Lauren McIver
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_18 |
| git_last_commit: 0ab531d |
| git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:23 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1124/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.16.0 (landing page) Lauren McIver
| kjohnson1 | macOS 13.6.1 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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2024-03-27 17:38:55 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 17:41:44 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 169.5 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/Maaslin2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* 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 R 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 90.521 1.609 92.532
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-arm64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.6 Current TMB version is 1.9.10 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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"
2024-03-27 17:41:01.92879 INFO::Writing function arguments to log file
2024-03-27 17:41:01.976172 INFO::Verifying options selected are valid
2024-03-27 17:41:02.024521 INFO::Determining format of input files
2024-03-27 17:41:02.026652 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-27 17:41:02.033476 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-27 17:41:02.0351 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-27 17:41:02.039375 INFO::Filter data based on min abundance and min prevalence
2024-03-27 17:41:02.040826 INFO::Total samples in data: 1595
2024-03-27 17:41:02.041747 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-27 17:41:02.047137 INFO::Total filtered features: 0
2024-03-27 17:41:02.048558 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-27 17:41:02.058696 INFO::Total filtered features with variance filtering: 0
2024-03-27 17:41:02.060005 INFO::Filtered feature names from variance filtering:
2024-03-27 17:41:02.060802 INFO::Running selected normalization method: TSS
2024-03-27 17:41:03.5138 INFO::Bypass z-score application to metadata
2024-03-27 17:41:03.515473 INFO::Running selected transform method: AST
2024-03-27 17:41:03.534323 INFO::Running selected analysis method: LM
2024-03-27 17:41:04.25569 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-27 17:41:04.701053 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-27 17:41:04.906544 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-27 17:41:05.08732 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-27 17:41:05.27036 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-27 17:41:05.448735 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-27 17:41:05.636322 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-27 17:41:05.833209 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-27 17:41:05.9733 WARNING::Fitting problem for feature 8 a warning was issued
2024-03-27 17:41:06.166493 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-27 17:41:06.340547 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-27 17:41:06.515801 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-27 17:41:06.689134 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-27 17:41:06.920243 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-27 17:41:07.068376 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-27 17:41:07.266726 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-27 17:41:07.462625 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-27 17:41:07.642083 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-27 17:41:07.818845 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-27 17:41:07.994406 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-27 17:41:08.180014 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-27 17:41:08.33943 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-27 17:41:08.510683 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-27 17:41:08.702379 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-27 17:41:08.870171 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-27 17:41:09.032083 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-27 17:41:09.208067 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-27 17:41:09.374604 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-27 17:41:09.536573 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-27 17:41:09.725671 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-27 17:41:09.905884 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-27 17:41:10.088166 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-27 17:41:10.265399 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-27 17:41:10.440441 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-27 17:41:10.61222 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-27 17:41:10.798629 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-27 17:41:10.960536 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-27 17:41:11.133251 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-27 17:41:11.312492 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-27 17:41:11.485262 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-27 17:41:11.656985 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-27 17:41:11.821211 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-27 17:41:11.995894 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-27 17:41:12.176277 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-27 17:41:12.346057 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-27 17:41:12.529435 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-27 17:41:12.696556 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-27 17:41:12.883047 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-27 17:41:13.057114 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-27 17:41:13.247852 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-27 17:41:13.414002 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-27 17:41:13.5921 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-27 17:41:13.757512 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-27 17:41:13.937044 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-27 17:41:14.110336 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-27 17:41:14.310519 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-27 17:41:14.486325 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-27 17:41:14.661955 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-27 17:41:14.851976 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-27 17:41:15.01923 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-27 17:41:15.194604 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-27 17:41:15.650802 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-27 17:41:15.821138 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-27 17:41:15.987908 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-27 17:41:16.170247 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-27 17:41:16.337199 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-27 17:41:16.504614 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-27 17:41:16.685862 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-27 17:41:16.848528 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-27 17:41:16.976089 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-27 17:41:17.150046 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-27 17:41:17.331599 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-27 17:41:17.522053 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-27 17:41:17.709946 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-27 17:41:17.906232 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-27 17:41:18.071941 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-27 17:41:18.213481 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-27 17:41:18.297346 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-27 17:41:18.382754 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-27 17:41:18.492758 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-27 17:41:18.616318 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-27 17:41:18.699743 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-27 17:41:18.828501 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-27 17:41:18.936926 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-27 17:41:19.07116 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-27 17:41:19.162477 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-27 17:41:19.305179 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-27 17:41:19.473482 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-27 17:41:19.655433 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-27 17:41:19.826002 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-27 17:41:20.053692 INFO::Counting total values for each feature
2024-03-27 17:41:20.091137 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-27 17:41:20.23892 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-27 17:41:20.412191 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-27 17:41:20.58695 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-27 17:41:20.691699 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-27 17:41:20.735914 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-27 17:41:20.74592 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-27 17:41:20.754428 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"
2024-03-27 17:41:20.770184 INFO::Writing function arguments to log file
2024-03-27 17:41:20.777889 INFO::Verifying options selected are valid
2024-03-27 17:41:20.779061 INFO::Determining format of input files
2024-03-27 17:41:20.780292 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-27 17:41:20.786208 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-27 17:41:20.787422 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-03-27 17:41:20.789093 INFO::Filter data based on min abundance and min prevalence
2024-03-27 17:41:20.789946 INFO::Total samples in data: 1595
2024-03-27 17:41:20.790749 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-27 17:41:20.796515 INFO::Total filtered features: 0
2024-03-27 17:41:20.797957 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-27 17:41:20.818851 INFO::Total filtered features with variance filtering: 0
2024-03-27 17:41:20.820373 INFO::Filtered feature names from variance filtering:
2024-03-27 17:41:20.821304 INFO::Running selected normalization method: NONE
2024-03-27 17:41:20.822109 INFO::Bypass z-score application to metadata
2024-03-27 17:41:20.822893 INFO::Running selected transform method: AST
2024-03-27 17:41:20.840057 INFO::Running selected analysis method: LM
2024-03-27 17:41:20.842256 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-27 17:41:21.006237 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-27 17:41:21.466701 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-27 17:41:21.629769 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-27 17:41:21.789772 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-27 17:41:21.951136 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-27 17:41:22.132262 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-27 17:41:22.292603 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-27 17:41:22.451642 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-27 17:41:22.598947 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-27 17:41:22.768215 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-27 17:41:22.937272 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-27 17:41:23.082875 WARNING::Fitting problem for feature 11 a warning was issued
2024-03-27 17:41:23.273225 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-27 17:41:23.430664 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-27 17:41:23.594881 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-27 17:41:23.758903 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-27 17:41:23.938032 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-27 17:41:24.095687 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-27 17:41:24.260502 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-27 17:41:24.437455 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-27 17:41:24.592891 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-27 17:41:24.758118 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-27 17:41:24.921114 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-27 17:41:25.091713 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-27 17:41:25.244474 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-27 17:41:25.416065 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-27 17:41:25.589319 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-27 17:41:25.756887 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-27 17:41:25.918917 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-27 17:41:26.080792 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-27 17:41:26.23085 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-27 17:41:26.387496 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-27 17:41:26.558294 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-27 17:41:26.722264 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-27 17:41:26.883735 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-27 17:41:27.357178 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-27 17:41:27.519643 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-27 17:41:27.687668 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-27 17:41:27.869232 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-27 17:41:28.053906 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-27 17:41:28.212225 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-27 17:41:28.383544 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-27 17:41:28.558761 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-27 17:41:28.715742 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-27 17:41:28.883768 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-27 17:41:29.061863 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-27 17:41:29.236076 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-27 17:41:29.400272 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-27 17:41:29.483694 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-27 17:41:29.561672 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-27 17:41:29.692293 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-27 17:41:29.790718 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-27 17:41:29.91458 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-27 17:41:30.03398 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-27 17:41:30.099837 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-27 17:41:30.171163 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-27 17:41:30.246234 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-27 17:41:30.333104 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-27 17:41:30.489526 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-27 17:41:30.646456 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-27 17:41:30.823596 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-27 17:41:30.978153 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-27 17:41:31.13358 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-27 17:41:31.29316 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-27 17:41:31.469486 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-27 17:41:31.630333 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-27 17:41:31.795113 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-27 17:41:31.967469 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-27 17:41:32.133916 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-27 17:41:32.291842 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-27 17:41:32.473134 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-27 17:41:32.64516 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-27 17:41:32.808142 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-27 17:41:32.875822 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-27 17:41:33.040841 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-27 17:41:33.212314 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-27 17:41:33.39488 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-27 17:41:33.563494 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-27 17:41:33.729476 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-27 17:41:33.90399 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-27 17:41:34.074071 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-27 17:41:34.244367 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-27 17:41:34.420809 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-27 17:41:34.593337 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-27 17:41:34.766001 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-27 17:41:34.921988 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-27 17:41:35.090619 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-27 17:41:35.251445 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-27 17:41:35.430581 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-27 17:41:35.645786 INFO::Counting total values for each feature
2024-03-27 17:41:35.67262 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-27 17:41:35.81961 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-27 17:41:35.96699 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-27 17:41:36.13682 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-27 17:41:36.245992 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-27 17:41:36.349644 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-27 17:41:36.358541 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-27 17:41:36.365058 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 6 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
34.937 0.775 35.930
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 90.521 | 1.609 | 92.532 | |