Lauren McIver
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1cacd4c |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:07 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1130/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.20.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the Maaslin2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.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: Maaslin2 |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2024-12-31 23:31:40 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 23:34:29 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 168.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* 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 ‘Maaslin2’ 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 ... NOTE
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
xnames
* 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
Maaslin2 90.088 1.614 91.929
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** 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 (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-12-31 23:33:45.986701 INFO::Writing function arguments to log file
2024-12-31 23:33:46.031234 INFO::Verifying options selected are valid
2024-12-31 23:33:46.056028 INFO::Determining format of input files
2024-12-31 23:33:46.057248 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 23:33:46.060993 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 23:33:46.061957 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-31 23:33:46.063105 INFO::Filter data based on min abundance and min prevalence
2024-12-31 23:33:46.063571 INFO::Total samples in data: 1595
2024-12-31 23:33:46.063927 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 23:33:46.0663 INFO::Total filtered features: 0
2024-12-31 23:33:46.067146 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 23:33:46.079844 INFO::Total filtered features with variance filtering: 0
2024-12-31 23:33:46.081104 INFO::Filtered feature names from variance filtering:
2024-12-31 23:33:46.081592 INFO::Running selected normalization method: TSS
2024-12-31 23:33:47.371269 INFO::Bypass z-score application to metadata
2024-12-31 23:33:47.373087 INFO::Running selected transform method: AST
2024-12-31 23:33:47.391643 INFO::Running selected analysis method: LM
2024-12-31 23:33:47.964909 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 23:33:48.387116 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 23:33:48.565065 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 23:33:48.752123 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 23:33:48.938999 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 23:33:49.1117 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 23:33:49.286786 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 23:33:49.454656 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 23:33:49.638102 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 23:33:49.77319 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-31 23:33:49.952108 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 23:33:50.129502 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 23:33:50.302212 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 23:33:50.478311 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 23:33:50.709044 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 23:33:50.880819 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 23:33:51.062944 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 23:33:51.233607 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 23:33:51.426774 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 23:33:51.610144 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 23:33:51.784098 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 23:33:51.973558 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 23:33:52.14571 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 23:33:52.316813 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 23:33:52.483834 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 23:33:52.666379 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 23:33:52.840278 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 23:33:53.0122 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 23:33:53.196178 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 23:33:53.362685 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 23:33:53.534767 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 23:33:53.70574 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 23:33:53.877785 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 23:33:54.048225 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 23:33:54.243718 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 23:33:54.406289 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 23:33:54.572263 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 23:33:54.750099 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 23:33:54.921872 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 23:33:55.088378 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 23:33:55.266508 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 23:33:55.441574 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 23:33:55.610715 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 23:33:55.802781 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 23:33:55.96843 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 23:33:56.140061 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 23:33:56.310604 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 23:33:56.482536 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 23:33:56.67039 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 23:33:56.833827 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 23:33:57.013551 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 23:33:57.173822 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 23:33:57.336399 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 23:33:57.513251 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 23:33:57.689494 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 23:33:57.867771 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 23:33:58.045922 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 23:33:58.23953 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 23:33:58.395334 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 23:33:58.573203 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 23:33:58.73431 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 23:33:58.903626 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 23:33:59.070302 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 23:33:59.250134 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 23:33:59.418039 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 23:33:59.59232 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 23:33:59.764563 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 23:33:59.932251 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 23:34:00.136032 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 23:34:00.313008 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 23:34:00.490138 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 23:34:00.678294 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 23:34:00.837863 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 23:34:00.999703 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 23:34:01.176454 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 23:34:01.342288 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 23:34:01.514184 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 23:34:01.694612 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 23:34:01.860313 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 23:34:02.040772 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 23:34:02.230773 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 23:34:02.394118 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 23:34:02.573754 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 23:34:02.76249 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 23:34:02.932782 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 23:34:03.109809 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 23:34:03.288094 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 23:34:03.455947 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 23:34:03.688969 INFO::Counting total values for each feature
2024-12-31 23:34:03.728634 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-31 23:34:03.879602 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-31 23:34:04.052976 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-31 23:34:04.22562 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-31 23:34:04.306017 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-31 23:34:04.349552 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-31 23:34:04.358955 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-31 23:34:04.367555 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-12-31 23:34:04.382934 INFO::Writing function arguments to log file
2024-12-31 23:34:04.389281 INFO::Verifying options selected are valid
2024-12-31 23:34:04.390285 INFO::Determining format of input files
2024-12-31 23:34:04.391432 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 23:34:04.408687 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 23:34:04.410644 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-12-31 23:34:04.413032 INFO::Filter data based on min abundance and min prevalence
2024-12-31 23:34:04.41437 INFO::Total samples in data: 1595
2024-12-31 23:34:04.415304 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 23:34:04.420221 INFO::Total filtered features: 0
2024-12-31 23:34:04.421318 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 23:34:04.429817 INFO::Total filtered features with variance filtering: 0
2024-12-31 23:34:04.430947 INFO::Filtered feature names from variance filtering:
2024-12-31 23:34:04.431764 INFO::Running selected normalization method: NONE
2024-12-31 23:34:04.432525 INFO::Bypass z-score application to metadata
2024-12-31 23:34:04.433293 INFO::Running selected transform method: AST
2024-12-31 23:34:04.450795 INFO::Running selected analysis method: LM
2024-12-31 23:34:04.452767 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 23:34:04.62457 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 23:34:04.785905 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 23:34:04.956919 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 23:34:05.122001 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 23:34:05.29897 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 23:34:05.462947 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 23:34:05.638573 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 23:34:05.800475 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 23:34:05.974948 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 23:34:06.142382 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 23:34:06.287644 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-31 23:34:06.477321 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 23:34:06.630986 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 23:34:07.052021 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-31 23:34:07.221084 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 23:34:07.382935 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 23:34:07.551348 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 23:34:07.719107 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 23:34:07.890167 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 23:34:08.058587 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 23:34:08.226816 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 23:34:08.382025 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 23:34:08.544055 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 23:34:08.705875 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 23:34:08.872962 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 23:34:09.039041 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 23:34:09.202464 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 23:34:09.381635 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 23:34:09.541785 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 23:34:09.695433 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 23:34:09.84573 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 23:34:10.014367 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 23:34:10.176842 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 23:34:10.337548 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 23:34:10.522439 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 23:34:10.683769 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 23:34:10.852692 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 23:34:11.026475 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 23:34:11.202326 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 23:34:11.365529 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 23:34:11.52144 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 23:34:11.960774 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 23:34:12.119755 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 23:34:12.276019 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 23:34:12.434982 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 23:34:12.603747 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 23:34:12.757598 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 23:34:12.916927 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 23:34:13.066322 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 23:34:13.23084 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 23:34:13.380995 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 23:34:13.526992 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 23:34:13.697121 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 23:34:13.842748 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 23:34:13.989967 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 23:34:14.153331 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 23:34:14.318011 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 23:34:14.47351 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 23:34:14.634136 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 23:34:14.803126 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 23:34:14.916597 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 23:34:14.990828 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 23:34:15.078867 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 23:34:15.176536 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 23:34:15.283158 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 23:34:15.394236 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 23:34:15.520034 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 23:34:15.676693 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 23:34:15.851422 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 23:34:16.007352 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 23:34:16.183467 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 23:34:16.372447 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 23:34:16.533918 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 23:34:16.5924 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-31 23:34:16.762559 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 23:34:16.925624 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 23:34:17.090522 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 23:34:17.263388 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 23:34:17.427746 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 23:34:17.595549 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 23:34:17.754512 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 23:34:17.919983 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 23:34:18.088803 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 23:34:18.261011 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 23:34:18.424923 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 23:34:18.582988 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 23:34:18.754881 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 23:34:18.914212 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 23:34:19.089389 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 23:34:19.27595 INFO::Counting total values for each feature
2024-12-31 23:34:19.312654 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-31 23:34:19.466678 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-31 23:34:19.611783 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-31 23:34:19.782166 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-31 23:34:19.896556 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-31 23:34:20.00288 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-31 23:34:20.012425 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-31 23:34:20.019536 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
34.473 0.769 35.317
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 90.088 | 1.614 | 91.929 | |