Lauren McIver
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_19 |
| git_last_commit: 35350f9 |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:41 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 1138/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.18.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2024-05-29 21:46:05 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 21:49:17 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 191.7 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* 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 100.843 2.245 104.06
* 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-3.19-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 Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.10 Current TMB version is 1.9.11 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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"
2024-05-29 21:48:31.793125 INFO::Writing function arguments to log file
2024-05-29 21:48:31.85378 INFO::Verifying options selected are valid
2024-05-29 21:48:31.899489 INFO::Determining format of input files
2024-05-29 21:48:31.901019 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-29 21:48:31.908781 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-29 21:48:31.911125 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-29 21:48:31.915233 INFO::Filter data based on min abundance and min prevalence
2024-05-29 21:48:31.916962 INFO::Total samples in data: 1595
2024-05-29 21:48:31.918923 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-29 21:48:31.935996 INFO::Total filtered features: 0
2024-05-29 21:48:31.937912 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-29 21:48:31.950335 INFO::Total filtered features with variance filtering: 0
2024-05-29 21:48:31.952182 INFO::Filtered feature names from variance filtering:
2024-05-29 21:48:31.953266 INFO::Running selected normalization method: TSS
2024-05-29 21:48:33.390003 INFO::Bypass z-score application to metadata
2024-05-29 21:48:33.391959 INFO::Running selected transform method: AST
2024-05-29 21:48:33.412874 INFO::Running selected analysis method: LM
2024-05-29 21:48:34.024677 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-29 21:48:34.463455 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-29 21:48:34.666104 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-29 21:48:34.850983 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-29 21:48:35.040339 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-29 21:48:35.219631 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-29 21:48:35.414458 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-29 21:48:35.599565 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-29 21:48:35.772978 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-29 21:48:35.986054 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-29 21:48:36.168848 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-29 21:48:36.340631 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-29 21:48:36.502512 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-29 21:48:36.654696 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-29 21:48:36.862557 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-29 21:48:37.043507 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-29 21:48:37.220271 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-29 21:48:37.384887 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-29 21:48:37.575802 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-29 21:48:37.75227 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-29 21:48:37.931938 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-29 21:48:38.113577 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-29 21:48:38.288985 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-29 21:48:38.480062 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-29 21:48:38.654951 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-29 21:48:38.852494 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-29 21:48:39.02806 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-29 21:48:39.205495 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-29 21:48:39.396582 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-29 21:48:39.588554 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-29 21:48:39.776221 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-29 21:48:39.965956 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-29 21:48:40.169201 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-29 21:48:40.357734 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-29 21:48:40.571161 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-29 21:48:40.759665 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-29 21:48:40.942093 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-29 21:48:41.103926 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-29 21:48:41.289265 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-29 21:48:41.461504 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-29 21:48:41.6546 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-29 21:48:41.834707 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-29 21:48:42.25848 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-29 21:48:42.432055 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-29 21:48:42.597494 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-29 21:48:42.763238 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-29 21:48:42.935274 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-29 21:48:43.109198 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-29 21:48:43.28585 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-29 21:48:43.451719 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-29 21:48:43.614984 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-29 21:48:43.77808 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-29 21:48:43.946058 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-29 21:48:44.126199 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-29 21:48:44.310699 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-29 21:48:44.498696 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-29 21:48:44.665773 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-29 21:48:44.853886 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-29 21:48:45.288499 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-29 21:48:45.444258 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-29 21:48:45.607147 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-29 21:48:45.790461 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-29 21:48:45.959707 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-29 21:48:46.130723 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-29 21:48:46.304616 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-29 21:48:46.482626 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-29 21:48:46.646997 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-29 21:48:46.825346 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-29 21:48:47.009827 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-29 21:48:47.181037 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-29 21:48:47.36144 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-29 21:48:47.559701 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-29 21:48:47.725155 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-29 21:48:47.897825 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-29 21:48:48.084336 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-29 21:48:48.25313 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-29 21:48:48.433824 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-29 21:48:48.626562 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-29 21:48:48.806685 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-29 21:48:49.003173 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-29 21:48:49.207928 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-29 21:48:49.378783 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-29 21:48:49.56613 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-29 21:48:49.75968 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-29 21:48:49.939147 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-29 21:48:50.126781 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-29 21:48:50.319839 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-29 21:48:50.509616 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-29 21:48:50.760336 INFO::Counting total values for each feature
2024-05-29 21:48:50.79964 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-29 21:48:50.944874 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-29 21:48:51.116549 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-29 21:48:51.293886 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-29 21:48:51.352096 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-29 21:48:51.387034 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-29 21:48:51.395057 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-29 21:48:51.405328 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"
2024-05-29 21:48:51.426636 INFO::Writing function arguments to log file
2024-05-29 21:48:51.437548 INFO::Verifying options selected are valid
2024-05-29 21:48:51.439493 INFO::Determining format of input files
2024-05-29 21:48:51.441675 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-29 21:48:51.449708 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-29 21:48:51.451757 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-05-29 21:48:51.454946 INFO::Filter data based on min abundance and min prevalence
2024-05-29 21:48:51.456592 INFO::Total samples in data: 1595
2024-05-29 21:48:51.458118 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-29 21:48:51.464325 INFO::Total filtered features: 0
2024-05-29 21:48:51.466435 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-29 21:48:51.489605 INFO::Total filtered features with variance filtering: 0
2024-05-29 21:48:51.492023 INFO::Filtered feature names from variance filtering:
2024-05-29 21:48:51.493664 INFO::Running selected normalization method: NONE
2024-05-29 21:48:51.495011 INFO::Bypass z-score application to metadata
2024-05-29 21:48:51.496363 INFO::Running selected transform method: AST
2024-05-29 21:48:51.515146 INFO::Running selected analysis method: LM
2024-05-29 21:48:51.517879 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-29 21:48:51.702555 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-29 21:48:51.887506 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-29 21:48:52.057755 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-29 21:48:52.252954 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-29 21:48:52.427181 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-29 21:48:52.617876 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-29 21:48:52.797399 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-29 21:48:52.974137 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-29 21:48:53.145288 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-29 21:48:53.324934 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-29 21:48:53.517351 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-29 21:48:53.686257 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-29 21:48:53.835061 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-29 21:48:54.058053 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-29 21:48:54.219134 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-29 21:48:54.37451 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-29 21:48:54.544771 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-29 21:48:54.713351 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-29 21:48:54.879085 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-29 21:48:55.058861 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-29 21:48:55.229656 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-29 21:48:55.407769 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-29 21:48:55.579723 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-29 21:48:55.740083 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-29 21:48:55.893444 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-29 21:48:56.063206 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-29 21:48:56.233299 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-29 21:48:56.404465 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-29 21:48:56.573159 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-29 21:48:56.732891 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-29 21:48:56.902893 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-29 21:48:57.079473 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-29 21:48:57.254251 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-29 21:48:57.436066 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-29 21:48:57.608343 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-29 21:48:57.77258 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-29 21:48:57.941681 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-29 21:48:58.102745 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-29 21:48:58.272222 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-29 21:48:58.437731 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-29 21:48:58.612067 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-29 21:48:58.801512 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-29 21:48:58.965222 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-29 21:48:59.137209 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-29 21:48:59.300453 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-29 21:48:59.453721 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-29 21:48:59.634328 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-29 21:48:59.798757 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-29 21:48:59.957132 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-29 21:49:00.114906 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-29 21:49:00.299446 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-29 21:49:00.471757 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-29 21:49:00.648476 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-29 21:49:00.823109 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-29 21:49:00.992353 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-29 21:49:01.152916 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-29 21:49:01.524158 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-29 21:49:01.680265 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-29 21:49:01.84553 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-29 21:49:02.002614 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-29 21:49:02.170803 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-29 21:49:02.335998 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-29 21:49:02.503889 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-29 21:49:02.677084 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-29 21:49:02.862263 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-29 21:49:03.027996 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-29 21:49:03.203119 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-29 21:49:03.351646 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-29 21:49:03.541594 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-29 21:49:03.717922 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-29 21:49:03.891693 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-29 21:49:04.069498 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-29 21:49:04.234005 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-29 21:49:04.294066 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-29 21:49:04.474417 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-29 21:49:04.647853 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-29 21:49:04.813268 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-29 21:49:04.98038 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-29 21:49:05.153618 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-29 21:49:05.311397 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-29 21:49:05.475515 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-29 21:49:05.668183 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-29 21:49:05.859598 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-29 21:49:06.03672 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-29 21:49:06.206919 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-29 21:49:06.383799 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-29 21:49:06.568898 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-29 21:49:06.741758 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-29 21:49:06.911955 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-29 21:49:07.120747 INFO::Counting total values for each feature
2024-05-29 21:49:07.160887 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-29 21:49:07.321363 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-29 21:49:07.487186 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-29 21:49:07.68357 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-29 21:49:07.764344 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-29 21:49:07.845918 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-29 21:49:07.853412 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-29 21:49:07.861191 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
36.367 0.936 37.673
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 100.843 | 2.245 | 104.060 | |