Lauren McIver
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.18.0 |
| 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: 2024-06-10 20:19:58 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 20:24:21 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 262.4 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/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 99.004 2.248 140.07
* 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/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"
2024-06-10 20:23:17.378537 INFO::Writing function arguments to log file
2024-06-10 20:23:17.461704 INFO::Verifying options selected are valid
2024-06-10 20:23:17.519062 INFO::Determining format of input files
2024-06-10 20:23:17.52164 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 20:23:17.52843 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 20:23:17.530548 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-10 20:23:17.533594 INFO::Filter data based on min abundance and min prevalence
2024-06-10 20:23:17.535117 INFO::Total samples in data: 1595
2024-06-10 20:23:17.536843 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 20:23:17.56635 INFO::Total filtered features: 0
2024-06-10 20:23:17.570145 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 20:23:17.586785 INFO::Total filtered features with variance filtering: 0
2024-06-10 20:23:17.592075 INFO::Filtered feature names from variance filtering:
2024-06-10 20:23:17.59366 INFO::Running selected normalization method: TSS
2024-06-10 20:23:19.665245 INFO::Bypass z-score application to metadata
2024-06-10 20:23:19.667485 INFO::Running selected transform method: AST
2024-06-10 20:23:19.690284 INFO::Running selected analysis method: LM
2024-06-10 20:23:20.692004 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 20:23:21.264083 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 20:23:21.535932 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 20:23:21.761563 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 20:23:22.014504 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 20:23:22.262606 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 20:23:22.50101 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 20:23:22.76207 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 20:23:23.002931 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 20:23:23.266007 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-10 20:23:23.5174 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 20:23:23.773439 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 20:23:23.994857 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 20:23:24.263212 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 20:23:24.510027 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 20:23:24.769898 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 20:23:25.027165 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 20:23:25.284629 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 20:23:25.529797 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 20:23:25.79853 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 20:23:26.021021 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 20:23:26.292784 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 20:23:26.531421 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 20:23:26.760896 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 20:23:27.027417 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 20:23:27.301924 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 20:23:27.542634 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 20:23:27.779411 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 20:23:28.016789 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 20:23:28.246576 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 20:23:28.535137 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 20:23:28.764493 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 20:23:29.020683 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 20:23:29.257943 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 20:23:29.543854 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 20:23:29.764697 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 20:23:30.002276 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 20:23:30.24617 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 20:23:30.514369 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 20:23:30.738552 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 20:23:31.016696 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 20:23:31.24654 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 20:23:31.495041 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 20:23:31.759557 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 20:23:31.981999 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 20:23:32.215253 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 20:23:32.466469 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 20:23:32.685897 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 20:23:33.530184 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 20:23:33.770004 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 20:23:34.00379 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 20:23:34.234743 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 20:23:34.462066 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 20:23:34.697924 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 20:23:35.519929 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 20:23:35.736824 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 20:23:35.991988 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 20:23:36.279283 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 20:23:36.524382 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 20:23:36.761829 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 20:23:36.996316 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 20:23:37.246653 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 20:23:37.476214 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 20:23:37.730994 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 20:23:37.996129 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 20:23:38.209974 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 20:23:38.435401 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 20:23:38.690561 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 20:23:38.921591 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 20:23:39.148682 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 20:23:39.416042 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 20:23:39.651258 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 20:23:39.891262 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 20:23:40.151772 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 20:23:40.368708 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 20:23:40.62441 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 20:23:40.894507 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 20:23:41.138005 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 20:23:41.400457 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 20:23:41.634891 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 20:23:42.440944 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 20:23:42.641634 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 20:23:42.870307 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 20:23:43.089161 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 20:23:43.341348 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 20:23:43.59532 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 20:23:43.787047 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 20:23:44.007941 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 20:23:44.32131 INFO::Counting total values for each feature
2024-06-10 20:23:44.364305 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-10 20:23:44.522534 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-10 20:23:44.696282 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-10 20:23:44.885876 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-10 20:23:44.954737 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-10 20:23:44.998875 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-10 20:23:45.01176 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-10 20:23:45.02085 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"
2024-06-10 20:23:45.055313 INFO::Writing function arguments to log file
2024-06-10 20:23:45.071843 INFO::Verifying options selected are valid
2024-06-10 20:23:45.07744 INFO::Determining format of input files
2024-06-10 20:23:45.079324 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 20:23:45.090715 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 20:23:45.092735 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-06-10 20:23:45.09965 INFO::Filter data based on min abundance and min prevalence
2024-06-10 20:23:45.102339 INFO::Total samples in data: 1595
2024-06-10 20:23:45.103759 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 20:23:45.113344 INFO::Total filtered features: 0
2024-06-10 20:23:45.118225 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 20:23:45.135089 INFO::Total filtered features with variance filtering: 0
2024-06-10 20:23:45.136966 INFO::Filtered feature names from variance filtering:
2024-06-10 20:23:45.142685 INFO::Running selected normalization method: NONE
2024-06-10 20:23:45.144253 INFO::Bypass z-score application to metadata
2024-06-10 20:23:45.145341 INFO::Running selected transform method: AST
2024-06-10 20:23:45.16413 INFO::Running selected analysis method: LM
2024-06-10 20:23:45.167822 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 20:23:45.420604 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 20:23:45.628674 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 20:23:45.830473 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 20:23:46.05212 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 20:23:46.30045 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 20:23:46.529188 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 20:23:46.773356 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 20:23:46.986521 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 20:23:47.237318 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 20:23:47.4628 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 20:23:47.66467 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-10 20:23:47.918397 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 20:23:48.166305 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 20:23:48.375866 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-10 20:23:48.621029 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 20:23:48.864285 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 20:23:49.08722 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 20:23:49.326298 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 20:23:49.577801 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 20:23:49.779982 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 20:23:49.985299 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 20:23:50.21592 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 20:23:50.448471 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 20:23:50.685318 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 20:23:50.859739 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 20:23:51.099464 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 20:23:51.278388 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 20:23:51.518896 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 20:23:51.782298 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 20:23:51.996392 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 20:23:52.215097 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 20:23:52.427015 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 20:23:52.676037 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 20:23:52.888818 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 20:23:53.095781 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 20:23:53.325441 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 20:23:53.639313 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 20:23:53.904294 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 20:23:54.136015 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 20:23:54.35634 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 20:23:54.577625 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 20:23:54.75381 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 20:23:54.99468 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 20:23:55.22193 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 20:23:55.460765 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 20:23:55.665539 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 20:23:55.897086 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 20:23:56.0745 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 20:23:56.282443 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 20:23:56.500031 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 20:23:56.71941 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 20:23:56.914068 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 20:23:57.170067 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 20:23:57.34921 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 20:23:57.555907 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 20:23:57.744506 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 20:23:57.986509 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 20:23:58.201515 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 20:23:58.39376 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 20:23:58.601414 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 20:23:58.78261 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 20:23:59.000247 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 20:23:59.194934 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 20:23:59.427135 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 20:23:59.663687 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 20:23:59.930082 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 20:24:00.130914 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 20:24:00.349433 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 20:24:01.128953 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 20:24:01.275155 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 20:24:01.42819 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 20:24:01.586183 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 20:24:01.810675 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 20:24:01.874229 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-10 20:24:02.114971 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 20:24:02.303822 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 20:24:02.525175 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 20:24:02.769917 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 20:24:03.005077 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 20:24:03.239425 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 20:24:03.487272 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 20:24:03.772876 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 20:24:03.941605 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 20:24:04.143272 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 20:24:04.35381 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 20:24:04.560297 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 20:24:04.752737 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 20:24:04.941669 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 20:24:05.090253 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 20:24:05.285287 INFO::Counting total values for each feature
2024-06-10 20:24:05.308795 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-10 20:24:05.417123 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-10 20:24:05.525763 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-10 20:24:05.682509 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-10 20:24:05.797207 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-10 20:24:05.904126 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-10 20:24:05.920562 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-10 20:24:05.932735 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
35.645 0.882 50.533
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 99.004 | 2.248 | 140.070 | |