Lauren McIver
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1cacd4c |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1130/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.20.0 (landing page) Lauren McIver
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.20.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2024-11-20 05:08:09 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 05:11:10 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 181.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* 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 loading without being on the library search path ... 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 61.268 0.387 61.695
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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"
2024-11-20 05:09:33.086199 INFO::Writing function arguments to log file
2024-11-20 05:09:33.115907 INFO::Verifying options selected are valid
2024-11-20 05:09:33.138802 INFO::Determining format of input files
2024-11-20 05:09:33.139793 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-20 05:09:33.143144 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-20 05:09:33.144048 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-20 05:09:33.145743 INFO::Filter data based on min abundance and min prevalence
2024-11-20 05:09:33.1464 INFO::Total samples in data: 1595
2024-11-20 05:09:33.14701 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-20 05:09:33.149694 INFO::Total filtered features: 0
2024-11-20 05:09:33.150633 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-20 05:09:33.16274 INFO::Total filtered features with variance filtering: 0
2024-11-20 05:09:33.163535 INFO::Filtered feature names from variance filtering:
2024-11-20 05:09:33.164209 INFO::Running selected normalization method: TSS
2024-11-20 05:09:34.045213 INFO::Bypass z-score application to metadata
2024-11-20 05:09:34.046242 INFO::Running selected transform method: AST
2024-11-20 05:09:34.060213 INFO::Running selected analysis method: LM
2024-11-20 05:09:34.492967 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-20 05:09:34.763422 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-20 05:09:34.877095 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-20 05:09:34.988018 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-20 05:09:35.102437 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-20 05:09:35.203991 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-20 05:09:35.306097 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-20 05:09:35.406394 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-20 05:09:35.494932 WARNING::Fitting problem for feature 8 a warning was issued
2024-11-20 05:09:35.596266 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-20 05:09:35.671468 WARNING::Fitting problem for feature 9 a warning was issued
2024-11-20 05:09:35.783472 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-20 05:09:35.877842 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-20 05:09:36.374485 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-20 05:09:36.503484 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-20 05:09:36.584266 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-20 05:09:36.68646 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-20 05:09:36.782311 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-20 05:09:36.887785 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-20 05:09:36.981897 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-20 05:09:37.07844 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-20 05:09:37.183251 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-20 05:09:37.274271 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-20 05:09:37.367791 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-20 05:09:37.464142 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-20 05:09:37.568782 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-20 05:09:37.666516 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-20 05:09:37.768035 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-20 05:09:37.880021 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-20 05:09:37.97835 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-20 05:09:38.080176 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-20 05:09:38.190403 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-20 05:09:38.293608 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-20 05:09:38.390872 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-20 05:09:38.504955 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-20 05:09:38.610281 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-20 05:09:38.715537 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-20 05:09:38.820612 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-20 05:09:38.922615 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-20 05:09:39.022521 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-20 05:09:39.133353 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-20 05:09:39.23058 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-20 05:09:39.337364 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-20 05:09:39.440421 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-20 05:09:39.542148 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-20 05:09:39.775585 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-20 05:09:39.880177 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-20 05:09:39.975438 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-20 05:09:40.081562 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-20 05:09:40.181517 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-20 05:09:40.292924 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-20 05:09:40.39199 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-20 05:09:40.491992 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-20 05:09:40.598698 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-20 05:09:40.697156 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-20 05:09:40.80582 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-20 05:09:40.911784 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-20 05:09:41.033077 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-20 05:09:41.139926 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-20 05:09:41.250484 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-20 05:09:41.356666 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-20 05:09:41.466228 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-20 05:09:41.571111 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-20 05:09:41.667493 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-20 05:09:41.776366 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-20 05:09:41.880877 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-20 05:09:41.981128 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-20 05:09:42.090454 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-20 05:09:42.1906 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-20 05:09:42.292547 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-20 05:09:42.399736 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-20 05:09:42.506211 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-20 05:09:42.615729 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-20 05:09:42.952214 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-20 05:09:43.050753 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-20 05:09:43.148488 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-20 05:09:43.507526 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-20 05:09:43.602221 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-20 05:09:43.697023 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-20 05:09:43.798436 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-20 05:09:43.895281 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-20 05:09:43.997867 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-20 05:09:44.111779 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-20 05:09:44.206724 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-20 05:09:44.307629 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-20 05:09:44.412437 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-20 05:09:44.503849 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-20 05:09:44.598367 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-20 05:09:44.699837 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-20 05:09:44.794628 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-20 05:09:44.920553 INFO::Counting total values for each feature
2024-11-20 05:09:44.951454 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-20 05:09:45.019078 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-20 05:09:45.086401 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-20 05:09:45.154154 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-20 05:09:45.189364 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-20 05:09:45.209544 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-20 05:09:45.213271 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-20 05:09:45.2168 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"
2024-11-20 05:09:45.225967 INFO::Writing function arguments to log file
2024-11-20 05:09:45.230137 INFO::Verifying options selected are valid
2024-11-20 05:09:45.230806 INFO::Determining format of input files
2024-11-20 05:09:45.231578 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-20 05:09:45.234784 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-20 05:09:45.23555 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-20 05:09:45.236743 INFO::Filter data based on min abundance and min prevalence
2024-11-20 05:09:45.237411 INFO::Total samples in data: 1595
2024-11-20 05:09:45.238033 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-20 05:09:45.240698 INFO::Total filtered features: 0
2024-11-20 05:09:45.241421 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-20 05:09:45.247607 INFO::Total filtered features with variance filtering: 0
2024-11-20 05:09:45.248315 INFO::Filtered feature names from variance filtering:
2024-11-20 05:09:45.248902 INFO::Running selected normalization method: NONE
2024-11-20 05:09:45.249516 INFO::Bypass z-score application to metadata
2024-11-20 05:09:45.25013 INFO::Running selected transform method: AST
2024-11-20 05:09:45.266287 INFO::Running selected analysis method: LM
2024-11-20 05:09:45.26756 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-20 05:09:45.360459 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-20 05:09:45.458482 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-20 05:09:45.546418 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-20 05:09:45.644749 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-20 05:09:45.734296 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-20 05:09:45.835389 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-20 05:09:45.927349 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-20 05:09:46.025018 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-20 05:09:46.11679 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-20 05:09:46.216876 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-20 05:09:46.306766 WARNING::Fitting problem for feature 11 a warning was issued
2024-11-20 05:09:46.405612 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-20 05:09:46.495525 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-20 05:09:46.595347 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-20 05:09:46.920835 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-20 05:09:47.015102 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-20 05:09:47.097246 WARNING::Fitting problem for feature 16 a warning was issued
2024-11-20 05:09:47.190757 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-20 05:09:47.285101 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-20 05:09:47.385817 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-20 05:09:47.473628 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-20 05:09:47.565844 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-20 05:09:47.665326 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-20 05:09:47.75771 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-20 05:09:47.856162 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-20 05:09:47.948821 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-20 05:09:48.041278 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-20 05:09:48.145152 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-20 05:09:48.241805 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-20 05:09:48.339348 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-20 05:09:48.429583 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-20 05:09:48.531692 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-20 05:09:48.623381 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-20 05:09:48.727372 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-20 05:09:48.821179 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-20 05:09:48.922679 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-20 05:09:49.015147 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-20 05:09:49.11413 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-20 05:09:49.205045 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-20 05:09:49.314436 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-20 05:09:49.399576 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-20 05:09:49.488421 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-20 05:09:49.588888 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-20 05:09:49.678202 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-20 05:09:49.770994 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-20 05:09:49.873471 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-20 05:09:49.963724 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-20 05:09:50.067806 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-20 05:09:50.15539 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-20 05:09:50.40565 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-20 05:09:50.505414 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-20 05:09:50.589963 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-20 05:09:50.681998 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-20 05:09:50.776287 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-20 05:09:50.859415 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-20 05:09:50.956464 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-20 05:09:51.044213 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-20 05:09:51.142765 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-20 05:09:51.230382 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-20 05:09:51.318829 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-20 05:09:51.420333 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-20 05:09:51.506923 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-20 05:09:51.604227 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-20 05:09:51.691679 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-20 05:09:51.79086 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-20 05:09:51.879356 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-20 05:09:51.978294 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-20 05:09:52.066395 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-20 05:09:52.150422 WARNING::Fitting problem for feature 67 a warning was issued
2024-11-20 05:09:52.254681 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-20 05:09:52.341919 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-20 05:09:52.443655 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-20 05:09:52.548642 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-20 05:09:52.64273 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-20 05:09:52.674576 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-20 05:09:52.76601 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-20 05:09:52.869182 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-20 05:09:52.960256 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-20 05:09:53.058676 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-20 05:09:53.15447 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-20 05:09:53.244804 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-20 05:09:53.348987 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-20 05:09:53.441714 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-20 05:09:53.531142 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-20 05:09:53.642157 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-20 05:09:53.730916 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-20 05:09:53.830666 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-20 05:09:53.918539 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-20 05:09:54.00915 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-20 05:09:54.115004 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-20 05:09:54.224529 INFO::Counting total values for each feature
2024-11-20 05:09:54.24885 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-20 05:09:54.316282 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-20 05:09:54.715991 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-20 05:09:54.786787 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-20 05:09:54.83233 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-20 05:09:54.875672 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-20 05:09:54.879482 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-20 05:09:54.882491 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 7 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
22.751 0.378 23.131
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 61.268 | 0.387 | 61.695 | |