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 14:42 -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: 2024-06-09 21:14:17 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 21:17:10 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 173.0 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: x86_64-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 Monterey 12.7.1
* 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 92.13 1.531 93.95
* 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-x86_64/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 1.9.10 Current TMB version is 1.9.11 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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"
2024-06-09 21:16:31.138203 INFO::Writing function arguments to log file
2024-06-09 21:16:31.179928 INFO::Verifying options selected are valid
2024-06-09 21:16:31.212694 INFO::Determining format of input files
2024-06-09 21:16:31.214292 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-09 21:16:31.220251 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-09 21:16:31.221707 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-09 21:16:31.224145 INFO::Filter data based on min abundance and min prevalence
2024-06-09 21:16:31.225138 INFO::Total samples in data: 1595
2024-06-09 21:16:31.22607 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-09 21:16:31.23598 INFO::Total filtered features: 0
2024-06-09 21:16:31.237272 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-09 21:16:31.245402 INFO::Total filtered features with variance filtering: 0
2024-06-09 21:16:31.246694 INFO::Filtered feature names from variance filtering:
2024-06-09 21:16:31.247673 INFO::Running selected normalization method: TSS
2024-06-09 21:16:32.437145 INFO::Bypass z-score application to metadata
2024-06-09 21:16:32.438471 INFO::Running selected transform method: AST
2024-06-09 21:16:32.45227 INFO::Running selected analysis method: LM
2024-06-09 21:16:32.986553 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-09 21:16:33.381057 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-09 21:16:33.582991 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-09 21:16:33.742784 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-09 21:16:33.905198 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-09 21:16:34.031863 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-09 21:16:34.154916 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-09 21:16:34.333645 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-09 21:16:34.474647 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-09 21:16:34.69351 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-09 21:16:34.864272 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-09 21:16:35.047585 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-09 21:16:35.217183 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-09 21:16:35.365132 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-09 21:16:35.54208 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-09 21:16:35.666598 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-09 21:16:35.853382 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-09 21:16:36.025295 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-09 21:16:36.210612 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-09 21:16:36.390043 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-09 21:16:36.571253 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-09 21:16:36.744262 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-09 21:16:36.902746 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-09 21:16:37.085084 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-09 21:16:37.234618 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-09 21:16:37.41911 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-09 21:16:37.553318 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-09 21:16:37.70636 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-09 21:16:37.858474 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-09 21:16:38.029522 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-09 21:16:38.206346 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-09 21:16:38.375271 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-09 21:16:38.586738 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-09 21:16:38.756861 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-09 21:16:39.159444 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-09 21:16:39.322107 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-09 21:16:39.451687 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-09 21:16:39.799841 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-09 21:16:39.921503 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-09 21:16:40.033125 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-09 21:16:40.153512 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-09 21:16:40.286611 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-09 21:16:40.400227 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-09 21:16:40.519455 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-09 21:16:40.648263 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-09 21:16:40.754795 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-09 21:16:40.86661 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-09 21:16:40.993731 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-09 21:16:41.106394 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-09 21:16:41.214325 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-09 21:16:41.340719 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-09 21:16:41.460536 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-09 21:16:41.623757 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-09 21:16:41.79496 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-09 21:16:41.946885 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-09 21:16:42.065678 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-09 21:16:42.190216 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-09 21:16:42.327803 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-09 21:16:42.483917 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-09 21:16:42.615331 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-09 21:16:42.758181 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-09 21:16:42.936523 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-09 21:16:43.095033 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-09 21:16:43.263886 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-09 21:16:43.65674 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-09 21:16:43.784554 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-09 21:16:43.936417 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-09 21:16:44.092338 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-09 21:16:44.232118 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-09 21:16:44.380752 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-09 21:16:44.530118 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-09 21:16:44.706937 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-09 21:16:44.852508 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-09 21:16:44.998135 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-09 21:16:45.118126 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-09 21:16:45.260165 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-09 21:16:45.419257 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-09 21:16:45.596843 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-09 21:16:45.734684 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-09 21:16:45.86682 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-09 21:16:46.042078 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-09 21:16:46.154347 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-09 21:16:46.268165 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-09 21:16:46.42881 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-09 21:16:46.58622 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-09 21:16:46.740394 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-09 21:16:46.889254 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-09 21:16:47.009083 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-09 21:16:47.216186 INFO::Counting total values for each feature
2024-06-09 21:16:47.250686 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-09 21:16:47.358346 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-09 21:16:47.511247 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-09 21:16:47.668738 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-09 21:16:47.730095 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-09 21:16:47.760602 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-09 21:16:47.767586 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-09 21:16:47.778709 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"
2024-06-09 21:16:47.792173 INFO::Writing function arguments to log file
2024-06-09 21:16:47.800371 INFO::Verifying options selected are valid
2024-06-09 21:16:47.801997 INFO::Determining format of input files
2024-06-09 21:16:47.803794 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-09 21:16:47.809657 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-09 21:16:47.811431 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-06-09 21:16:47.814036 INFO::Filter data based on min abundance and min prevalence
2024-06-09 21:16:47.815546 INFO::Total samples in data: 1595
2024-06-09 21:16:47.816566 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-09 21:16:47.830255 INFO::Total filtered features: 0
2024-06-09 21:16:47.831626 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-09 21:16:47.83741 INFO::Total filtered features with variance filtering: 0
2024-06-09 21:16:47.838726 INFO::Filtered feature names from variance filtering:
2024-06-09 21:16:47.839753 INFO::Running selected normalization method: NONE
2024-06-09 21:16:47.840661 INFO::Bypass z-score application to metadata
2024-06-09 21:16:47.841522 INFO::Running selected transform method: AST
2024-06-09 21:16:47.855916 INFO::Running selected analysis method: LM
2024-06-09 21:16:47.858097 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-09 21:16:47.993818 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-09 21:16:48.145487 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-09 21:16:48.297033 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-09 21:16:48.444555 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-09 21:16:48.583255 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-09 21:16:48.720976 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-09 21:16:48.848661 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-09 21:16:48.976178 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-09 21:16:49.10417 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-09 21:16:49.237351 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-09 21:16:49.371858 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-09 21:16:49.770266 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-09 21:16:49.901322 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-09 21:16:50.054181 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-09 21:16:50.217401 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-09 21:16:50.367678 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-09 21:16:50.519691 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-09 21:16:50.662651 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-09 21:16:50.821327 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-09 21:16:50.937008 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-09 21:16:51.045555 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-09 21:16:51.161628 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-09 21:16:51.33321 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-09 21:16:51.437973 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-09 21:16:51.556781 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-09 21:16:51.725807 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-09 21:16:51.900445 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-09 21:16:52.059732 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-09 21:16:52.211002 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-09 21:16:52.349961 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-09 21:16:52.453967 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-09 21:16:52.584238 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-09 21:16:52.744356 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-09 21:16:52.906698 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-09 21:16:53.044803 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-09 21:16:53.187729 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-09 21:16:53.359671 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-09 21:16:53.516284 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-09 21:16:53.663707 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-09 21:16:53.813472 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-09 21:16:53.988289 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-09 21:16:54.142369 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-09 21:16:54.281905 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-09 21:16:54.457465 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-09 21:16:54.628602 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-09 21:16:54.741222 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-09 21:16:54.854896 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-09 21:16:54.970726 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-09 21:16:55.092883 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-09 21:16:55.238868 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-09 21:16:55.348195 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-09 21:16:55.49573 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-09 21:16:55.625234 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-09 21:16:55.77487 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-09 21:16:55.95426 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-09 21:16:56.106147 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-09 21:16:56.267842 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-09 21:16:56.393246 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-09 21:16:56.531709 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-09 21:16:56.682493 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-09 21:16:56.840913 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-09 21:16:57.009419 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-09 21:16:57.151014 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-09 21:16:57.290705 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-09 21:16:57.441272 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-09 21:16:57.574218 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-09 21:16:57.681043 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-09 21:16:57.802508 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-09 21:16:57.971638 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-09 21:16:58.123983 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-09 21:16:58.286727 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-09 21:16:58.399293 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-09 21:16:58.510572 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-09 21:16:58.560746 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-09 21:16:58.72086 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-09 21:16:58.881581 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-09 21:16:59.059304 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-09 21:16:59.216797 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-09 21:16:59.390566 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-09 21:16:59.536715 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-09 21:16:59.679689 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-09 21:16:59.827737 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-09 21:16:59.958524 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-09 21:17:00.112794 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-09 21:17:00.289416 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-09 21:17:00.450803 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-09 21:17:00.582584 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-09 21:17:00.748222 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-09 21:17:00.909431 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-09 21:17:01.098027 INFO::Counting total values for each feature
2024-06-09 21:17:01.133025 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-09 21:17:01.259748 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-09 21:17:01.389018 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-09 21:17:01.542792 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-09 21:17:01.617913 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-09 21:17:01.690241 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-09 21:17:01.698338 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-09 21:17:01.706521 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
31.349 0.715 32.127
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 92.130 | 1.531 | 93.950 | |