Lauren McIver
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 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 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| 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: 2024-12-20 05:23:45 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 05:29:36 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 350.4 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: x86_64-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 Monterey 12.7.6
* 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 182.205 2.862 202.865
* 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-x86_64/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: x86_64-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"
2024-12-20 05:28:17.997694 INFO::Writing function arguments to log file
2024-12-20 05:28:18.245448 INFO::Verifying options selected are valid
2024-12-20 05:28:18.321356 INFO::Determining format of input files
2024-12-20 05:28:18.324751 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 05:28:18.339448 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 05:28:18.342843 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-20 05:28:18.349466 INFO::Filter data based on min abundance and min prevalence
2024-12-20 05:28:18.352188 INFO::Total samples in data: 1595
2024-12-20 05:28:18.354782 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 05:28:18.366202 INFO::Total filtered features: 0
2024-12-20 05:28:18.369037 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 05:28:18.400986 INFO::Total filtered features with variance filtering: 0
2024-12-20 05:28:18.403627 INFO::Filtered feature names from variance filtering:
2024-12-20 05:28:18.405872 INFO::Running selected normalization method: TSS
2024-12-20 05:28:21.071686 INFO::Bypass z-score application to metadata
2024-12-20 05:28:21.07437 INFO::Running selected transform method: AST
2024-12-20 05:28:21.109135 INFO::Running selected analysis method: LM
2024-12-20 05:28:22.291765 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 05:28:23.087771 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 05:28:23.440737 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 05:28:23.800535 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 05:28:24.133384 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 05:28:24.449761 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 05:28:24.774988 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 05:28:25.103311 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 05:28:25.4508 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 05:28:25.768497 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 05:28:26.094737 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 05:28:26.422741 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 05:28:26.733091 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 05:28:27.001674 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-20 05:28:27.38944 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 05:28:27.710959 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 05:28:28.033156 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 05:28:28.348085 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 05:28:28.69137 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 05:28:29.015725 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 05:28:29.319567 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 05:28:29.694097 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 05:28:30.019904 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 05:28:30.350551 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 05:28:30.687562 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 05:28:31.044538 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 05:28:31.372083 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 05:28:31.682326 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 05:28:32.018363 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 05:28:32.336149 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 05:28:32.667842 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 05:28:32.993108 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 05:28:33.324663 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 05:28:33.644659 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 05:28:33.977305 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 05:28:34.282772 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 05:28:34.597756 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 05:28:34.950049 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 05:28:35.275605 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 05:28:35.600072 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 05:28:35.932767 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 05:28:36.258999 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 05:28:36.590389 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 05:28:36.90286 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 05:28:37.213317 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 05:28:37.508268 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 05:28:37.82962 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 05:28:38.195785 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 05:28:38.618995 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 05:28:38.941019 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 05:28:39.318198 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 05:28:39.621939 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 05:28:39.915247 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 05:28:40.239054 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 05:28:40.575439 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 05:28:40.88544 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 05:28:41.209536 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 05:28:41.539466 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 05:28:41.84494 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 05:28:42.186758 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 05:28:42.495872 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 05:28:42.788578 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 05:28:43.107593 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 05:28:43.439969 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 05:28:43.800621 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 05:28:44.121265 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 05:28:44.43824 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 05:28:44.809053 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 05:28:45.110086 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 05:28:45.437113 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 05:28:45.753989 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 05:28:46.089649 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 05:28:46.406583 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 05:28:46.71352 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 05:28:47.045692 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 05:28:47.360588 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 05:28:47.940409 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 05:28:48.251511 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 05:28:48.562579 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 05:28:48.90549 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 05:28:49.24797 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 05:28:49.560725 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 05:28:49.892281 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 05:28:50.217747 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 05:28:50.524962 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 05:28:50.858951 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 05:28:51.165707 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 05:28:51.469218 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 05:28:51.929734 INFO::Counting total values for each feature
2024-12-20 05:28:52.025237 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-20 05:28:52.323673 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-20 05:28:52.691661 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-20 05:28:53.061306 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-20 05:28:53.158576 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-20 05:28:53.214763 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-20 05:28:53.226381 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-20 05:28:53.243892 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"
2024-12-20 05:28:53.275432 INFO::Writing function arguments to log file
2024-12-20 05:28:53.295622 INFO::Verifying options selected are valid
2024-12-20 05:28:53.298735 INFO::Determining format of input files
2024-12-20 05:28:53.303818 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 05:28:53.317258 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 05:28:53.320248 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-12-20 05:28:53.324424 INFO::Filter data based on min abundance and min prevalence
2024-12-20 05:28:53.326899 INFO::Total samples in data: 1595
2024-12-20 05:28:53.329011 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 05:28:53.33951 INFO::Total filtered features: 0
2024-12-20 05:28:53.342209 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 05:28:53.359714 INFO::Total filtered features with variance filtering: 0
2024-12-20 05:28:53.362569 INFO::Filtered feature names from variance filtering:
2024-12-20 05:28:53.365022 INFO::Running selected normalization method: NONE
2024-12-20 05:28:53.367401 INFO::Bypass z-score application to metadata
2024-12-20 05:28:53.37046 INFO::Running selected transform method: AST
2024-12-20 05:28:53.403089 INFO::Running selected analysis method: LM
2024-12-20 05:28:53.406513 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 05:28:53.732539 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 05:28:54.048735 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 05:28:54.370459 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 05:28:54.689014 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 05:28:54.985115 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 05:28:55.297458 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 05:28:55.594759 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 05:28:55.916946 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 05:28:56.22749 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 05:28:56.617831 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 05:28:56.974181 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 05:28:57.257902 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 05:28:57.504971 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-20 05:28:57.850913 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 05:28:58.141111 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 05:28:58.447562 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 05:28:58.737806 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 05:28:59.034162 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 05:28:59.339062 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 05:28:59.632275 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 05:28:59.940776 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 05:29:00.248305 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 05:29:00.57323 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 05:29:00.854762 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 05:29:01.16204 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 05:29:01.464336 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 05:29:01.774929 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 05:29:02.075714 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 05:29:02.357351 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 05:29:02.65193 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 05:29:02.962074 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 05:29:03.263692 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 05:29:03.57183 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 05:29:03.891561 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 05:29:04.186948 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 05:29:04.479632 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 05:29:04.77295 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 05:29:05.084178 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 05:29:05.380951 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 05:29:05.714028 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 05:29:06.013797 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 05:29:06.298268 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 05:29:06.588912 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 05:29:06.899648 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 05:29:07.225368 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 05:29:07.456688 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 05:29:07.778488 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 05:29:08.072994 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 05:29:08.373833 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 05:29:08.891821 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 05:29:09.253395 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 05:29:09.574357 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 05:29:09.881746 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 05:29:10.213315 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 05:29:10.524542 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 05:29:10.865842 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 05:29:11.189687 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 05:29:11.509647 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 05:29:11.821316 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 05:29:12.154844 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 05:29:12.454483 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 05:29:12.758344 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 05:29:13.068483 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 05:29:13.399475 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 05:29:13.711047 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 05:29:14.00553 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 05:29:14.294477 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 05:29:14.568972 WARNING::Fitting problem for feature 67 a warning was issued
2024-12-20 05:29:14.887459 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 05:29:15.190903 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 05:29:15.505595 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 05:29:15.8332 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 05:29:16.130823 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 05:29:16.232826 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-20 05:29:16.537439 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 05:29:16.83241 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 05:29:17.399583 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 05:29:17.689544 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 05:29:17.981108 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 05:29:18.267421 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 05:29:18.5754 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 05:29:18.877742 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 05:29:19.198953 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 05:29:19.490714 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 05:29:19.777333 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 05:29:20.070899 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 05:29:20.348518 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 05:29:20.638039 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 05:29:20.933666 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 05:29:21.309757 INFO::Counting total values for each feature
2024-12-20 05:29:21.37619 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-20 05:29:21.670282 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-20 05:29:21.96686 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-20 05:29:22.331761 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-20 05:29:22.449628 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-20 05:29:22.563871 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-20 05:29:22.575462 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-20 05:29:22.589336 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
61.817 1.106 67.266
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 182.205 | 2.862 | 202.865 | |