Lauren McIver
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1cacd4c |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1130/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.20.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the Maaslin2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Maaslin2 |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2024-12-20 23:47:55 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 23:50:43 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 167.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Maaslin2 91.232 1.759 93.163
* 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-arm64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-12-20 23:50:00.596486 INFO::Writing function arguments to log file
2024-12-20 23:50:00.643588 INFO::Verifying options selected are valid
2024-12-20 23:50:00.686356 INFO::Determining format of input files
2024-12-20 23:50:00.688224 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 23:50:00.694097 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 23:50:00.695656 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-20 23:50:00.698276 INFO::Filter data based on min abundance and min prevalence
2024-12-20 23:50:00.699386 INFO::Total samples in data: 1595
2024-12-20 23:50:00.70025 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 23:50:00.705394 INFO::Total filtered features: 0
2024-12-20 23:50:00.706756 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 23:50:00.724777 INFO::Total filtered features with variance filtering: 0
2024-12-20 23:50:00.726287 INFO::Filtered feature names from variance filtering:
2024-12-20 23:50:00.727218 INFO::Running selected normalization method: TSS
2024-12-20 23:50:02.027923 INFO::Bypass z-score application to metadata
2024-12-20 23:50:02.029063 INFO::Running selected transform method: AST
2024-12-20 23:50:02.037147 INFO::Running selected analysis method: LM
2024-12-20 23:50:02.560849 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 23:50:02.967224 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 23:50:03.144886 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 23:50:03.322453 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 23:50:03.525357 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 23:50:03.703166 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 23:50:03.872317 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 23:50:04.039986 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 23:50:04.224442 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 23:50:04.360756 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-20 23:50:04.535745 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 23:50:04.712774 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 23:50:04.880478 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 23:50:05.043471 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 23:50:05.259583 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 23:50:05.429018 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 23:50:05.608978 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 23:50:05.774161 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 23:50:05.965276 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 23:50:06.140452 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 23:50:06.309154 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 23:50:06.490862 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 23:50:06.66118 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 23:50:06.829078 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 23:50:06.998006 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 23:50:07.185274 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 23:50:07.362124 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 23:50:07.522111 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 23:50:07.713464 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 23:50:07.835385 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 23:50:07.916679 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 23:50:08.024365 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 23:50:08.11574 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 23:50:08.231614 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 23:50:08.393421 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 23:50:08.472532 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 23:50:08.557444 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 23:50:08.726053 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 23:50:08.890766 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 23:50:09.05253 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 23:50:09.238951 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 23:50:09.416197 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 23:50:09.600799 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 23:50:09.784027 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 23:50:09.949501 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 23:50:10.120897 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 23:50:10.292058 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 23:50:10.464156 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 23:50:10.650347 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 23:50:10.815281 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 23:50:10.992672 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 23:50:11.156094 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 23:50:11.325586 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 23:50:11.508769 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 23:50:11.684843 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 23:50:11.852979 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 23:50:12.023638 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 23:50:12.213912 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 23:50:12.37032 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 23:50:12.55437 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 23:50:12.722407 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 23:50:12.897232 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 23:50:13.062193 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 23:50:13.24277 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 23:50:13.408909 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 23:50:13.581948 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 23:50:13.750111 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 23:50:13.913635 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 23:50:14.113486 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 23:50:14.28257 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 23:50:14.467604 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 23:50:14.660016 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 23:50:14.823514 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 23:50:14.98931 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 23:50:15.169261 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 23:50:15.332312 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 23:50:15.501296 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 23:50:15.684506 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 23:50:15.858449 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 23:50:16.038355 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 23:50:16.227336 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 23:50:16.393229 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 23:50:16.569594 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 23:50:16.751209 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 23:50:16.908209 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 23:50:17.076715 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 23:50:17.249716 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 23:50:17.411928 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 23:50:17.640378 INFO::Counting total values for each feature
2024-12-20 23:50:17.680035 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-20 23:50:17.82775 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-20 23:50:18.009485 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-20 23:50:18.18574 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-20 23:50:18.284228 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-20 23:50:18.327971 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-20 23:50:18.337195 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-20 23:50:18.345727 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-12-20 23:50:18.361461 INFO::Writing function arguments to log file
2024-12-20 23:50:18.367943 INFO::Verifying options selected are valid
2024-12-20 23:50:18.369014 INFO::Determining format of input files
2024-12-20 23:50:18.370231 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 23:50:18.375965 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 23:50:18.377167 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-12-20 23:50:18.378814 INFO::Filter data based on min abundance and min prevalence
2024-12-20 23:50:18.37975 INFO::Total samples in data: 1595
2024-12-20 23:50:18.380579 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 23:50:18.395299 INFO::Total filtered features: 0
2024-12-20 23:50:18.39734 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 23:50:18.4075 INFO::Total filtered features with variance filtering: 0
2024-12-20 23:50:18.40881 INFO::Filtered feature names from variance filtering:
2024-12-20 23:50:18.40965 INFO::Running selected normalization method: NONE
2024-12-20 23:50:18.41044 INFO::Bypass z-score application to metadata
2024-12-20 23:50:18.411231 INFO::Running selected transform method: AST
2024-12-20 23:50:18.427787 INFO::Running selected analysis method: LM
2024-12-20 23:50:18.429766 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 23:50:18.6012 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 23:50:18.763164 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 23:50:18.931795 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 23:50:19.091499 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 23:50:19.259915 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 23:50:19.424056 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 23:50:19.596359 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 23:50:19.757736 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 23:50:19.9358 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 23:50:20.108281 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 23:50:20.258808 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-20 23:50:20.443613 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 23:50:20.613458 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 23:50:21.04132 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-20 23:50:21.205888 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 23:50:21.362013 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 23:50:21.525281 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 23:50:21.69068 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 23:50:21.858437 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 23:50:22.020525 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 23:50:22.175364 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 23:50:22.341387 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 23:50:22.502956 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 23:50:22.664313 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 23:50:22.829176 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 23:50:22.988998 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 23:50:23.147516 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 23:50:23.306921 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 23:50:23.478577 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 23:50:23.631611 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 23:50:23.782146 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 23:50:23.948794 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 23:50:24.107648 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 23:50:24.270749 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 23:50:24.463209 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 23:50:24.616244 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 23:50:24.777922 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 23:50:24.951483 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 23:50:25.134049 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 23:50:25.29885 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 23:50:25.462484 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 23:50:25.616965 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 23:50:25.788829 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 23:50:25.94904 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 23:50:26.117767 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 23:50:26.295022 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 23:50:26.456814 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 23:50:26.625654 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 23:50:26.783033 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 23:50:26.963747 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 23:50:27.12425 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 23:50:27.274677 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 23:50:27.446299 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 23:50:27.590916 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 23:50:27.739413 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 23:50:27.902492 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 23:50:28.054159 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 23:50:28.21224 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 23:50:28.376186 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 23:50:28.532553 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 23:50:28.692845 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 23:50:28.855202 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 23:50:29.011331 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 23:50:29.168915 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 23:50:29.340071 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 23:50:29.497184 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 23:50:29.658939 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 23:50:29.82532 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 23:50:29.989781 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 23:50:30.442569 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 23:50:30.60876 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 23:50:30.780287 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 23:50:30.938941 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 23:50:30.997121 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-20 23:50:31.171741 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 23:50:31.332991 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 23:50:31.494522 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 23:50:31.653521 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 23:50:31.82116 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 23:50:32.007609 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 23:50:32.168218 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 23:50:32.33583 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 23:50:32.503028 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 23:50:32.68739 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 23:50:32.839851 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 23:50:32.995999 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 23:50:33.1509 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 23:50:33.321129 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 23:50:33.487774 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 23:50:33.676829 INFO::Counting total values for each feature
2024-12-20 23:50:33.703985 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-20 23:50:33.848531 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-20 23:50:33.992785 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-20 23:50:34.164448 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-20 23:50:34.275582 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-20 23:50:34.383555 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-20 23:50:34.393077 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-20 23:50:34.400173 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
34.308 0.806 35.170
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 91.232 | 1.759 | 93.163 | |