Lauren McIver
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 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 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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. |
| 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: 2024-11-09 05:59:29 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 06:03:58 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 269.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 23.661 0.367 24.047
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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"
2024-11-09 06:03:47.200131 INFO::Writing function arguments to log file
2024-11-09 06:03:47.212065 INFO::Verifying options selected are valid
2024-11-09 06:03:47.223599 INFO::Determining format of input files
2024-11-09 06:03:47.224035 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-09 06:03:47.225766 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-09 06:03:47.226152 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-09 06:03:47.226838 INFO::Filter data based on min abundance and min prevalence
2024-11-09 06:03:47.22709 INFO::Total samples in data: 1595
2024-11-09 06:03:47.227331 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-09 06:03:47.23056 INFO::Total filtered features: 0
2024-11-09 06:03:47.230863 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-09 06:03:47.233347 INFO::Total filtered features with variance filtering: 0
2024-11-09 06:03:47.233607 INFO::Filtered feature names from variance filtering:
2024-11-09 06:03:47.233841 INFO::Running selected normalization method: TSS
2024-11-09 06:03:47.580933 INFO::Bypass z-score application to metadata
2024-11-09 06:03:47.581371 INFO::Running selected transform method: AST
2024-11-09 06:03:47.58651 INFO::Running selected analysis method: LM
2024-11-09 06:03:47.736752 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-09 06:03:47.842505 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-09 06:03:47.890703 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-09 06:03:47.93408 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-09 06:03:47.980569 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-09 06:03:48.02392 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-09 06:03:48.066449 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-09 06:03:48.120968 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-09 06:03:48.163981 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-09 06:03:48.200299 WARNING::Fitting problem for feature 9 a warning was issued
2024-11-09 06:03:48.244806 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-09 06:03:48.29187 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-09 06:03:48.334819 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-09 06:03:48.375965 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-09 06:03:48.421912 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-09 06:03:48.46418 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-09 06:03:48.510485 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-09 06:03:48.551995 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-09 06:03:48.598709 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-09 06:03:48.642285 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-09 06:03:48.684772 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-09 06:03:48.727869 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-09 06:03:48.773747 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-09 06:03:48.815804 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-09 06:03:48.8593 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-09 06:03:48.902197 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-09 06:03:48.948059 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-09 06:03:48.990806 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-09 06:03:49.034718 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-09 06:03:49.0793 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-09 06:03:49.124808 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-09 06:03:49.165532 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-09 06:03:49.210743 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-09 06:03:49.328404 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-09 06:03:49.372317 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-09 06:03:49.413251 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-09 06:03:49.458357 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-09 06:03:49.500271 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-09 06:03:49.54296 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-09 06:03:49.583563 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-09 06:03:49.626928 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-09 06:03:49.670241 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-09 06:03:49.712114 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-09 06:03:49.758273 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-09 06:03:49.798953 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-09 06:03:49.838413 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-09 06:03:49.88302 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-09 06:03:49.925598 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-09 06:03:49.969398 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-09 06:03:50.012837 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-09 06:03:50.053526 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-09 06:03:50.094003 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-09 06:03:50.137495 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-09 06:03:50.17924 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-09 06:03:50.224253 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-09 06:03:50.266521 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-09 06:03:50.309198 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-09 06:03:50.354108 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-09 06:03:50.39743 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-09 06:03:50.44077 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-09 06:03:50.484655 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-09 06:03:50.525081 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-09 06:03:50.566782 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-09 06:03:50.615949 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-09 06:03:50.657794 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-09 06:03:50.699255 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-09 06:03:50.74244 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-09 06:03:50.783831 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-09 06:03:50.82257 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-09 06:03:50.867358 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-09 06:03:50.911409 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-09 06:03:50.955216 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-09 06:03:50.998767 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-09 06:03:51.039767 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-09 06:03:51.080503 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-09 06:03:51.122163 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-09 06:03:51.167528 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-09 06:03:51.20965 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-09 06:03:51.252177 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-09 06:03:51.299696 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-09 06:03:51.343694 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-09 06:03:51.38815 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-09 06:03:51.431918 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-09 06:03:51.474778 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-09 06:03:51.517291 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-09 06:03:51.558548 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-09 06:03:51.599242 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-09 06:03:51.642597 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-09 06:03:51.697187 INFO::Counting total values for each feature
2024-11-09 06:03:51.710588 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-09 06:03:51.751691 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-09 06:03:51.799562 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-09 06:03:51.846786 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-09 06:03:51.870171 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-09 06:03:51.882725 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-09 06:03:51.885139 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-09 06:03:51.887357 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"
2024-11-09 06:03:51.891427 INFO::Writing function arguments to log file
2024-11-09 06:03:51.893073 INFO::Verifying options selected are valid
2024-11-09 06:03:51.893339 INFO::Determining format of input files
2024-11-09 06:03:51.893639 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-09 06:03:51.89519 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-09 06:03:51.895468 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-09 06:03:51.895921 INFO::Filter data based on min abundance and min prevalence
2024-11-09 06:03:51.896146 INFO::Total samples in data: 1595
2024-11-09 06:03:51.89637 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-09 06:03:51.897543 INFO::Total filtered features: 0
2024-11-09 06:03:51.897788 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-09 06:03:51.900102 INFO::Total filtered features with variance filtering: 0
2024-11-09 06:03:51.900351 INFO::Filtered feature names from variance filtering:
2024-11-09 06:03:51.900573 INFO::Running selected normalization method: NONE
2024-11-09 06:03:51.900789 INFO::Bypass z-score application to metadata
2024-11-09 06:03:51.901008 INFO::Running selected transform method: AST
2024-11-09 06:03:51.907612 INFO::Running selected analysis method: LM
2024-11-09 06:03:51.908092 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-09 06:03:51.949131 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-09 06:03:51.991978 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-09 06:03:52.036542 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-09 06:03:52.077047 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-09 06:03:52.116699 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-09 06:03:52.16207 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-09 06:03:52.20247 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-09 06:03:52.242617 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-09 06:03:52.286384 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-09 06:03:52.327946 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-09 06:03:52.362912 WARNING::Fitting problem for feature 11 a warning was issued
2024-11-09 06:03:52.412133 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-09 06:03:52.451664 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-09 06:03:52.485903 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-09 06:03:52.531403 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-09 06:03:52.571443 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-09 06:03:52.61611 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-09 06:03:52.655136 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-09 06:03:52.697261 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-09 06:03:52.740961 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-09 06:03:52.779801 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-09 06:03:52.822842 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-09 06:03:52.863728 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-09 06:03:52.907479 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-09 06:03:52.945858 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-09 06:03:52.989681 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-09 06:03:53.03019 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-09 06:03:53.073005 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-09 06:03:53.114129 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-09 06:03:53.156974 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-09 06:03:53.195062 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-09 06:03:53.234828 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-09 06:03:53.278353 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-09 06:03:53.319219 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-09 06:03:53.35869 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-09 06:03:53.402504 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-09 06:03:53.443405 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-09 06:03:53.484652 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-09 06:03:53.52909 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-09 06:03:53.569759 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-09 06:03:53.611345 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-09 06:03:53.649816 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-09 06:03:53.689843 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-09 06:03:53.733129 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-09 06:03:53.774255 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-09 06:03:53.815596 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-09 06:03:53.859249 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-09 06:03:53.901311 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-09 06:03:54.017812 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-09 06:03:54.058661 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-09 06:03:54.098471 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-09 06:03:54.136617 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-09 06:03:54.180423 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-09 06:03:54.21692 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-09 06:03:54.253626 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-09 06:03:54.294681 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-09 06:03:54.333431 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-09 06:03:54.373339 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-09 06:03:54.412896 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-09 06:03:54.455183 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-09 06:03:54.495796 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-09 06:03:54.534535 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-09 06:03:54.576486 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-09 06:03:54.615345 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-09 06:03:54.655659 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-09 06:03:54.698485 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-09 06:03:54.738424 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-09 06:03:54.777755 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-09 06:03:54.818955 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-09 06:03:54.860434 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-09 06:03:54.902421 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-09 06:03:54.945533 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-09 06:03:54.988533 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-09 06:03:55.002918 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-09 06:03:55.042774 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-09 06:03:55.083288 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-09 06:03:55.126903 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-09 06:03:55.16681 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-09 06:03:55.207967 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-09 06:03:55.247679 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-09 06:03:55.290789 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-09 06:03:55.332589 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-09 06:03:55.372496 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-09 06:03:55.418437 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-09 06:03:55.457767 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-09 06:03:55.496441 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-09 06:03:55.538335 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-09 06:03:55.57785 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-09 06:03:55.619914 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-09 06:03:55.670085 INFO::Counting total values for each feature
2024-11-09 06:03:55.677314 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-09 06:03:55.717587 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-09 06:03:55.758038 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-09 06:03:55.805081 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-09 06:03:55.836203 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-09 06:03:55.866115 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-09 06:03:55.868553 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-09 06:03:55.870337 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
8.928 0.094 9.021
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 23.661 | 0.367 | 24.047 | |