Lauren McIver
| Snapshot Date: 2023-12-07 14:00:14 -0500 (Thu, 07 Dec 2023) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: a8d86b0 |
| git_last_commit_date: 2023-10-24 11:15:22 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2023-12-08 12:24:40 -0500 (Fri, 08 Dec 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4617 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" | 4377 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4386 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" | 4270 |
| 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 1106/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.17.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | 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: 1.17.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings Maaslin2_1.17.0.tar.gz |
| StartedAt: 2023-12-08 05:41:20 -0000 (Fri, 08 Dec 2023) |
| EndedAt: 2023-12-08 05:44:45 -0000 (Fri, 08 Dec 2023) |
| EllapsedTime: 205.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings Maaslin2_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.17.0’
* 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 R 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 119.859 0.934 121.062
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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 1.9.6 Current TMB version is 1.9.9 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 Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 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"
2023-12-08 05:43:57.643427 INFO::Writing function arguments to log file
2023-12-08 05:43:57.680752 INFO::Verifying options selected are valid
2023-12-08 05:43:57.727554 INFO::Determining format of input files
2023-12-08 05:43:57.729642 INFO::Input format is data samples as rows and metadata samples as rows
2023-12-08 05:43:57.737615 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-12-08 05:43:57.739697 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-12-08 05:43:57.743598 INFO::Filter data based on min abundance and min prevalence
2023-12-08 05:43:57.745189 INFO::Total samples in data: 1595
2023-12-08 05:43:57.746599 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-12-08 05:43:57.757823 INFO::Total filtered features: 0
2023-12-08 05:43:57.759652 INFO::Filtered feature names from abundance and prevalence filtering:
2023-12-08 05:43:57.792506 INFO::Total filtered features with variance filtering: 0
2023-12-08 05:43:57.794162 INFO::Filtered feature names from variance filtering:
2023-12-08 05:43:57.795569 INFO::Running selected normalization method: TSS
2023-12-08 05:43:59.253545 INFO::Bypass z-score application to metadata
2023-12-08 05:43:59.255164 INFO::Running selected transform method: AST
2023-12-08 05:43:59.280818 INFO::Running selected analysis method: LM
2023-12-08 05:44:00.018697 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-12-08 05:44:00.49485 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-12-08 05:44:00.75411 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-12-08 05:44:00.991284 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-12-08 05:44:01.236286 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-12-08 05:44:01.473983 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-12-08 05:44:01.730099 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-12-08 05:44:01.969856 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-12-08 05:44:02.164604 WARNING::Fitting problem for feature 8 a warning was issued
2023-12-08 05:44:02.437777 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-12-08 05:44:02.641712 WARNING::Fitting problem for feature 9 a warning was issued
2023-12-08 05:44:02.91822 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-12-08 05:44:03.149156 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-12-08 05:44:03.431342 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-12-08 05:44:03.665689 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-12-08 05:44:03.902406 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-12-08 05:44:04.141133 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-12-08 05:44:04.385896 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-12-08 05:44:04.62412 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-12-08 05:44:04.881254 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-12-08 05:44:05.13438 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-12-08 05:44:05.358494 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-12-08 05:44:05.586792 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-12-08 05:44:05.83685 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-12-08 05:44:06.073514 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-12-08 05:44:06.302462 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-12-08 05:44:06.548448 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-12-08 05:44:06.78805 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-12-08 05:44:07.02767 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-12-08 05:44:07.297331 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-12-08 05:44:07.546135 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-12-08 05:44:07.807685 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-12-08 05:44:08.056562 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-12-08 05:44:08.30354 INFO::Fitting model to feature number 32, Prevotella.copri
2023-12-08 05:44:08.546001 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-12-08 05:44:08.803496 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-12-08 05:44:09.035114 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-12-08 05:44:09.266902 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-12-08 05:44:09.507471 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-12-08 05:44:09.746557 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-12-08 05:44:09.977864 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-12-08 05:44:10.218353 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-12-08 05:44:10.461221 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-12-08 05:44:10.710602 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-12-08 05:44:10.964052 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-12-08 05:44:11.191655 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-12-08 05:44:11.421937 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-12-08 05:44:11.655297 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-12-08 05:44:11.899238 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-12-08 05:44:12.14258 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-12-08 05:44:12.37659 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-12-08 05:44:12.606562 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-12-08 05:44:12.846191 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-12-08 05:44:13.09555 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-12-08 05:44:13.366438 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-12-08 05:44:13.629018 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-12-08 05:44:13.863591 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-12-08 05:44:14.104747 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-12-08 05:44:14.363333 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-12-08 05:44:14.584303 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-12-08 05:44:14.833648 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-12-08 05:44:15.077023 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-12-08 05:44:15.305625 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-12-08 05:44:15.552013 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-12-08 05:44:16.102078 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-12-08 05:44:16.342282 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-12-08 05:44:16.567119 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-12-08 05:44:16.815896 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-12-08 05:44:17.048195 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-12-08 05:44:17.219961 WARNING::Fitting problem for feature 67 a warning was issued
2023-12-08 05:44:17.440559 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-12-08 05:44:17.690967 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-12-08 05:44:17.944674 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-12-08 05:44:18.205019 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-12-08 05:44:18.441791 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-12-08 05:44:18.671744 INFO::Fitting model to feature number 73, Dialister.invisus
2023-12-08 05:44:18.89811 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-12-08 05:44:19.135281 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-12-08 05:44:19.372134 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-12-08 05:44:19.606559 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-12-08 05:44:19.856962 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-12-08 05:44:20.112782 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-12-08 05:44:20.36002 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-12-08 05:44:20.606124 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-12-08 05:44:20.888 INFO::Fitting model to feature number 82, Escherichia.coli
2023-12-08 05:44:21.137072 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-12-08 05:44:21.381717 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-12-08 05:44:21.613936 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-12-08 05:44:21.852287 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-12-08 05:44:22.077867 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-12-08 05:44:22.377244 INFO::Counting total values for each feature
2023-12-08 05:44:22.438649 INFO::Writing filtered data to file output/features/filtered_data.tsv
2023-12-08 05:44:22.566755 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2023-12-08 05:44:22.694832 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2023-12-08 05:44:22.825924 INFO::Writing residuals to file output/fits/residuals.rds
2023-12-08 05:44:22.875992 INFO::Writing fitted values to file output/fits/fitted.rds
2023-12-08 05:44:22.902589 INFO::Writing extracted random effects to file output/fits/ranef.rds
2023-12-08 05:44:22.908919 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-12-08 05:44:22.915927 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"
2023-12-08 05:44:22.9341 INFO::Writing function arguments to log file
2023-12-08 05:44:22.942728 INFO::Verifying options selected are valid
2023-12-08 05:44:22.944213 INFO::Determining format of input files
2023-12-08 05:44:22.945873 INFO::Input format is data samples as rows and metadata samples as rows
2023-12-08 05:44:22.953343 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-12-08 05:44:22.954962 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2023-12-08 05:44:22.957452 INFO::Filter data based on min abundance and min prevalence
2023-12-08 05:44:22.958849 INFO::Total samples in data: 1595
2023-12-08 05:44:22.960212 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-12-08 05:44:22.970937 INFO::Total filtered features: 0
2023-12-08 05:44:22.972536 INFO::Filtered feature names from abundance and prevalence filtering:
2023-12-08 05:44:23.004572 INFO::Total filtered features with variance filtering: 0
2023-12-08 05:44:23.006108 INFO::Filtered feature names from variance filtering:
2023-12-08 05:44:23.00745 INFO::Running selected normalization method: NONE
2023-12-08 05:44:23.008679 INFO::Bypass z-score application to metadata
2023-12-08 05:44:23.020127 INFO::Running selected transform method: AST
2023-12-08 05:44:23.044199 INFO::Running selected analysis method: LM
2023-12-08 05:44:23.046357 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-12-08 05:44:23.264612 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-12-08 05:44:23.488588 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-12-08 05:44:23.694734 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-12-08 05:44:23.921633 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-12-08 05:44:24.134474 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-12-08 05:44:24.364106 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-12-08 05:44:24.579267 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-12-08 05:44:24.805875 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-12-08 05:44:25.019059 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-12-08 05:44:25.247445 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-12-08 05:44:25.477348 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-12-08 05:44:25.709378 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-12-08 05:44:25.922996 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-12-08 05:44:26.144305 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-12-08 05:44:26.383226 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-12-08 05:44:26.554946 WARNING::Fitting problem for feature 16 a warning was issued
2023-12-08 05:44:26.773979 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-12-08 05:44:27.011399 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-12-08 05:44:27.228686 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-12-08 05:44:27.397608 WARNING::Fitting problem for feature 19 a warning was issued
2023-12-08 05:44:27.620178 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-12-08 05:44:27.839768 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-12-08 05:44:28.061129 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-12-08 05:44:28.298547 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-12-08 05:44:28.503317 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-12-08 05:44:28.721538 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-12-08 05:44:28.947552 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-12-08 05:44:29.16198 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-12-08 05:44:29.407366 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-12-08 05:44:29.613726 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-12-08 05:44:29.823684 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-12-08 05:44:30.048076 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-12-08 05:44:30.261982 INFO::Fitting model to feature number 32, Prevotella.copri
2023-12-08 05:44:30.491345 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-12-08 05:44:30.714518 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-12-08 05:44:30.928822 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-12-08 05:44:31.168001 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-12-08 05:44:31.420683 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-12-08 05:44:31.653676 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-12-08 05:44:31.883685 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-12-08 05:44:32.086238 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-12-08 05:44:32.294566 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-12-08 05:44:32.519922 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-12-08 05:44:32.733072 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-12-08 05:44:32.969959 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-12-08 05:44:33.187642 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-12-08 05:44:33.415185 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-12-08 05:44:33.645881 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-12-08 05:44:33.865958 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-12-08 05:44:34.094771 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-12-08 05:44:34.306237 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-12-08 05:44:34.517136 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-12-08 05:44:34.734795 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-12-08 05:44:34.944646 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-12-08 05:44:35.152567 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-12-08 05:44:35.358479 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-12-08 05:44:35.583287 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-12-08 05:44:35.804205 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-12-08 05:44:36.043812 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-12-08 05:44:36.258968 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-12-08 05:44:36.485019 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-12-08 05:44:36.706788 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-12-08 05:44:36.926083 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-12-08 05:44:37.140663 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-12-08 05:44:37.377332 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-12-08 05:44:37.592756 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-12-08 05:44:37.8083 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-12-08 05:44:38.037041 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-12-08 05:44:38.261528 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-12-08 05:44:38.488876 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-12-08 05:44:38.722194 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-12-08 05:44:38.959348 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-12-08 05:44:39.189576 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-12-08 05:44:39.264272 WARNING::Fitting problem for feature 72 a warning was issued
2023-12-08 05:44:39.477773 INFO::Fitting model to feature number 73, Dialister.invisus
2023-12-08 05:44:39.710646 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-12-08 05:44:39.928258 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-12-08 05:44:40.145518 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-12-08 05:44:40.376199 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-12-08 05:44:40.587826 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-12-08 05:44:40.817811 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-12-08 05:44:41.043458 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-12-08 05:44:41.255411 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-12-08 05:44:41.770847 INFO::Fitting model to feature number 82, Escherichia.coli
2023-12-08 05:44:41.98451 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-12-08 05:44:42.190303 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-12-08 05:44:42.400343 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-12-08 05:44:42.619165 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-12-08 05:44:42.857941 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-12-08 05:44:43.117945 INFO::Counting total values for each feature
2023-12-08 05:44:43.154761 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2023-12-08 05:44:43.279088 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2023-12-08 05:44:43.402977 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2023-12-08 05:44:43.53192 INFO::Writing residuals to file output2/fits/residuals.rds
2023-12-08 05:44:43.597642 INFO::Writing fitted values to file output2/fits/fitted.rds
2023-12-08 05:44:43.662084 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2023-12-08 05:44:43.668306 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-12-08 05:44:43.67418 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 6 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
46.991 0.486 47.574
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 119.859 | 0.934 | 121.062 | |