Lauren McIver
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 3dacd30 |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 1122/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.21.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.21.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz |
| StartedAt: 2024-11-25 02:04:18 -0500 (Mon, 25 Nov 2024) |
| EndedAt: 2024-11-25 02:07:45 -0500 (Mon, 25 Nov 2024) |
| EllapsedTime: 206.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.21.0'
* 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 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 111.62 6.85 118.72
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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"
2024-11-25 02:06:58.49695 INFO::Writing function arguments to log file
2024-11-25 02:06:58.550116 INFO::Verifying options selected are valid
2024-11-25 02:06:58.601774 INFO::Determining format of input files
2024-11-25 02:06:58.605218 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-25 02:06:58.615924 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-25 02:06:58.629765 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-25 02:06:58.634609 INFO::Filter data based on min abundance and min prevalence
2024-11-25 02:06:58.637218 INFO::Total samples in data: 1595
2024-11-25 02:06:58.639685 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-25 02:06:58.647057 INFO::Total filtered features: 0
2024-11-25 02:06:58.650063 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-25 02:06:58.662754 INFO::Total filtered features with variance filtering: 0
2024-11-25 02:06:58.665768 INFO::Filtered feature names from variance filtering:
2024-11-25 02:06:58.668439 INFO::Running selected normalization method: TSS
2024-11-25 02:06:59.967318 INFO::Bypass z-score application to metadata
2024-11-25 02:06:59.9703 INFO::Running selected transform method: AST
2024-11-25 02:07:00.218026 INFO::Running selected analysis method: LM
2024-11-25 02:07:00.678303 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-25 02:07:01.189653 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-25 02:07:01.433897 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-25 02:07:01.635446 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-25 02:07:01.859837 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-25 02:07:02.089629 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-25 02:07:02.319978 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-25 02:07:02.586855 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-25 02:07:02.795846 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-25 02:07:03.003423 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-25 02:07:03.153205 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-25 02:07:03.336179 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-25 02:07:03.549731 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-25 02:07:03.677863 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-25 02:07:03.855161 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-25 02:07:04.033121 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-25 02:07:04.257891 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-25 02:07:04.389757 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-25 02:07:04.557854 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-25 02:07:04.73293 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-25 02:07:04.932865 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-25 02:07:05.144481 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-25 02:07:05.368029 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-25 02:07:05.596382 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-25 02:07:05.761821 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-25 02:07:05.935287 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-25 02:07:06.115128 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-25 02:07:06.273504 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-25 02:07:06.450424 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-25 02:07:06.657503 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-25 02:07:06.858451 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-25 02:07:06.996162 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-25 02:07:07.168353 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-25 02:07:07.352891 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-25 02:07:07.575415 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-25 02:07:07.711495 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-25 02:07:07.846062 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-25 02:07:07.978149 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-25 02:07:08.131669 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-25 02:07:08.273012 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-25 02:07:08.405612 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-25 02:07:08.896305 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-25 02:07:09.097335 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-25 02:07:09.301062 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-25 02:07:09.503213 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-25 02:07:09.679351 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-25 02:07:09.869114 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-25 02:07:10.060068 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-25 02:07:10.28232 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-25 02:07:10.483521 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-25 02:07:10.690068 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-25 02:07:10.906258 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-25 02:07:11.047496 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-25 02:07:11.175003 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-25 02:07:11.313054 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-25 02:07:11.433552 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-25 02:07:11.636537 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-25 02:07:11.870281 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-25 02:07:12.050688 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-25 02:07:12.199279 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-25 02:07:12.617946 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-25 02:07:12.789483 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-25 02:07:12.92893 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-25 02:07:13.077725 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-25 02:07:13.242627 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-25 02:07:13.433283 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-25 02:07:13.650718 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-25 02:07:13.857373 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-25 02:07:14.005286 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-25 02:07:14.135252 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-25 02:07:14.275137 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-25 02:07:14.402868 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-25 02:07:14.584691 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-25 02:07:14.719833 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-25 02:07:14.876187 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-25 02:07:15.071839 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-25 02:07:15.270916 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-25 02:07:15.474243 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-25 02:07:15.704575 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-25 02:07:15.851901 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-25 02:07:15.987992 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-25 02:07:16.124785 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-25 02:07:16.269101 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-25 02:07:16.444306 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-25 02:07:16.645228 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-25 02:07:16.844618 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-25 02:07:16.997892 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-25 02:07:17.118677 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-25 02:07:17.286572 INFO::Counting total values for each feature
2024-11-25 02:07:17.319826 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-25 02:07:17.618294 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-25 02:07:18.088992 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-25 02:07:18.549107 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-25 02:07:18.591863 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-25 02:07:18.615586 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-25 02:07:18.622388 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-25 02:07:18.638014 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"
2024-11-25 02:07:18.681011 INFO::Writing function arguments to log file
2024-11-25 02:07:18.700464 INFO::Verifying options selected are valid
2024-11-25 02:07:18.70302 INFO::Determining format of input files
2024-11-25 02:07:18.705878 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-25 02:07:18.716148 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-25 02:07:18.719053 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-25 02:07:18.722746 INFO::Filter data based on min abundance and min prevalence
2024-11-25 02:07:18.725218 INFO::Total samples in data: 1595
2024-11-25 02:07:18.727628 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-25 02:07:18.746679 INFO::Total filtered features: 0
2024-11-25 02:07:18.749633 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-25 02:07:18.760294 INFO::Total filtered features with variance filtering: 0
2024-11-25 02:07:18.763264 INFO::Filtered feature names from variance filtering:
2024-11-25 02:07:18.765754 INFO::Running selected normalization method: NONE
2024-11-25 02:07:18.768165 INFO::Bypass z-score application to metadata
2024-11-25 02:07:18.770554 INFO::Running selected transform method: AST
2024-11-25 02:07:18.79258 INFO::Running selected analysis method: LM
2024-11-25 02:07:18.796287 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-25 02:07:18.978671 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-25 02:07:19.164721 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-25 02:07:19.358592 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-25 02:07:19.547957 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-25 02:07:19.73278 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-25 02:07:19.931383 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-25 02:07:20.135983 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-25 02:07:20.340386 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-25 02:07:20.459569 WARNING::Fitting problem for feature 9 a warning was issued
2024-11-25 02:07:20.669415 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-25 02:07:20.84221 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-25 02:07:20.990601 WARNING::Fitting problem for feature 11 a warning was issued
2024-11-25 02:07:21.155272 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-25 02:07:21.280656 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-25 02:07:21.437519 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-25 02:07:21.620449 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-25 02:07:21.801097 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-25 02:07:21.902421 WARNING::Fitting problem for feature 16 a warning was issued
2024-11-25 02:07:22.106834 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-25 02:07:22.231329 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-25 02:07:22.406682 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-25 02:07:22.608855 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-25 02:07:22.796676 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-25 02:07:23.014299 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-25 02:07:23.210124 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-25 02:07:23.392963 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-25 02:07:23.607541 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-25 02:07:23.794349 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-25 02:07:23.983127 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-25 02:07:24.197646 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-25 02:07:24.349307 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-25 02:07:24.488911 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-25 02:07:24.637477 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-25 02:07:24.777645 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-25 02:07:24.969282 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-25 02:07:25.139962 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-25 02:07:25.300756 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-25 02:07:25.436872 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-25 02:07:25.568574 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-25 02:07:25.695055 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-25 02:07:25.831434 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-25 02:07:26.010409 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-25 02:07:26.205978 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-25 02:07:26.400465 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-25 02:07:26.609781 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-25 02:07:26.794866 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-25 02:07:26.975797 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-25 02:07:27.148778 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-25 02:07:27.338812 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-25 02:07:27.473362 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-25 02:07:27.647625 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-25 02:07:27.823622 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-25 02:07:28.011738 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-25 02:07:28.217367 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-25 02:07:28.378712 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-25 02:07:28.579657 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-25 02:07:28.764552 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-25 02:07:28.955547 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-25 02:07:29.157332 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-25 02:07:29.328106 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-25 02:07:29.452949 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-25 02:07:29.623724 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-25 02:07:29.811513 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-25 02:07:30.019052 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-25 02:07:30.198273 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-25 02:07:30.347101 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-25 02:07:30.49814 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-25 02:07:30.647974 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-25 02:07:30.848366 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-25 02:07:31.043784 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-25 02:07:31.231759 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-25 02:07:31.439123 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-25 02:07:31.592596 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-25 02:07:31.731087 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-25 02:07:31.776743 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-25 02:07:31.900797 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-25 02:07:32.058052 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-25 02:07:32.185445 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-25 02:07:32.608079 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-25 02:07:32.784668 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-25 02:07:32.942571 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-25 02:07:33.126793 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-25 02:07:33.345985 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-25 02:07:33.538172 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-25 02:07:33.75153 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-25 02:07:33.90861 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-25 02:07:34.043146 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-25 02:07:34.228204 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-25 02:07:34.356845 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-25 02:07:34.492753 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-25 02:07:34.732142 INFO::Counting total values for each feature
2024-11-25 02:07:34.768811 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-25 02:07:35.144015 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-25 02:07:35.524323 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-25 02:07:35.920325 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-25 02:07:35.992664 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-25 02:07:36.046657 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-25 02:07:36.05278 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-25 02:07:36.072027 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 5 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
38.12 0.90 39.07
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 111.62 | 6.85 | 118.72 | |