Lauren McIver
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: a8d86b0 |
| git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:57 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1123/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.17.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.17.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.17.0.tar.gz |
| StartedAt: 2024-03-28 03:32:51 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:36:09 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 198.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.17.0'
* 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 104.61 6.78 112.91
* 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
'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.
Maaslin2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion(getOption("TMB.check.Matrix", TRUE)) :
Package version inconsistency detected.
TMB was built with Matrix version 1.6.5
Current Matrix version is 1.7.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** 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) (2024-03-16 r86144 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"
2024-03-28 03:35:24.14906 INFO::Writing function arguments to log file
2024-03-28 03:35:24.217119 INFO::Verifying options selected are valid
2024-03-28 03:35:24.260177 INFO::Determining format of input files
2024-03-28 03:35:24.26349 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-28 03:35:24.283729 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-28 03:35:24.287093 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-28 03:35:24.291832 INFO::Filter data based on min abundance and min prevalence
2024-03-28 03:35:24.294501 INFO::Total samples in data: 1595
2024-03-28 03:35:24.297099 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-28 03:35:24.304833 INFO::Total filtered features: 0
2024-03-28 03:35:24.307758 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-28 03:35:24.320773 INFO::Total filtered features with variance filtering: 0
2024-03-28 03:35:24.323753 INFO::Filtered feature names from variance filtering:
2024-03-28 03:35:24.326397 INFO::Running selected normalization method: TSS
2024-03-28 03:35:25.923364 INFO::Bypass z-score application to metadata
2024-03-28 03:35:25.926758 INFO::Running selected transform method: AST
2024-03-28 03:35:25.954723 INFO::Running selected analysis method: LM
2024-03-28 03:35:26.321775 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-28 03:35:26.730234 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-28 03:35:26.872813 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-28 03:35:27.030977 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-28 03:35:27.170885 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-28 03:35:27.319967 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-28 03:35:27.463504 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-28 03:35:27.643726 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-28 03:35:27.854167 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-28 03:35:28.083839 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-28 03:35:28.245198 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-28 03:35:28.381336 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-28 03:35:28.575179 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-28 03:35:28.750859 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-28 03:35:28.930502 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-28 03:35:29.101479 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-28 03:35:29.303996 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-28 03:35:29.487823 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-28 03:35:29.688575 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-28 03:35:29.871175 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-28 03:35:30.052307 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-28 03:35:30.213216 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-28 03:35:30.371803 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-28 03:35:30.548365 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-28 03:35:30.770556 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-28 03:35:30.967908 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-28 03:35:31.151532 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-28 03:35:31.299096 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-28 03:35:31.466161 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-28 03:35:31.648618 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-28 03:35:31.844722 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-28 03:35:31.985879 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-28 03:35:32.138641 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-28 03:35:32.336896 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-28 03:35:32.558696 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-28 03:35:32.773698 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-28 03:35:32.985011 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-28 03:35:33.125869 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-28 03:35:33.299468 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-28 03:35:33.448681 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-28 03:35:33.648293 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-28 03:35:33.825177 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-28 03:35:33.963227 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-28 03:35:34.121171 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-28 03:35:34.30995 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-28 03:35:34.539832 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-28 03:35:35.045353 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-28 03:35:35.227116 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-28 03:35:35.373242 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-28 03:35:35.58893 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-28 03:35:35.781973 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-28 03:35:35.946632 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-28 03:35:36.151129 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-28 03:35:36.3145 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-28 03:35:36.544116 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-28 03:35:36.747215 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-28 03:35:36.975796 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-28 03:35:37.19107 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-28 03:35:37.399948 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-28 03:35:37.635818 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-28 03:35:37.773366 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-28 03:35:37.928154 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-28 03:35:38.107327 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-28 03:35:38.242441 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-28 03:35:38.37824 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-28 03:35:38.552681 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-28 03:35:38.685541 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-28 03:35:38.82861 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-28 03:35:38.969679 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-28 03:35:39.115453 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-28 03:35:39.262327 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-28 03:35:39.401335 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-28 03:35:39.580127 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-28 03:35:39.796535 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-28 03:35:39.990948 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-28 03:35:40.133657 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-28 03:35:40.26842 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-28 03:35:40.41054 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-28 03:35:40.616693 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-28 03:35:40.844976 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-28 03:35:41.084232 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-28 03:35:41.290024 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-28 03:35:41.488213 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-28 03:35:41.634646 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-28 03:35:41.76033 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-28 03:35:41.889508 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-28 03:35:42.030118 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-28 03:35:42.157449 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-28 03:35:42.347532 INFO::Counting total values for each feature
2024-03-28 03:35:42.388023 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-28 03:35:42.792236 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-28 03:35:43.316546 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-28 03:35:43.696482 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-28 03:35:43.751329 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-28 03:35:43.779725 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-28 03:35:43.786724 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-28 03:35:43.806982 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"
2024-03-28 03:35:43.849874 INFO::Writing function arguments to log file
2024-03-28 03:35:43.866775 INFO::Verifying options selected are valid
2024-03-28 03:35:43.868696 INFO::Determining format of input files
2024-03-28 03:35:43.870721 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-28 03:35:43.877538 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-28 03:35:43.879657 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-03-28 03:35:43.882643 INFO::Filter data based on min abundance and min prevalence
2024-03-28 03:35:43.884438 INFO::Total samples in data: 1595
2024-03-28 03:35:43.88631 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-28 03:35:43.891201 INFO::Total filtered features: 0
2024-03-28 03:35:43.893082 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-28 03:35:43.90158 INFO::Total filtered features with variance filtering: 0
2024-03-28 03:35:43.90419 INFO::Filtered feature names from variance filtering:
2024-03-28 03:35:43.906554 INFO::Running selected normalization method: NONE
2024-03-28 03:35:43.908749 INFO::Bypass z-score application to metadata
2024-03-28 03:35:43.910717 INFO::Running selected transform method: AST
2024-03-28 03:35:43.927633 INFO::Running selected analysis method: LM
2024-03-28 03:35:43.931318 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-28 03:35:44.106755 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-28 03:35:44.248563 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-28 03:35:44.408484 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-28 03:35:44.565631 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-28 03:35:44.797542 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-28 03:35:45.008513 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-28 03:35:45.226261 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-28 03:35:45.427228 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-28 03:35:45.584748 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-28 03:35:45.816263 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-28 03:35:46.005906 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-28 03:35:46.208786 WARNING::Fitting problem for feature 11 a warning was issued
2024-03-28 03:35:46.430377 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-28 03:35:46.626111 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-28 03:35:46.780076 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-28 03:35:46.907376 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-28 03:35:47.063236 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-28 03:35:47.259519 WARNING::Fitting problem for feature 16 a warning was issued
2024-03-28 03:35:47.469512 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-28 03:35:47.623321 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-28 03:35:47.784572 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-28 03:35:47.980208 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-28 03:35:48.174763 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-28 03:35:48.325747 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-28 03:35:48.519917 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-28 03:35:48.726133 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-28 03:35:48.891975 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-28 03:35:49.03057 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-28 03:35:49.171075 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-28 03:35:49.308752 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-28 03:35:49.438172 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-28 03:35:49.570082 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-28 03:35:49.693231 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-28 03:35:49.830104 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-28 03:35:49.962014 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-28 03:35:50.142241 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-28 03:35:50.288347 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-28 03:35:50.429206 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-28 03:35:50.627959 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-28 03:35:50.834256 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-28 03:35:51.023788 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-28 03:35:51.210501 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-28 03:35:51.3792 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-28 03:35:51.552986 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-28 03:35:51.731202 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-28 03:35:51.905035 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-28 03:35:52.038746 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-28 03:35:52.176152 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-28 03:35:52.301324 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-28 03:35:52.434979 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-28 03:35:52.57002 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-28 03:35:52.702554 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-28 03:35:52.834042 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-28 03:35:52.958089 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-28 03:35:53.325829 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-28 03:35:53.454388 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-28 03:35:53.582574 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-28 03:35:53.710998 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-28 03:35:53.864351 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-28 03:35:53.991169 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-28 03:35:54.126233 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-28 03:35:54.25826 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-28 03:35:54.393347 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-28 03:35:54.530929 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-28 03:35:54.653078 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-28 03:35:54.777164 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-28 03:35:54.915516 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-28 03:35:55.042429 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-28 03:35:55.166128 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-28 03:35:55.292999 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-28 03:35:55.443978 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-28 03:35:55.660956 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-28 03:35:55.874135 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-28 03:35:56.07535 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-28 03:35:56.154126 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-28 03:35:56.410499 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-28 03:35:56.606425 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-28 03:35:56.732374 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-28 03:35:56.879757 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-28 03:35:57.02674 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-28 03:35:57.149938 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-28 03:35:57.280889 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-28 03:35:57.472846 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-28 03:35:57.639304 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-28 03:35:57.764189 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-28 03:35:57.883582 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-28 03:35:58.015863 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-28 03:35:58.157612 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-28 03:35:58.282948 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-28 03:35:58.413127 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-28 03:35:58.588092 INFO::Counting total values for each feature
2024-03-28 03:35:58.636327 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-28 03:35:58.93019 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-28 03:35:59.26341 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-28 03:35:59.621352 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-28 03:35:59.682915 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-28 03:35:59.758764 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-28 03:35:59.768181 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-28 03:35:59.787763 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
35.75 1.28 37.03
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 104.61 | 6.78 | 112.91 | |