Lauren McIver
| Snapshot Date: 2024-11-04 13:40 -0500 (Mon, 04 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 2024-11-05 12:07 -0500 (Tue, 05 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" | 4503 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| 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" | 4539 |
| 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 | | ||||||||
| nebbiolo2 | 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 | | ||||||||
| 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: 2024-11-05 00:11:32 -0500 (Tue, 05 Nov 2024) |
| EndedAt: 2024-11-05 00:17:14 -0500 (Tue, 05 Nov 2024) |
| EllapsedTime: 341.3 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 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 62.002 1.21 63.581
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-11-05 00:16:47.53779 INFO::Writing function arguments to log file
2024-11-05 00:16:47.57378 INFO::Verifying options selected are valid
2024-11-05 00:16:47.601167 INFO::Determining format of input files
2024-11-05 00:16:47.602476 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-05 00:16:47.607233 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-05 00:16:47.60842 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-05 00:16:47.610339 INFO::Filter data based on min abundance and min prevalence
2024-11-05 00:16:47.611101 INFO::Total samples in data: 1595
2024-11-05 00:16:47.611847 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-05 00:16:47.620027 INFO::Total filtered features: 0
2024-11-05 00:16:47.621018 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-05 00:16:47.627891 INFO::Total filtered features with variance filtering: 0
2024-11-05 00:16:47.628756 INFO::Filtered feature names from variance filtering:
2024-11-05 00:16:47.629627 INFO::Running selected normalization method: TSS
2024-11-05 00:16:48.454464 INFO::Bypass z-score application to metadata
2024-11-05 00:16:48.455596 INFO::Running selected transform method: AST
2024-11-05 00:16:48.468895 INFO::Running selected analysis method: LM
2024-11-05 00:16:48.840766 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-05 00:16:49.091693 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-05 00:16:49.372428 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-05 00:16:49.470527 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-05 00:16:49.572199 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-05 00:16:49.67162 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-05 00:16:49.772395 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-05 00:16:49.868039 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-05 00:16:49.965319 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-05 00:16:50.062879 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-05 00:16:50.150618 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-05 00:16:50.241246 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-05 00:16:50.331038 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-05 00:16:50.415674 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-05 00:16:50.516499 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-05 00:16:50.606249 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-05 00:16:50.721231 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-05 00:16:50.813423 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-05 00:16:50.917076 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-05 00:16:51.019744 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-05 00:16:51.111783 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-05 00:16:51.209092 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-05 00:16:51.302315 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-05 00:16:51.404102 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-05 00:16:51.496054 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-05 00:16:51.592899 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-05 00:16:51.697941 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-05 00:16:51.789776 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-05 00:16:51.894131 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-05 00:16:52.000385 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-05 00:16:52.098571 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-05 00:16:52.202166 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-05 00:16:52.321201 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-05 00:16:52.426684 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-05 00:16:52.531633 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-05 00:16:52.638817 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-05 00:16:52.740274 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-05 00:16:52.844263 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-05 00:16:52.954143 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-05 00:16:53.052538 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-05 00:16:53.15145 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-05 00:16:53.265134 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-05 00:16:53.370354 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-05 00:16:53.478678 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-05 00:16:53.582962 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-05 00:16:53.681629 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-05 00:16:53.786745 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-05 00:16:53.902848 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-05 00:16:54.007579 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-05 00:16:54.107996 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-05 00:16:54.212316 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-05 00:16:54.502575 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-05 00:16:54.602032 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-05 00:16:54.711744 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-05 00:16:54.826318 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-05 00:16:54.923567 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-05 00:16:55.026685 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-05 00:16:55.147651 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-05 00:16:55.243579 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-05 00:16:55.34932 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-05 00:16:55.460561 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-05 00:16:55.55793 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-05 00:16:55.657248 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-05 00:16:55.775207 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-05 00:16:55.879524 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-05 00:16:55.982648 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-05 00:16:56.092562 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-05 00:16:56.194201 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-05 00:16:56.29587 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-05 00:16:56.408408 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-05 00:16:56.515968 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-05 00:16:56.622022 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-05 00:16:56.733279 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-05 00:16:56.836685 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-05 00:16:56.948255 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-05 00:16:57.060035 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-05 00:16:57.164678 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-05 00:16:57.270247 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-05 00:16:57.369977 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-05 00:16:57.484974 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-05 00:16:57.592467 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-05 00:16:57.701481 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-05 00:16:57.805314 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-05 00:16:57.922339 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-05 00:16:58.01426 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-05 00:16:58.108709 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-05 00:16:58.206906 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-05 00:16:58.307911 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-05 00:16:58.439837 INFO::Counting total values for each feature
2024-11-05 00:16:58.473792 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-05 00:16:58.563167 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-05 00:16:58.669075 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-05 00:16:58.780444 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-05 00:16:58.823396 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-05 00:16:58.846239 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-05 00:16:58.851598 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-05 00:16:58.857834 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"
2024-11-05 00:16:58.872266 INFO::Writing function arguments to log file
2024-11-05 00:16:58.906792 INFO::Verifying options selected are valid
2024-11-05 00:16:58.907833 INFO::Determining format of input files
2024-11-05 00:16:58.908934 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-05 00:16:58.913356 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-05 00:16:58.914398 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-05 00:16:58.915889 INFO::Filter data based on min abundance and min prevalence
2024-11-05 00:16:58.916788 INFO::Total samples in data: 1595
2024-11-05 00:16:58.917665 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-05 00:16:58.921178 INFO::Total filtered features: 0
2024-11-05 00:16:58.922151 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-05 00:16:58.928512 INFO::Total filtered features with variance filtering: 0
2024-11-05 00:16:58.929486 INFO::Filtered feature names from variance filtering:
2024-11-05 00:16:58.930321 INFO::Running selected normalization method: NONE
2024-11-05 00:16:58.931116 INFO::Bypass z-score application to metadata
2024-11-05 00:16:58.931961 INFO::Running selected transform method: AST
2024-11-05 00:16:58.945299 INFO::Running selected analysis method: LM
2024-11-05 00:16:58.946737 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-05 00:16:59.055727 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-05 00:16:59.156579 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-05 00:16:59.263348 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-05 00:16:59.36467 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-05 00:16:59.462123 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-05 00:16:59.573238 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-05 00:16:59.675555 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-05 00:16:59.781325 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-05 00:16:59.88202 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-05 00:16:59.986119 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-05 00:17:00.102987 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-05 00:17:00.201281 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-05 00:17:00.291865 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-05 00:17:00.403626 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-05 00:17:00.514074 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-05 00:17:00.61426 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-05 00:17:00.713461 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-05 00:17:00.812861 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-05 00:17:00.919996 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-05 00:17:01.014013 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-05 00:17:01.120158 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-05 00:17:01.225155 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-05 00:17:01.320809 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-05 00:17:01.433499 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-05 00:17:01.529737 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-05 00:17:01.633042 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-05 00:17:01.734711 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-05 00:17:01.833728 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-05 00:17:01.922749 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-05 00:17:02.022873 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-05 00:17:02.117264 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-05 00:17:02.216138 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-05 00:17:02.329243 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-05 00:17:02.423755 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-05 00:17:02.531664 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-05 00:17:02.623451 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-05 00:17:02.716815 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-05 00:17:02.815873 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-05 00:17:02.911653 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-05 00:17:03.005014 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-05 00:17:03.114221 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-05 00:17:03.213673 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-05 00:17:03.482161 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-05 00:17:03.576321 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-05 00:17:03.669848 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-05 00:17:03.770484 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-05 00:17:03.880563 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-05 00:17:03.975783 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-05 00:17:04.072112 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-05 00:17:04.185881 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-05 00:17:04.303595 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-05 00:17:04.423783 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-05 00:17:04.521148 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-05 00:17:04.619827 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-05 00:17:04.713139 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-05 00:17:04.804496 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-05 00:17:04.902945 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-05 00:17:05.008579 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-05 00:17:05.111274 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-05 00:17:05.205411 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-05 00:17:05.300953 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-05 00:17:05.3899 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-05 00:17:05.482376 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-05 00:17:05.582397 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-05 00:17:05.686932 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-05 00:17:05.781622 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-05 00:17:05.880265 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-05 00:17:05.96803 WARNING::Fitting problem for feature 67 a warning was issued
2024-11-05 00:17:06.071114 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-05 00:17:06.162115 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-05 00:17:06.267438 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-05 00:17:06.375531 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-05 00:17:06.468822 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-05 00:17:06.503296 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-05 00:17:06.616875 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-05 00:17:06.707492 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-05 00:17:06.796007 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-05 00:17:06.892527 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-05 00:17:06.996909 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-05 00:17:07.088121 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-05 00:17:07.18544 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-05 00:17:07.290398 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-05 00:17:07.387134 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-05 00:17:07.486338 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-05 00:17:07.583623 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-05 00:17:07.674118 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-05 00:17:07.7679 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-05 00:17:07.867069 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-05 00:17:07.966199 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-05 00:17:08.088798 INFO::Counting total values for each feature
2024-11-05 00:17:08.105128 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-05 00:17:08.192857 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-05 00:17:08.281631 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-05 00:17:08.385201 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-05 00:17:08.435209 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-05 00:17:08.482961 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-05 00:17:08.487549 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-05 00:17:08.492003 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
21.301 0.517 21.873
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 62.002 | 1.210 | 63.581 | |