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 15:38 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1129/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 0.99.3 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 0.99.3 |
| Command: 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: 2025-01-25 02:58:31 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 03:09:36 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 665.2 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 47.61 2.44 50.04
maaslin_plot_results_from_output 46.33 2.04 48.36
maaslin3 28.73 1.07 30.17
maaslin_contrast_test 24.70 1.75 26.44
maaslin_write_results 20.98 1.63 22.65
maaslin_fit 20.74 1.72 22.46
maaslin_write_results_lefse_format 20.35 1.32 21.65
* 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")
2025-01-25 03:06:12.327564 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:06:13.209585 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:06:13.368823 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:06:13.414369 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:06:13.480199 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:06:13.625582 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:06:13.636624 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:06:13.659904 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:06:13.834568 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:06:13.847504 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:06:13.958419 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:06:14.016054 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:06:14.039134 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:06:14.120471 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:06:14.257138 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:06:34.480102 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:06:34.635675 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:06:34.755639 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:06:34.798197 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:06:34.853217 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:06:34.94836 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:06:34.955687 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:06:34.971003 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:06:35.150987 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:06:35.162786 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:06:35.267079 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:06:35.353522 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:06:35.379797 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:06:35.468083 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:06:35.631448 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:06:58.643018 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:06:58.778057 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:06:58.87812 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:06:58.920926 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:06:58.971945 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:06:59.072112 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:06:59.079745 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:06:59.095957 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:06:59.219491 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:07:00.181316 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:07:00.267115 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:07:00.335525 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:07:00.356782 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:07:00.426656 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:07:00.542115 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:07:18.164353 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:07:18.344963 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:07:18.470189 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:07:18.513919 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:07:18.582094 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:07:18.72256 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:07:18.733754 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:07:18.757141 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:07:18.936668 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:07:18.947989 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:07:19.034706 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:07:19.106376 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:07:19.129552 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:07:19.209846 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:07:19.334984 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:07:19.603641 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_linear.rds
2025-01-25 03:07:19.678327 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_linear.rds
2025-01-25 03:07:19.754865 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_logistic.rds
2025-01-25 03:07:20.054481 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_logistic.rds
2025-01-25 03:07:41.658156 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:07:41.791347 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:07:41.934003 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:07:41.962581 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:07:42.005618 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:07:42.122833 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:07:42.1348 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:07:42.160281 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:07:42.360077 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:07:42.374236 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:07:42.480716 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:07:42.56532 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:07:42.5906 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:07:42.709482 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:07:42.796821 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:08:00.771476 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:08:00.921572 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:08:01.069964 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:08:01.114901 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:08:01.184921 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:08:01.341115 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:08:01.353125 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:08:01.378684 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:08:01.571175 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:08:01.583947 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:08:01.779072 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:08:01.858378 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:08:01.882901 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:08:01.962694 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:08:02.099239 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:08:02.37675 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_linear.rds
2025-01-25 03:08:02.443102 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_linear.rds
2025-01-25 03:08:02.520175 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_logistic.rds
2025-01-25 03:08:02.85041 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_logistic.rds
2025-01-25 03:08:23.673206 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:08:23.817293 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:08:23.958109 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:08:23.998634 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:08:24.062373 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:08:24.174239 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:08:24.18154 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:08:24.19656 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:08:24.323296 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:08:24.332402 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:08:24.428794 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:08:24.49741 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:08:24.512746 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:08:24.562996 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:08:24.680686 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:08:41.122027 WARNING::Fitting problem for feature 50 returning NA
2025-01-25 03:08:41.264259 WARNING::Fitting problem for feature 62 returning NA
2025-01-25 03:08:41.409869 WARNING::Fitting problem for feature 74 returning NA
2025-01-25 03:08:41.451597 WARNING::Fitting problem for feature 78 returning NA
2025-01-25 03:08:41.517272 WARNING::Fitting problem for feature 84 returning NA
2025-01-25 03:08:41.67156 WARNING::Fitting problem for feature 96 returning NA
2025-01-25 03:08:41.682567 WARNING::Fitting problem for feature 97 returning NA
2025-01-25 03:08:41.705735 WARNING::Fitting problem for feature 99 returning NA
2025-01-25 03:08:41.885654 WARNING::Fitting problem for feature 114 returning NA
2025-01-25 03:08:41.897949 WARNING::Fitting problem for feature 115 returning NA
2025-01-25 03:08:41.995424 WARNING::Fitting problem for feature 123 returning NA
2025-01-25 03:08:42.080563 WARNING::Fitting problem for feature 130 returning NA
2025-01-25 03:08:42.106647 WARNING::Fitting problem for feature 132 returning NA
2025-01-25 03:08:42.19316 WARNING::Fitting problem for feature 139 returning NA
2025-01-25 03:08:42.336188 WARNING::Fitting problem for feature 150 returning NA
2025-01-25 03:08:42.628197 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_linear.rds
2025-01-25 03:08:42.684952 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_linear.rds
2025-01-25 03:08:42.754468 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/residuals_logistic.rds
2025-01-25 03:08:43.077537 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc1f9b6df0/fits/fitted_logistic.rds
2025-01-25 03:09:03.266814 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-01-25 03:09:03.285164 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-01-25 03:09:03.295259 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-01-25 03:09:03.374464 ERROR::No fixed, group, or
ordered effects included in formula.
2025-01-25 03:09:03.392842 ERROR::Effect name not found in metadata: d
2025-01-25 03:09:03.402965 ERROR::No user formula provided
2025-01-25 03:09:03.450478 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-01-25 03:09:03.461027 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-01-25 03:09:07.757302 INFO::Writing function arguments to log file
2025-01-25 03:09:07.805951 INFO::Verifying options selected are valid
2025-01-25 03:09:10.460609 INFO::Writing function arguments to log file
2025-01-25 03:09:10.490938 INFO::Verifying options selected are valid
2025-01-25 03:09:10.493006 INFO::Determining format of input files
2025-01-25 03:09:10.49568 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 03:09:10.502303 INFO::Running selected normalization method: TSS
2025-01-25 03:09:10.505201 INFO::Creating output feature tables folder
2025-01-25 03:09:10.507682 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/features/data_norm.tsv
2025-01-25 03:09:10.512131 INFO::Filter data based on min abundance and min prevalence
2025-01-25 03:09:10.514846 INFO::Total samples in data: 16
2025-01-25 03:09:10.517462 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-01-25 03:09:10.521805 INFO::Total filtered features: 0
2025-01-25 03:09:10.524599 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-25 03:09:10.527621 INFO::Total features filtered by non-zero variance filtering: 0
2025-01-25 03:09:10.530294 INFO::Filtered feature names from variance filtering:
2025-01-25 03:09:10.533084 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/features/filtered_data.tsv
2025-01-25 03:09:10.537259 INFO::Running selected transform method: LOG
2025-01-25 03:09:10.540326 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/features/data_transformed.tsv
2025-01-25 03:09:10.544716 INFO::Applying z-score to standardize continuous metadata
2025-01-25 03:09:10.554567 INFO::Running the linear model component
2025-01-25 03:09:10.568012 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:10.578487 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:10.588199 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:10.602508 INFO::Counting total values for each feature
2025-01-25 03:09:10.606988 INFO::Running the logistic model component
2025-01-25 03:09:10.619935 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:10.633202 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:10.647122 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:10.665288 INFO::Counting total values for each feature
2025-01-25 03:09:10.670267 INFO::Re-running abundances for warn_prevalence
2025-01-25 03:09:10.67352 INFO::Running selected normalization method: TSS
2025-01-25 03:09:10.677501 INFO::Running selected transform method: LOG
2025-01-25 03:09:10.691177 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:10.698401 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:10.70509 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:10.839521 INFO::Creating fits folder
2025-01-25 03:09:10.842697 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/fits/residuals_linear.rds
2025-01-25 03:09:10.84623 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/fits/fitted_linear.rds
2025-01-25 03:09:10.849573 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/fits/residuals_logistic.rds
2025-01-25 03:09:10.852878 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/fits/fitted_logistic.rds
2025-01-25 03:09:10.85801 INFO::Writing all the results to file (ordered
by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/all_results.tsv
2025-01-25 03:09:10.862722 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\Rtmp44XuDY\file9ebc5e8e32b3/significant_results.tsv
2025-01-25 03:09:10.866685 INFO::Creating output figures folder
2025-01-25 03:09:10.870995 INFO::Writing summary plot of significant
results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/figures/summary_plot.pdf
2025-01-25 03:09:12.327166 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/figures
2025-01-25 03:09:12.331143 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 03:09:12.340852 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 03:09:12.842892 INFO::Writing summary plot of
significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/figures/summary_plot.pdf
2025-01-25 03:09:14.606464 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc5e8e32b3/figures
2025-01-25 03:09:14.609168 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 03:09:14.617754 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 03:09:15.054951 INFO::Running the linear model component
2025-01-25 03:09:15.06735 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:15.07624 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:15.084898 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:15.0977 INFO::Counting total values for each feature
2025-01-25 03:09:15.101155 INFO::Running the logistic model component
2025-01-25 03:09:15.113013 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:15.120493 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:15.127489 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:15.137284 INFO::Counting total values for each feature
2025-01-25 03:09:15.139639 INFO::Re-running abundances for warn_prevalence
2025-01-25 03:09:15.140728 INFO::Running selected normalization method: TSS
2025-01-25 03:09:15.14234 INFO::Running selected transform method: LOG
2025-01-25 03:09:15.149043 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:15.154532 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:15.159816 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:15.270749 INFO::Creating output folder
2025-01-25 03:09:15.27307 INFO::Creating output figures folder
2025-01-25 03:09:15.275802 INFO::Writing summary plot of significant
results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc4593ef3/figures/summary_plot.pdf
2025-01-25 03:09:16.941579 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc4593ef3/figures
2025-01-25 03:09:16.944417 INFO::Plotting associations from most to least significant, grouped by metadata
2025-01-25 03:09:16.952841 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-01-25 03:09:18.162643 INFO::Applying z-score to standardize continuous metadata
2025-01-25 03:09:18.170819 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-01-25 03:09:18.171982 INFO::Bypass z-score application to metadata
2025-01-25 03:09:18.174877 INFO::Bypass z-score application to metadata
2025-01-25 03:09:18.227195 INFO::Determining format of input files
2025-01-25 03:09:18.228459 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 03:09:18.229555 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-01-25 03:09:18.237353 INFO::Determining format of input files
2025-01-25 03:09:18.238737 INFO::Input format is data samples as columns and metadata samples as rows
2025-01-25 03:09:18.240356 INFO::Input format is feature_specific_covariate samples as columns
2025-01-25 03:09:18.248874 INFO::Determining format of input files
2025-01-25 03:09:18.25018 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 03:09:18.251473 INFO::Input format is feature_specific_covariate samples as columns
2025-01-25 03:09:18.253414 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 03:09:18.254444 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 03:09:18.267582 INFO::Running selected transform method: LOG
2025-01-25 03:09:18.269159 INFO::Creating output feature tables folder
2025-01-25 03:09:18.270865 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc310822a3/features/data_transformed.tsv
2025-01-25 03:09:18.275885 INFO::Running selected transform method: LOG
2025-01-25 03:09:18.277461 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc310822a3/features/data_transformed.tsv
2025-01-25 03:09:18.292371 INFO::Running selected transform method: PLOG
2025-01-25 03:09:18.295494 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc310822a3/features/data_transformed.tsv
2025-01-25 03:09:18.306774 INFO::Running selected transform method: NONE
2025-01-25 03:09:18.308752 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc310822a3/features/data_transformed.tsv
2025-01-25 03:09:18.343645 INFO::Running the linear model component
2025-01-25 03:09:18.355968 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:18.365618 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:18.374944 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:18.387763 INFO::Counting total values for each feature
2025-01-25 03:09:18.390684 INFO::Running the logistic model component
2025-01-25 03:09:18.400054 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:18.411043 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:18.421501 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:18.435748 INFO::Counting total values for each feature
2025-01-25 03:09:18.439322 INFO::Re-running abundances for warn_prevalence
2025-01-25 03:09:18.441039 INFO::Running selected normalization method: TSS
2025-01-25 03:09:18.443555 INFO::Running selected transform method: LOG
2025-01-25 03:09:18.455493 INFO::Fitting model to feature number 1, a
2025-01-25 03:09:18.463828 INFO::Fitting model to feature number 2, b
2025-01-25 03:09:18.471926 INFO::Fitting model to feature number 3, c
2025-01-25 03:09:18.617334 INFO::Creating output folder
2025-01-25 03:09:18.619451 INFO::Creating fits folder
2025-01-25 03:09:18.621449 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc371c6342/fits/residuals_linear.rds
2025-01-25 03:09:18.623748 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc371c6342/fits/fitted_linear.rds
2025-01-25 03:09:18.625983 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc371c6342/fits/residuals_logistic.rds
2025-01-25 03:09:18.628147 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc371c6342/fits/fitted_logistic.rds
2025-01-25 03:09:18.63228 INFO::Writing all the results to file (ordered
by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp44XuDY\file9ebc371c6342/all_results.tsv
2025-01-25 03:09:18.635687 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\Rtmp44XuDY\file9ebc371c6342/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
>
>
> proc.time()
user system elapsed
193.00 6.92 199.98
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.73 | 1.07 | 30.17 | |
| maaslin_check_arguments | 0.33 | 0.00 | 0.33 | |
| maaslin_check_formula | 0.35 | 0.02 | 0.37 | |
| maaslin_compute_formula | 0.27 | 0.02 | 0.28 | |
| maaslin_contrast_test | 24.70 | 1.75 | 26.44 | |
| maaslin_filter | 1.58 | 0.15 | 1.75 | |
| maaslin_fit | 20.74 | 1.72 | 22.46 | |
| maaslin_log_arguments | 0.29 | 0.05 | 0.36 | |
| maaslin_normalize | 0.86 | 0.03 | 0.89 | |
| maaslin_plot_results | 47.61 | 2.44 | 50.04 | |
| maaslin_plot_results_from_output | 46.33 | 2.04 | 48.36 | |
| maaslin_process_metadata | 1.64 | 0.11 | 1.75 | |
| maaslin_read_data | 0.33 | 0.02 | 0.36 | |
| maaslin_reorder_data | 0.31 | 0.00 | 0.33 | |
| maaslin_transform | 2.41 | 0.06 | 2.48 | |
| maaslin_write_results | 20.98 | 1.63 | 22.65 | |
| maaslin_write_results_lefse_format | 20.35 | 1.32 | 21.65 | |
| preprocess_dna_mtx | 0 | 0 | 0 | |