Lauren McIver
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_19 |
| git_last_commit: 35350f9 |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:37 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1138/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.18.0 (landing page) Lauren McIver
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the Maaslin2 package: - 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: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2024-05-06 22:38:11 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 22:39:08 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 56.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* 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 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 27.952 0.512 28.488
* 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-3.19-bioc-mac-arm64/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-05-06 22:38:54.5756 INFO::Writing function arguments to log file
2024-05-06 22:38:54.589382 INFO::Verifying options selected are valid
2024-05-06 22:38:54.602799 INFO::Determining format of input files
2024-05-06 22:38:54.603288 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-06 22:38:54.605063 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-06 22:38:54.605455 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-06 22:38:54.606176 INFO::Filter data based on min abundance and min prevalence
2024-05-06 22:38:54.606438 INFO::Total samples in data: 1595
2024-05-06 22:38:54.60668 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-06 22:38:54.610491 INFO::Total filtered features: 0
2024-05-06 22:38:54.610876 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-06 22:38:54.613997 INFO::Total filtered features with variance filtering: 0
2024-05-06 22:38:54.614311 INFO::Filtered feature names from variance filtering:
2024-05-06 22:38:54.614569 INFO::Running selected normalization method: TSS
2024-05-06 22:38:55.112661 INFO::Bypass z-score application to metadata
2024-05-06 22:38:55.113184 INFO::Running selected transform method: AST
2024-05-06 22:38:55.124965 INFO::Running selected analysis method: LM
2024-05-06 22:38:55.236573 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-06 22:38:55.361883 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-06 22:38:55.415375 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-06 22:38:55.471479 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-06 22:38:55.525992 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-06 22:38:55.58037 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-06 22:38:55.635162 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-06 22:38:55.710617 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-06 22:38:55.762882 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-06 22:38:55.90891 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-06 22:38:55.962611 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-06 22:38:56.01233 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-06 22:38:56.066616 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-06 22:38:56.115305 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-06 22:38:56.165947 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-06 22:38:56.218156 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-06 22:38:56.270364 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-06 22:38:56.323283 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-06 22:38:56.377914 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-06 22:38:56.433288 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-06 22:38:56.487381 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-06 22:38:56.539926 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-06 22:38:56.596154 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-06 22:38:56.646692 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-06 22:38:56.69777 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-06 22:38:56.753952 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-06 22:38:56.805596 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-06 22:38:56.855062 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-06 22:38:56.9144 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-06 22:38:56.965636 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-06 22:38:57.022598 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-06 22:38:57.071359 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-06 22:38:57.125607 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-06 22:38:57.18181 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-06 22:38:57.236451 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-06 22:38:57.291559 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-06 22:38:57.344651 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-06 22:38:57.397577 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-06 22:38:57.455912 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-06 22:38:57.504284 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-06 22:38:57.555325 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-06 22:38:57.612123 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-06 22:38:57.662557 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-06 22:38:57.719751 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-06 22:38:57.768783 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-06 22:38:57.816951 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-06 22:38:57.871266 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-06 22:38:57.924639 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-06 22:38:57.985843 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-06 22:38:58.037974 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-06 22:38:58.092277 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-06 22:38:58.147274 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-06 22:38:58.198969 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-06 22:38:58.254921 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-06 22:38:58.314176 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-06 22:38:58.366553 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-06 22:38:58.424315 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-06 22:38:58.479301 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-06 22:38:58.528163 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-06 22:38:58.586048 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-06 22:38:58.636582 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-06 22:38:58.687372 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-06 22:38:58.842618 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-06 22:38:58.895949 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-06 22:38:58.955533 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-06 22:38:59.005838 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-06 22:38:59.055408 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-06 22:38:59.109802 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-06 22:38:59.156951 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-06 22:38:59.213062 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-06 22:38:59.268658 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-06 22:38:59.321981 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-06 22:38:59.379611 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-06 22:38:59.430257 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-06 22:38:59.48129 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-06 22:38:59.540197 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-06 22:38:59.591841 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-06 22:38:59.648646 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-06 22:38:59.698687 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-06 22:38:59.753901 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-06 22:38:59.811767 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-06 22:38:59.863282 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-06 22:38:59.919682 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-06 22:38:59.975146 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-06 22:39:00.023535 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-06 22:39:00.078725 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-06 22:39:00.128837 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-06 22:39:00.180042 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-06 22:39:00.251768 INFO::Counting total values for each feature
2024-05-06 22:39:00.265189 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-06 22:39:00.31367 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-06 22:39:00.369816 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-06 22:39:00.426558 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-06 22:39:00.453682 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-06 22:39:00.468388 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-06 22:39:00.471506 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-06 22:39:00.47431 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"
2024-05-06 22:39:00.479536 INFO::Writing function arguments to log file
2024-05-06 22:39:00.481605 INFO::Verifying options selected are valid
2024-05-06 22:39:00.481935 INFO::Determining format of input files
2024-05-06 22:39:00.482307 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-06 22:39:00.488436 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-06 22:39:00.4889 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-05-06 22:39:00.489491 INFO::Filter data based on min abundance and min prevalence
2024-05-06 22:39:00.489783 INFO::Total samples in data: 1595
2024-05-06 22:39:00.490058 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-06 22:39:00.491516 INFO::Total filtered features: 0
2024-05-06 22:39:00.49182 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-06 22:39:00.494564 INFO::Total filtered features with variance filtering: 0
2024-05-06 22:39:00.494892 INFO::Filtered feature names from variance filtering:
2024-05-06 22:39:00.495156 INFO::Running selected normalization method: NONE
2024-05-06 22:39:00.495416 INFO::Bypass z-score application to metadata
2024-05-06 22:39:00.495675 INFO::Running selected transform method: AST
2024-05-06 22:39:00.50147 INFO::Running selected analysis method: LM
2024-05-06 22:39:00.502 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-06 22:39:00.555399 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-06 22:39:00.605752 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-06 22:39:00.654201 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-06 22:39:00.708702 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-06 22:39:00.759253 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-06 22:39:00.8192 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-06 22:39:00.87092 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-06 22:39:00.925131 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-06 22:39:00.97504 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-06 22:39:01.031273 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-06 22:39:01.073826 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-06 22:39:01.137755 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-06 22:39:01.187387 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-06 22:39:01.228943 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-06 22:39:01.277043 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-06 22:39:01.324562 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-06 22:39:01.381384 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-06 22:39:01.425654 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-06 22:39:01.473792 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-06 22:39:01.525425 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-06 22:39:01.570023 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-06 22:39:01.615376 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-06 22:39:01.665935 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-06 22:39:01.712359 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-06 22:39:01.760858 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-06 22:39:01.807453 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-06 22:39:01.854154 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-06 22:39:01.905565 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-06 22:39:01.954221 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-06 22:39:01.999354 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-06 22:39:02.048573 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-06 22:39:02.093017 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-06 22:39:02.143292 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-06 22:39:02.189158 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-06 22:39:02.236245 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-06 22:39:02.28736 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-06 22:39:02.333971 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-06 22:39:02.381232 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-06 22:39:02.431599 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-06 22:39:02.477239 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-06 22:39:02.524458 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-06 22:39:02.567106 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-06 22:39:02.612147 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-06 22:39:02.66028 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-06 22:39:02.706232 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-06 22:39:02.753253 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-06 22:39:02.80325 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-06 22:39:02.853418 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-06 22:39:02.906979 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-06 22:39:02.957584 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-06 22:39:03.010185 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-06 22:39:03.051771 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-06 22:39:03.109757 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-06 22:39:03.153844 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-06 22:39:03.198938 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-06 22:39:03.252062 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-06 22:39:03.298891 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-06 22:39:03.347222 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-06 22:39:03.399534 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-06 22:39:03.447708 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-06 22:39:03.5013 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-06 22:39:03.544805 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-06 22:39:03.591094 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-06 22:39:03.644851 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-06 22:39:03.694113 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-06 22:39:03.748432 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-06 22:39:03.798548 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-06 22:39:03.848167 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-06 22:39:03.904453 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-06 22:39:03.951677 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-06 22:39:04.007383 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-06 22:39:04.059056 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-06 22:39:04.111105 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-06 22:39:04.128168 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-06 22:39:04.179649 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-06 22:39:04.22525 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-06 22:39:04.27937 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-06 22:39:04.326903 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-06 22:39:04.37798 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-06 22:39:04.422192 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-06 22:39:04.474205 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-06 22:39:04.529732 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-06 22:39:04.574796 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-06 22:39:04.625913 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-06 22:39:04.779667 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-06 22:39:04.8269 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-06 22:39:04.877277 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-06 22:39:04.929938 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-06 22:39:04.981938 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-06 22:39:05.043495 INFO::Counting total values for each feature
2024-05-06 22:39:05.051886 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-06 22:39:05.096182 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-06 22:39:05.14076 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-06 22:39:05.193476 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-06 22:39:05.227243 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-06 22:39:05.26061 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-06 22:39:05.263614 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-06 22:39:05.265774 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
10.853 0.257 11.121
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 27.952 | 0.512 | 28.488 | |