Lauren McIver
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 2f9ea7a |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 1106/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.19.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 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: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2024-06-10 05:35:44 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 05:41:56 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 372.8 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.19.0’
* 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 184.959 2.945 216.64
* 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 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 Patched (2024-04-24 r86482) -- "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"
2024-06-10 05:40:30.337655 INFO::Writing function arguments to log file
2024-06-10 05:40:30.451744 INFO::Verifying options selected are valid
2024-06-10 05:40:30.546898 INFO::Determining format of input files
2024-06-10 05:40:30.550429 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 05:40:30.568463 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 05:40:30.572643 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-10 05:40:30.581269 INFO::Filter data based on min abundance and min prevalence
2024-06-10 05:40:30.583871 INFO::Total samples in data: 1595
2024-06-10 05:40:30.586276 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 05:40:30.613221 INFO::Total filtered features: 0
2024-06-10 05:40:30.618108 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 05:40:30.641703 INFO::Total filtered features with variance filtering: 0
2024-06-10 05:40:30.644444 INFO::Filtered feature names from variance filtering:
2024-06-10 05:40:30.648971 INFO::Running selected normalization method: TSS
2024-06-10 05:40:33.462497 INFO::Bypass z-score application to metadata
2024-06-10 05:40:33.465656 INFO::Running selected transform method: AST
2024-06-10 05:40:33.50568 INFO::Running selected analysis method: LM
2024-06-10 05:40:34.770676 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 05:40:35.644189 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 05:40:36.05373 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 05:40:36.429491 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 05:40:36.822546 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 05:40:37.186633 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 05:40:37.551373 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 05:40:37.934572 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 05:40:38.306917 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 05:40:38.72187 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 05:40:39.090378 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 05:40:39.451362 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 05:40:39.808345 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 05:40:40.104653 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-10 05:40:40.518118 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 05:40:40.871844 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 05:40:41.248547 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 05:40:41.60305 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 05:40:41.986293 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 05:40:42.350224 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 05:40:42.704376 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 05:40:43.074322 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 05:40:43.437827 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 05:40:43.814216 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 05:40:44.165549 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 05:40:44.561084 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 05:40:44.934421 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 05:40:45.31906 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 05:40:45.69806 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 05:40:46.079943 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 05:40:46.430002 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 05:40:46.789843 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 05:40:47.195403 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 05:40:47.565476 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 05:40:47.950264 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 05:40:48.299672 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 05:40:48.672968 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 05:40:49.045401 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 05:40:49.413429 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 05:40:49.767811 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 05:40:50.133069 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 05:40:50.495016 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 05:40:50.871818 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 05:40:51.236432 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 05:40:51.605931 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 05:40:51.961153 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 05:40:52.308316 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 05:40:52.672614 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 05:40:53.349754 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 05:40:53.693172 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 05:40:54.038057 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 05:40:54.390714 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 05:40:54.76498 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 05:40:55.125556 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 05:40:55.500301 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 05:40:55.889734 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 05:40:56.240215 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 05:40:56.614497 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 05:40:56.981026 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 05:40:57.321572 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 05:40:57.66894 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 05:40:58.032454 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 05:40:58.393916 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 05:40:58.76165 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 05:40:59.13248 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 05:40:59.495775 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 05:40:59.847472 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 05:41:00.232005 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 05:41:00.579359 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 05:41:00.938685 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 05:41:01.320153 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 05:41:01.695367 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 05:41:02.037568 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 05:41:02.38918 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 05:41:02.75054 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 05:41:03.102782 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 05:41:03.459681 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 05:41:03.811753 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 05:41:04.157396 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 05:41:04.541792 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 05:41:04.910283 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 05:41:05.266222 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 05:41:05.935986 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 05:41:06.294728 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 05:41:06.639614 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 05:41:07.002448 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 05:41:07.38149 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 05:41:07.735455 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 05:41:08.231559 INFO::Counting total values for each feature
2024-06-10 05:41:08.342328 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-10 05:41:08.665544 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-10 05:41:09.065619 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-10 05:41:09.467344 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-10 05:41:09.575919 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-10 05:41:09.635216 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-10 05:41:09.647955 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-10 05:41:09.669604 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"
2024-06-10 05:41:09.722828 INFO::Writing function arguments to log file
2024-06-10 05:41:09.743334 INFO::Verifying options selected are valid
2024-06-10 05:41:09.747628 INFO::Determining format of input files
2024-06-10 05:41:09.750775 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 05:41:09.766254 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 05:41:09.770379 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-06-10 05:41:09.775575 INFO::Filter data based on min abundance and min prevalence
2024-06-10 05:41:09.778268 INFO::Total samples in data: 1595
2024-06-10 05:41:09.780721 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 05:41:09.793589 INFO::Total filtered features: 0
2024-06-10 05:41:09.797514 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 05:41:09.817651 INFO::Total filtered features with variance filtering: 0
2024-06-10 05:41:09.821347 INFO::Filtered feature names from variance filtering:
2024-06-10 05:41:09.823726 INFO::Running selected normalization method: NONE
2024-06-10 05:41:09.825915 INFO::Bypass z-score application to metadata
2024-06-10 05:41:09.828101 INFO::Running selected transform method: AST
2024-06-10 05:41:09.864777 INFO::Running selected analysis method: LM
2024-06-10 05:41:09.870527 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 05:41:10.226538 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 05:41:10.582697 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 05:41:10.916937 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 05:41:11.251146 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 05:41:11.565104 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 05:41:11.919814 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 05:41:12.296897 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 05:41:12.678194 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 05:41:13.025157 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 05:41:13.381261 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 05:41:13.725086 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 05:41:14.061067 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 05:41:14.344803 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-10 05:41:14.724603 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 05:41:15.091685 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 05:41:15.485566 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 05:41:15.805345 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 05:41:16.138629 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 05:41:16.457163 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 05:41:16.781271 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 05:41:17.116733 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 05:41:17.430738 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 05:41:17.746505 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 05:41:18.071218 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 05:41:18.396077 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 05:41:18.711598 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 05:41:19.022231 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 05:41:19.360878 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 05:41:19.664174 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 05:41:19.961843 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 05:41:20.273281 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 05:41:20.614726 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 05:41:20.962501 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 05:41:21.276197 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 05:41:21.621809 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 05:41:21.960669 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 05:41:22.296713 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 05:41:22.630139 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 05:41:22.982081 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 05:41:23.364655 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 05:41:23.696096 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 05:41:24.037379 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 05:41:24.373752 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 05:41:24.762474 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 05:41:25.10641 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 05:41:25.445607 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 05:41:25.790358 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 05:41:26.1328 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 05:41:26.460217 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 05:41:26.794787 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 05:41:27.109817 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 05:41:27.452712 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 05:41:27.765257 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 05:41:28.069872 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 05:41:28.406417 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 05:41:28.792454 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 05:41:29.129487 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 05:41:29.555984 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 05:41:29.951178 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 05:41:30.343927 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 05:41:30.680192 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 05:41:31.032082 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 05:41:31.360043 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 05:41:31.711218 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 05:41:32.053089 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 05:41:32.385787 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 05:41:32.706477 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 05:41:32.986088 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-10 05:41:33.355324 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 05:41:33.67883 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 05:41:34.031653 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 05:41:34.390444 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 05:41:34.749498 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 05:41:34.874016 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-10 05:41:35.221729 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 05:41:35.566842 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 05:41:35.925149 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 05:41:36.260638 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 05:41:36.607103 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 05:41:36.943483 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 05:41:37.296439 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 05:41:37.625853 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 05:41:37.9642 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 05:41:38.35125 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 05:41:38.688626 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 05:41:39.016997 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 05:41:39.370164 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 05:41:39.735762 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 05:41:40.097501 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 05:41:40.537483 INFO::Counting total values for each feature
2024-06-10 05:41:40.636319 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-10 05:41:40.94882 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-10 05:41:41.268843 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-10 05:41:41.673881 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-10 05:41:41.833237 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-10 05:41:41.970025 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-10 05:41:41.981657 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-10 05:41:41.99861 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
62.947 1.162 74.806
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 184.959 | 2.945 | 216.640 | |