Lauren McIver
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| 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 2025-02-04 11:41 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 1132/2295 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.21.0 |
| 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: 2025-02-04 02:56:37 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 03:00:07 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 210.0 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) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 114.52 7.25 122.08
* 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' ... ** this is package 'Maaslin2' version '1.21.0' ** 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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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"
2025-02-04 02:59:20.435665 INFO::Writing function arguments to log file
2025-02-04 02:59:20.468904 INFO::Verifying options selected are valid
2025-02-04 02:59:20.518497 INFO::Determining format of input files
2025-02-04 02:59:20.520858 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 02:59:20.542201 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 02:59:20.545925 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-04 02:59:20.551259 INFO::Filter data based on min abundance and min prevalence
2025-02-04 02:59:20.554208 INFO::Total samples in data: 1595
2025-02-04 02:59:20.556987 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 02:59:20.565178 INFO::Total filtered features: 0
2025-02-04 02:59:20.568432 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 02:59:20.582209 INFO::Total filtered features with variance filtering: 0
2025-02-04 02:59:20.585566 INFO::Filtered feature names from variance filtering:
2025-02-04 02:59:20.588436 INFO::Running selected normalization method: TSS
2025-02-04 02:59:22.023351 INFO::Bypass z-score application to metadata
2025-02-04 02:59:22.026203 INFO::Running selected transform method: AST
2025-02-04 02:59:22.052179 INFO::Running selected analysis method: LM
2025-02-04 02:59:22.520104 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 02:59:22.888041 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 02:59:23.028888 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 02:59:23.206597 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 02:59:23.350949 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 02:59:23.562558 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 02:59:23.7819 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 02:59:23.936857 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 02:59:24.099908 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 02:59:24.292871 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 02:59:24.515711 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 02:59:24.718353 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 02:59:24.913416 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 02:59:25.03619 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-04 02:59:25.226043 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 02:59:25.421711 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 02:59:25.576395 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 02:59:25.737685 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 02:59:25.915936 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 02:59:26.083548 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 02:59:26.262548 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 02:59:26.445539 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 02:59:26.660431 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 02:59:26.881018 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 02:59:27.088643 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 02:59:27.30443 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 02:59:27.438176 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 02:59:27.647394 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 02:59:27.861375 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 02:59:28.084891 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 02:59:28.264148 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 02:59:28.462034 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 02:59:28.692442 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 02:59:28.879188 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 02:59:29.07969 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 02:59:29.271826 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 02:59:29.471947 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 02:59:29.878393 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 02:59:30.044454 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 02:59:30.238166 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 02:59:30.463902 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 02:59:30.647932 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 02:59:30.773823 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 02:59:30.916592 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 02:59:31.13337 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 02:59:31.320421 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 02:59:31.528663 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 02:59:31.678953 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 02:59:31.807816 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 02:59:31.932505 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 02:59:32.063091 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 02:59:32.193158 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 02:59:32.395652 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 02:59:32.547487 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 02:59:32.678356 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 02:59:32.802036 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 02:59:33.174114 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 02:59:33.315591 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 02:59:33.44013 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 02:59:33.596244 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 02:59:33.726155 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 02:59:33.851309 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 02:59:33.991551 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 02:59:34.129993 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 02:59:34.294975 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 02:59:34.434739 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 02:59:34.568576 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 02:59:34.740277 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 02:59:34.943627 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 02:59:35.165242 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 02:59:35.377274 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 02:59:35.582576 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 02:59:35.765126 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 02:59:35.98619 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 02:59:36.180047 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 02:59:36.381217 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 02:59:36.556446 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 02:59:36.690228 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 02:59:36.899278 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 02:59:37.072184 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 02:59:37.236084 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 02:59:37.39719 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 02:59:37.612988 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 02:59:37.809814 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 02:59:38.007161 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 02:59:38.2323 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 02:59:38.399008 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 02:59:38.609772 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 02:59:38.858035 INFO::Counting total values for each feature
2025-02-04 02:59:38.899169 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-04 02:59:39.329565 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-04 02:59:39.823988 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-04 02:59:40.268229 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-04 02:59:40.328869 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-04 02:59:40.363609 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-04 02:59:40.372136 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-04 02:59:40.397101 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"
2025-02-04 02:59:40.440378 INFO::Writing function arguments to log file
2025-02-04 02:59:40.457136 INFO::Verifying options selected are valid
2025-02-04 02:59:40.459395 INFO::Determining format of input files
2025-02-04 02:59:40.461457 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 02:59:40.469565 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 02:59:40.471427 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-02-04 02:59:40.473805 INFO::Filter data based on min abundance and min prevalence
2025-02-04 02:59:40.475448 INFO::Total samples in data: 1595
2025-02-04 02:59:40.477031 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 02:59:40.491096 INFO::Total filtered features: 0
2025-02-04 02:59:40.493605 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 02:59:40.506218 INFO::Total filtered features with variance filtering: 0
2025-02-04 02:59:40.509371 INFO::Filtered feature names from variance filtering:
2025-02-04 02:59:40.512127 INFO::Running selected normalization method: NONE
2025-02-04 02:59:40.514732 INFO::Bypass z-score application to metadata
2025-02-04 02:59:40.517318 INFO::Running selected transform method: AST
2025-02-04 02:59:40.541575 INFO::Running selected analysis method: LM
2025-02-04 02:59:40.545458 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 02:59:40.71606 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 02:59:40.941413 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 02:59:41.128998 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 02:59:41.307029 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 02:59:41.516395 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 02:59:41.645224 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 02:59:41.814672 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 02:59:41.964389 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 02:59:42.073468 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-04 02:59:42.257051 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 02:59:42.41038 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 02:59:42.573229 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-04 02:59:42.784742 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 02:59:42.973831 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 02:59:43.185123 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 02:59:43.316713 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 02:59:43.439865 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 02:59:43.568686 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-04 02:59:43.732691 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 02:59:43.931964 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 02:59:44.101176 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 02:59:44.276841 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 02:59:44.39726 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 02:59:44.56906 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 02:59:44.721205 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 02:59:44.918598 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 02:59:45.137627 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 02:59:45.283809 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 02:59:45.411884 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 02:59:45.544751 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 02:59:45.663761 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 02:59:45.779736 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 02:59:45.906129 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 02:59:46.023169 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 02:59:46.170223 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 02:59:46.317536 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 02:59:46.486411 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 02:59:46.633694 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 02:59:46.802137 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 02:59:46.94048 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 02:59:47.056679 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 02:59:47.184957 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 02:59:47.314913 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 02:59:47.439552 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 02:59:47.601371 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 02:59:47.783782 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 02:59:47.970992 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 02:59:48.090346 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 02:59:48.272413 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 02:59:48.45826 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 02:59:48.669977 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 02:59:48.860409 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 02:59:48.995249 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 02:59:49.1784 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 02:59:49.357003 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 02:59:49.520135 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 02:59:49.691908 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 02:59:49.882594 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 02:59:50.083467 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 02:59:50.245651 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 02:59:50.377535 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 02:59:50.549644 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 02:59:50.744574 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 02:59:50.936885 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 02:59:51.14519 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 02:59:51.329565 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 02:59:51.45107 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 02:59:51.628274 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 02:59:51.757446 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 02:59:51.875536 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 02:59:52.005883 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 02:59:52.138676 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 02:59:52.285335 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 02:59:52.477704 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 02:59:52.548844 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-04 02:59:52.780066 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 02:59:52.98273 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 02:59:53.188796 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 02:59:53.400056 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 02:59:53.599963 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 02:59:53.813843 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 02:59:54.006791 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 02:59:54.147244 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 02:59:54.319249 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 02:59:54.448304 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 02:59:54.623921 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 02:59:54.784094 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 02:59:54.929051 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 02:59:55.062767 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 02:59:55.19979 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 02:59:55.409412 INFO::Counting total values for each feature
2025-02-04 02:59:55.447743 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-04 02:59:55.867073 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-04 02:59:56.308618 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-04 02:59:56.674652 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-04 02:59:56.746792 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-04 02:59:56.81835 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-04 02:59:56.82681 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-04 02:59:56.845614 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
36.90 0.92 37.96
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 114.52 | 7.25 | 122.08 | |