Lauren McIver
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_18 |
| git_last_commit: 0ab531d |
| git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:12 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1124/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.16.0 (landing page) Lauren McIver
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the Maaslin2 package: - 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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2024-04-17 18:00:15 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 18:03:05 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 170.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/Maaslin2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* 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 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 90.334 1.685 92.603
* 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
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/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 1.9.6 Current TMB version is 1.9.10 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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"
2024-04-17 18:02:20.898007 INFO::Writing function arguments to log file
2024-04-17 18:02:20.944811 INFO::Verifying options selected are valid
2024-04-17 18:02:20.991953 INFO::Determining format of input files
2024-04-17 18:02:20.993832 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-17 18:02:20.999874 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-17 18:02:21.001506 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-04-17 18:02:21.004214 INFO::Filter data based on min abundance and min prevalence
2024-04-17 18:02:21.005343 INFO::Total samples in data: 1595
2024-04-17 18:02:21.006214 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-17 18:02:21.011226 INFO::Total filtered features: 0
2024-04-17 18:02:21.012508 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-17 18:02:21.022515 INFO::Total filtered features with variance filtering: 0
2024-04-17 18:02:21.023772 INFO::Filtered feature names from variance filtering:
2024-04-17 18:02:21.024588 INFO::Running selected normalization method: TSS
2024-04-17 18:02:22.417495 INFO::Bypass z-score application to metadata
2024-04-17 18:02:22.419122 INFO::Running selected transform method: AST
2024-04-17 18:02:22.437748 INFO::Running selected analysis method: LM
2024-04-17 18:02:23.133167 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-17 18:02:23.566687 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-17 18:02:23.767338 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-17 18:02:23.939148 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-17 18:02:24.112785 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-17 18:02:24.285682 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-17 18:02:24.467985 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-17 18:02:24.656611 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-17 18:02:24.78924 WARNING::Fitting problem for feature 8 a warning was issued
2024-04-17 18:02:24.983203 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-17 18:02:25.143562 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-17 18:02:25.311827 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-17 18:02:25.488573 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-17 18:02:25.713624 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-17 18:02:25.862621 WARNING::Fitting problem for feature 13 a warning was issued
2024-04-17 18:02:26.068746 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-17 18:02:26.259727 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-17 18:02:26.440615 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-17 18:02:26.609877 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-17 18:02:26.789297 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-17 18:02:26.977658 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-17 18:02:27.135565 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-17 18:02:27.299449 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-17 18:02:27.483885 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-17 18:02:27.656981 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-17 18:02:27.821905 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-17 18:02:28.003505 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-17 18:02:28.184548 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-17 18:02:28.354432 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-17 18:02:28.549243 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-17 18:02:28.731898 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-17 18:02:28.92106 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-17 18:02:29.099979 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-17 18:02:29.284173 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-17 18:02:29.462599 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-17 18:02:29.653681 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-17 18:02:29.82339 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-17 18:02:29.99358 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-17 18:02:30.18267 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-17 18:02:30.359097 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-17 18:02:30.537735 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-17 18:02:30.706736 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-17 18:02:30.890753 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-17 18:02:31.074142 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-17 18:02:31.257968 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-17 18:02:31.445901 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-17 18:02:31.608997 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-17 18:02:31.791527 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-17 18:02:31.96384 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-17 18:02:32.146405 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-17 18:02:32.306003 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-17 18:02:32.482806 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-17 18:02:32.643615 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-17 18:02:32.817278 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-17 18:02:32.984351 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-17 18:02:33.170094 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-17 18:02:33.340964 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-17 18:02:33.515078 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-17 18:02:33.984536 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-17 18:02:34.14759 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-17 18:02:34.326191 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-17 18:02:34.50918 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-17 18:02:34.678273 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-17 18:02:34.847128 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-17 18:02:35.023141 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-17 18:02:35.209031 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-17 18:02:35.377696 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-17 18:02:35.545315 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-17 18:02:35.74089 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-17 18:02:35.871901 WARNING::Fitting problem for feature 67 a warning was issued
2024-04-17 18:02:36.033542 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-17 18:02:36.232834 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-17 18:02:36.414387 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-17 18:02:36.600691 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-17 18:02:36.785822 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-17 18:02:36.958821 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-17 18:02:37.138011 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-17 18:02:37.323142 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-17 18:02:37.497274 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-17 18:02:37.664851 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-17 18:02:37.848302 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-17 18:02:38.032318 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-17 18:02:38.219818 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-17 18:02:38.398518 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-17 18:02:38.576349 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-17 18:02:38.748446 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-17 18:02:38.911246 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-17 18:02:39.078565 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-17 18:02:39.244193 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-17 18:02:39.417574 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-17 18:02:39.633719 INFO::Counting total values for each feature
2024-04-17 18:02:39.682226 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-04-17 18:02:39.83033 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-04-17 18:02:39.999777 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-04-17 18:02:40.171526 INFO::Writing residuals to file output/fits/residuals.rds
2024-04-17 18:02:40.252848 INFO::Writing fitted values to file output/fits/fitted.rds
2024-04-17 18:02:40.297482 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-04-17 18:02:40.306806 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-04-17 18:02:40.315309 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"
2024-04-17 18:02:40.33156 INFO::Writing function arguments to log file
2024-04-17 18:02:40.338143 INFO::Verifying options selected are valid
2024-04-17 18:02:40.33943 INFO::Determining format of input files
2024-04-17 18:02:40.342247 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-17 18:02:40.348608 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-17 18:02:40.349779 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-04-17 18:02:40.351449 INFO::Filter data based on min abundance and min prevalence
2024-04-17 18:02:40.352314 INFO::Total samples in data: 1595
2024-04-17 18:02:40.353121 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-17 18:02:40.357298 INFO::Total filtered features: 0
2024-04-17 18:02:40.358384 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-17 18:02:40.368394 INFO::Total filtered features with variance filtering: 0
2024-04-17 18:02:40.370099 INFO::Filtered feature names from variance filtering:
2024-04-17 18:02:40.370981 INFO::Running selected normalization method: NONE
2024-04-17 18:02:40.371772 INFO::Bypass z-score application to metadata
2024-04-17 18:02:40.372538 INFO::Running selected transform method: AST
2024-04-17 18:02:40.397624 INFO::Running selected analysis method: LM
2024-04-17 18:02:40.399822 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-17 18:02:40.563054 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-17 18:02:40.734129 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-17 18:02:40.889026 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-17 18:02:41.065306 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-17 18:02:41.23878 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-17 18:02:41.407991 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-17 18:02:41.594061 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-17 18:02:41.760064 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-17 18:02:41.893652 WARNING::Fitting problem for feature 9 a warning was issued
2024-04-17 18:02:42.074909 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-17 18:02:42.240337 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-17 18:02:42.377748 WARNING::Fitting problem for feature 11 a warning was issued
2024-04-17 18:02:42.561965 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-17 18:02:42.723798 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-17 18:02:42.890747 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-17 18:02:43.071187 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-17 18:02:43.236862 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-17 18:02:43.395958 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-17 18:02:43.575641 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-17 18:02:43.741478 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-17 18:02:43.922134 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-17 18:02:44.093053 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-17 18:02:44.255721 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-17 18:02:44.431142 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-17 18:02:44.586639 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-17 18:02:44.764695 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-17 18:02:44.929833 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-17 18:02:45.09489 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-17 18:02:45.271911 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-17 18:02:45.428982 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-17 18:02:45.600585 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-17 18:02:45.76221 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-17 18:02:45.95816 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-17 18:02:46.118696 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-17 18:02:46.271702 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-17 18:02:46.459128 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-17 18:02:46.623324 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-17 18:02:46.790592 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-17 18:02:46.968693 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-17 18:02:47.136056 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-17 18:02:47.296349 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-17 18:02:47.467767 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-17 18:02:47.632407 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-17 18:02:47.81278 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-17 18:02:47.978096 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-17 18:02:48.146614 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-17 18:02:48.325012 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-17 18:02:48.494381 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-17 18:02:48.671216 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-17 18:02:48.831552 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-17 18:02:48.990221 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-17 18:02:49.14983 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-17 18:02:49.311817 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-17 18:02:49.471646 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-17 18:02:49.618912 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-17 18:02:49.784817 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-17 18:02:49.937413 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-17 18:02:50.101713 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-17 18:02:50.253562 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-17 18:02:50.419317 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-17 18:02:50.586302 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-17 18:02:50.7491 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-17 18:02:50.904641 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-17 18:02:51.070984 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-17 18:02:51.243736 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-17 18:02:51.39995 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-17 18:02:51.580567 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-17 18:02:51.740288 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-17 18:02:51.924736 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-17 18:02:52.077194 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-17 18:02:52.24133 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-17 18:02:52.424743 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-17 18:02:52.584172 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-17 18:02:52.641239 WARNING::Fitting problem for feature 72 a warning was issued
2024-04-17 18:02:52.8158 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-17 18:02:52.981482 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-17 18:02:53.148591 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-17 18:02:53.330373 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-17 18:02:53.496899 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-17 18:02:53.675029 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-17 18:02:53.835587 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-17 18:02:54.023223 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-17 18:02:54.186991 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-17 18:02:54.378042 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-17 18:02:54.545959 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-17 18:02:54.703116 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-17 18:02:54.880408 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-17 18:02:55.04171 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-17 18:02:55.213523 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-17 18:02:55.42679 INFO::Counting total values for each feature
2024-04-17 18:02:55.455054 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-04-17 18:02:55.602967 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-04-17 18:02:55.750678 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-04-17 18:02:55.922951 INFO::Writing residuals to file output2/fits/residuals.rds
2024-04-17 18:02:56.033188 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-04-17 18:02:56.138045 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-04-17 18:02:56.147431 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-04-17 18:02:56.154236 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
35.941 0.747 36.761
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 90.334 | 1.685 | 92.603 | |