2025-01-29 02:19:38.572989 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-29 02:19:38.574971 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-29 02:19:38.587921 INFO::Determining format of input files
2025-01-29 02:19:38.590305 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-29 02:19:38.592838 INFO::Input format is feature_specific_covariate samples as columns
2025-01-29 02:19:38.601761 INFO::Determining format of input files
2025-01-29 02:19:38.603096 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-29 02:19:38.604432 INFO::Input format is feature_specific_covariate samples as columns
2025-01-29 02:19:38.607052 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-01-29 02:19:38.608737 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-01-29 02:19:38.629136 INFO::Running selected transform method: LOG
2025-01-29 02:19:38.631581 INFO::Creating output feature tables folder
2025-01-29 02:19:38.634133 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175541473107f/features/data_transformed.tsv
2025-01-29 02:19:38.64154 INFO::Running selected transform method: LOG
2025-01-29 02:19:38.643844 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175541473107f/features/data_transformed.tsv
2025-01-29 02:19:38.6559 INFO::Running selected transform method: PLOG
2025-01-29 02:19:38.658102 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175541473107f/features/data_transformed.tsv
2025-01-29 02:19:38.661949 INFO::Running selected transform method: NONE
2025-01-29 02:19:38.663197 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file175541473107f/features/data_transformed.tsv
2025-01-29 02:19:38.677613 INFO::Running the linear model component
2025-01-29 02:19:38.688281 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:38.695529 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:38.703623 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:38.716337 INFO::Counting total values for each feature
2025-01-29 02:19:38.719393 INFO::Running the logistic model component
2025-01-29 02:19:38.729723 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:38.741143 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:38.752501 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:38.767735 INFO::Counting total values for each feature
2025-01-29 02:19:38.771601 INFO::Re-running abundances for warn_prevalence
2025-01-29 02:19:38.773441 INFO::Running selected normalization method: TSS
2025-01-29 02:19:38.776112 INFO::Running selected transform method: LOG
2025-01-29 02:19:38.7886 INFO::Fitting model to feature number 1, a
2025-01-29 02:19:38.797206 INFO::Fitting model to feature number 2, b
2025-01-29 02:19:38.805182 INFO::Fitting model to feature number 3, c
2025-01-29 02:19:38.970837 INFO::Creating output folder
2025-01-29 02:19:38.973279 INFO::Creating fits folder
2025-01-29 02:19:38.975631 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/fits/residuals_linear.rds
2025-01-29 02:19:38.978379 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/fits/fitted_linear.rds
2025-01-29 02:19:38.981061 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/fits/residuals_logistic.rds
2025-01-29 02:19:38.983746 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/fits/fitted_logistic.rds
2025-01-29 02:19:38.988456 INFO::Writing all the results to file (ordered
by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/all_results.tsv
2025-01-29 02:19:38.992514 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp8Sqytk\file17554515464d9/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
195.29 7.26 202.62
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.34 | 1.14 | 29.70 | |
| maaslin_check_arguments | 0.21 | 0.03 | 0.24 | |
| maaslin_check_formula | 0.33 | 0.01 | 0.35 | |
| maaslin_compute_formula | 0.28 | 0.02 | 0.29 | |
| maaslin_contrast_test | 24.86 | 2.06 | 26.94 | |
| maaslin_filter | 1.61 | 0.10 | 1.70 | |
| maaslin_fit | 19.36 | 1.92 | 21.28 | |
| maaslin_log_arguments | 0.27 | 0.01 | 0.32 | |
| maaslin_normalize | 1.00 | 0.02 | 1.01 | |
| maaslin_plot_results | 47.54 | 1.97 | 49.50 | |
| maaslin_plot_results_from_output | 46.99 | 1.95 | 49.39 | |
| maaslin_process_metadata | 1.42 | 0.06 | 1.49 | |
| maaslin_read_data | 0.25 | 0.00 | 0.26 | |
| maaslin_reorder_data | 0.25 | 0.00 | 0.25 | |
| maaslin_transform | 2.30 | 0.13 | 2.43 | |
| maaslin_write_results | 20.56 | 1.28 | 21.87 | |
| maaslin_write_results_lefse_format | 21.89 | 1.51 | 23.41 | |
| preprocess_dna_mtx | 0 | 0 | 0 | |