Lauren McIver
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Maaslin2 |
| Version: 1.20.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2024-11-20 09:23:45 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 09:27:19 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 214.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 118.965 0.647 119.88
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-11-20 09:26:31.704779 INFO::Writing function arguments to log file
2024-11-20 09:26:31.764341 INFO::Verifying options selected are valid
2024-11-20 09:26:31.809858 INFO::Determining format of input files
2024-11-20 09:26:31.811903 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-20 09:26:31.819589 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-20 09:26:31.82156 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-20 09:26:31.825184 INFO::Filter data based on min abundance and min prevalence
2024-11-20 09:26:31.826639 INFO::Total samples in data: 1595
2024-11-20 09:26:31.828052 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-20 09:26:31.838824 INFO::Total filtered features: 0
2024-11-20 09:26:31.840534 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-20 09:26:31.882009 INFO::Total filtered features with variance filtering: 0
2024-11-20 09:26:31.883719 INFO::Filtered feature names from variance filtering:
2024-11-20 09:26:31.885131 INFO::Running selected normalization method: TSS
2024-11-20 09:26:33.413506 INFO::Bypass z-score application to metadata
2024-11-20 09:26:33.415141 INFO::Running selected transform method: AST
2024-11-20 09:26:33.439415 INFO::Running selected analysis method: LM
2024-11-20 09:26:34.087156 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-20 09:26:34.590165 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-20 09:26:34.835282 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-20 09:26:35.068856 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-20 09:26:35.324039 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-20 09:26:35.561104 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-20 09:26:35.894381 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-20 09:26:36.176638 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-20 09:26:36.502429 WARNING::Fitting problem for feature 8 a warning was issued
2024-11-20 09:26:36.801835 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-20 09:26:36.993314 WARNING::Fitting problem for feature 9 a warning was issued
2024-11-20 09:26:37.259549 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-20 09:26:37.477438 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-20 09:26:37.696171 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-20 09:26:37.983332 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-20 09:26:38.169487 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-20 09:26:38.406084 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-20 09:26:38.62857 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-20 09:26:38.874818 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-20 09:26:39.104562 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-20 09:26:39.333298 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-20 09:26:39.569644 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-20 09:26:39.774528 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-20 09:26:39.992486 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-20 09:26:40.215727 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-20 09:26:40.445484 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-20 09:26:40.658649 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-20 09:26:40.901081 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-20 09:26:41.158426 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-20 09:26:41.37824 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-20 09:26:41.615624 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-20 09:26:41.860024 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-20 09:26:42.085818 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-20 09:26:42.299475 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-20 09:26:42.557937 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-20 09:26:42.79406 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-20 09:26:43.030828 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-20 09:26:43.266169 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-20 09:26:43.450969 WARNING::Fitting problem for feature 35 a warning was issued
2024-11-20 09:26:43.68087 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-20 09:26:43.91734 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-20 09:26:44.140094 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-20 09:26:44.349273 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-20 09:26:44.599381 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-20 09:26:44.833605 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-20 09:26:45.068371 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-20 09:26:45.301897 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-20 09:26:45.520762 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-20 09:26:45.751301 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-20 09:26:45.982142 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-20 09:26:46.222139 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-20 09:26:46.453134 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-20 09:26:46.668934 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-20 09:26:46.897812 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-20 09:26:47.133979 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-20 09:26:47.380568 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-20 09:26:47.609182 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-20 09:26:47.858392 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-20 09:26:48.070137 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-20 09:26:48.313383 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-20 09:26:48.570167 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-20 09:26:48.813436 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-20 09:26:49.066865 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-20 09:26:49.320071 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-20 09:26:49.538524 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-20 09:26:49.769999 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-20 09:26:50.006679 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-20 09:26:50.232552 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-20 09:26:50.523341 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-20 09:26:50.747887 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-20 09:26:50.979715 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-20 09:26:51.205351 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-20 09:26:51.441393 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-20 09:26:51.685336 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-20 09:26:51.931999 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-20 09:26:52.153533 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-20 09:26:52.379899 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-20 09:26:52.611833 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-20 09:26:52.833956 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-20 09:26:53.061096 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-20 09:26:53.302573 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-20 09:26:53.532434 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-20 09:26:53.780286 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-20 09:26:54.041748 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-20 09:26:54.28809 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-20 09:26:54.528865 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-20 09:26:54.792898 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-20 09:26:55.022873 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-20 09:26:55.27172 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-20 09:26:55.490676 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-20 09:26:55.707247 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-20 09:26:56.005754 INFO::Counting total values for each feature
2024-11-20 09:26:56.058365 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-20 09:26:56.185606 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-20 09:26:56.314252 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-20 09:26:56.458178 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-20 09:26:56.514942 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-20 09:26:56.546605 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-20 09:26:56.55387 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-20 09:26:56.561093 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"
2024-11-20 09:26:56.57882 INFO::Writing function arguments to log file
2024-11-20 09:26:56.587025 INFO::Verifying options selected are valid
2024-11-20 09:26:56.588463 INFO::Determining format of input files
2024-11-20 09:26:56.589988 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-20 09:26:56.598529 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-20 09:26:56.600173 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-20 09:26:56.602433 INFO::Filter data based on min abundance and min prevalence
2024-11-20 09:26:56.603736 INFO::Total samples in data: 1595
2024-11-20 09:26:56.604922 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-20 09:26:56.614979 INFO::Total filtered features: 0
2024-11-20 09:26:56.616523 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-20 09:26:56.647093 INFO::Total filtered features with variance filtering: 0
2024-11-20 09:26:56.648588 INFO::Filtered feature names from variance filtering:
2024-11-20 09:26:56.649747 INFO::Running selected normalization method: NONE
2024-11-20 09:26:56.650877 INFO::Bypass z-score application to metadata
2024-11-20 09:26:56.652069 INFO::Running selected transform method: AST
2024-11-20 09:26:56.684672 INFO::Running selected analysis method: LM
2024-11-20 09:26:56.68773 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-20 09:26:56.897845 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-20 09:26:57.480755 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-20 09:26:57.680513 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-20 09:26:57.895648 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-20 09:26:58.103192 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-20 09:26:58.332195 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-20 09:26:58.548336 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-20 09:26:58.765122 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-20 09:26:58.988848 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-20 09:26:59.198103 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-20 09:26:59.413763 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-20 09:26:59.613467 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-20 09:26:59.82921 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-20 09:27:00.035775 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-20 09:27:00.267419 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-20 09:27:00.441038 WARNING::Fitting problem for feature 16 a warning was issued
2024-11-20 09:27:00.679105 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-20 09:27:00.905327 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-20 09:27:01.111703 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-20 09:27:01.673398 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-20 09:27:01.891761 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-20 09:27:02.116279 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-20 09:27:02.334041 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-20 09:27:02.560635 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-20 09:27:02.776809 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-20 09:27:02.98651 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-20 09:27:03.195526 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-20 09:27:03.423133 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-20 09:27:03.630301 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-20 09:27:03.827551 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-20 09:27:04.032424 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-20 09:27:04.252278 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-20 09:27:04.464243 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-20 09:27:04.665953 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-20 09:27:04.879149 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-20 09:27:05.085505 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-20 09:27:05.295568 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-20 09:27:05.508621 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-20 09:27:05.717279 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-20 09:27:05.910957 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-20 09:27:06.105638 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-20 09:27:06.317019 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-20 09:27:06.517404 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-20 09:27:06.724107 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-20 09:27:06.94595 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-20 09:27:07.148907 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-20 09:27:07.355985 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-20 09:27:07.562267 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-20 09:27:07.792492 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-20 09:27:08.001878 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-20 09:27:08.198521 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-20 09:27:08.421025 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-20 09:27:08.609848 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-20 09:27:08.798961 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-20 09:27:08.995935 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-20 09:27:09.208285 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-20 09:27:09.416129 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-20 09:27:09.618276 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-20 09:27:09.826427 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-20 09:27:10.03184 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-20 09:27:10.230443 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-20 09:27:10.439357 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-20 09:27:10.641633 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-20 09:27:10.846706 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-20 09:27:11.04659 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-20 09:27:11.259956 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-20 09:27:11.461544 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-20 09:27:11.634821 WARNING::Fitting problem for feature 67 a warning was issued
2024-11-20 09:27:11.872871 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-20 09:27:12.072824 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-20 09:27:12.287106 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-20 09:27:12.519396 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-20 09:27:12.722435 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-20 09:27:12.79227 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-20 09:27:13.006196 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-20 09:27:13.214929 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-20 09:27:13.423619 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-20 09:27:13.639899 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-20 09:27:13.851315 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-20 09:27:14.057406 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-20 09:27:14.281248 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-20 09:27:14.493195 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-20 09:27:14.70958 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-20 09:27:14.925175 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-20 09:27:15.12539 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-20 09:27:15.331968 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-20 09:27:15.53134 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-20 09:27:15.744161 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-20 09:27:15.953623 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-20 09:27:16.20607 INFO::Counting total values for each feature
2024-11-20 09:27:16.242376 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-20 09:27:16.369849 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-20 09:27:16.496544 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-20 09:27:16.62623 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-20 09:27:16.701224 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-20 09:27:16.772317 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-20 09:27:16.778852 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-20 09:27:16.784378 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 7 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
45.439 1.221 46.657
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 118.965 | 0.647 | 119.880 | |