Lauren McIver
| Snapshot Date: 2024-06-27 14:00 -0400 (Thu, 27 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 2f9ea7a |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-28 11:40 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4089 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
| 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 1108/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.19.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | see weekly results here | ||||||||||||
|
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: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2024-06-27 22:04:58 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 22:05:56 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 57.6 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 ‘1.19.0’
* 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 28.718 0.56 29.304
* 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-3.20-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 Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.11 Current TMB version is 1.9.12 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 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
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"
2024-06-27 22:05:41.472901 INFO::Writing function arguments to log file
2024-06-27 22:05:41.489433 INFO::Verifying options selected are valid
2024-06-27 22:05:41.5035 INFO::Determining format of input files
2024-06-27 22:05:41.504105 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 22:05:41.506037 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 22:05:41.506514 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-27 22:05:41.50731 INFO::Filter data based on min abundance and min prevalence
2024-06-27 22:05:41.507606 INFO::Total samples in data: 1595
2024-06-27 22:05:41.507879 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 22:05:41.512379 INFO::Total filtered features: 0
2024-06-27 22:05:41.512756 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 22:05:41.515746 INFO::Total filtered features with variance filtering: 0
2024-06-27 22:05:41.516089 INFO::Filtered feature names from variance filtering:
2024-06-27 22:05:41.516357 INFO::Running selected normalization method: TSS
2024-06-27 22:05:41.963147 INFO::Bypass z-score application to metadata
2024-06-27 22:05:41.963687 INFO::Running selected transform method: AST
2024-06-27 22:05:41.970096 INFO::Running selected analysis method: LM
2024-06-27 22:05:42.167158 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 22:05:42.298995 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 22:05:42.358466 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 22:05:42.411446 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 22:05:42.468649 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 22:05:42.521727 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 22:05:42.574956 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 22:05:42.630212 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 22:05:42.684007 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 22:05:42.741337 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-27 22:05:42.79656 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 22:05:42.851685 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 22:05:42.904685 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 22:05:42.95892 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 22:05:43.012453 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 22:05:43.067318 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 22:05:43.120535 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 22:05:43.173651 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 22:05:43.228182 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 22:05:43.285036 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 22:05:43.334626 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 22:05:43.390317 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 22:05:43.448923 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 22:05:43.502863 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 22:05:43.558658 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 22:05:43.616518 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 22:05:43.673989 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 22:05:43.736805 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 22:05:43.791106 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 22:05:43.843446 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 22:05:43.901098 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 22:05:43.951195 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 22:05:44.009247 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 22:05:44.062077 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 22:05:44.121743 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 22:05:44.17241 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 22:05:44.227959 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 22:05:44.279233 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 22:05:44.335913 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 22:05:44.386993 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 22:05:44.440848 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 22:05:44.497429 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 22:05:44.549933 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 22:05:44.710413 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 22:05:44.761151 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 22:05:44.810181 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 22:05:44.868898 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 22:05:44.921572 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 22:05:44.974971 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 22:05:45.02538 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 22:05:45.081993 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 22:05:45.134116 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 22:05:45.187786 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 22:05:45.245692 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 22:05:45.301159 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 22:05:45.350942 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 22:05:45.515847 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 22:05:45.572952 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 22:05:45.623215 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 22:05:45.683914 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 22:05:45.735553 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 22:05:45.786193 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 22:05:45.839338 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 22:05:45.897109 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 22:05:45.951659 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 22:05:46.001442 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 22:05:46.053804 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 22:05:46.103679 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 22:05:46.151595 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 22:05:46.206656 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 22:05:46.259615 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 22:05:46.311745 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 22:05:46.363677 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 22:05:46.413091 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 22:05:46.574385 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 22:05:46.623341 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 22:05:46.674176 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 22:05:46.725344 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 22:05:46.885068 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 22:05:46.940978 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 22:05:46.995306 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 22:05:47.051245 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 22:05:47.111147 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 22:05:47.163072 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 22:05:47.211689 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 22:05:47.263303 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 22:05:47.318974 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 22:05:47.368867 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 22:05:47.436026 INFO::Counting total values for each feature
2024-06-27 22:05:47.448722 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-27 22:05:47.497177 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-27 22:05:47.554596 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-27 22:05:47.611089 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-27 22:05:47.638004 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-27 22:05:47.65265 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-27 22:05:47.655568 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-27 22:05:47.658291 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"
2024-06-27 22:05:47.663562 INFO::Writing function arguments to log file
2024-06-27 22:05:47.665664 INFO::Verifying options selected are valid
2024-06-27 22:05:47.665993 INFO::Determining format of input files
2024-06-27 22:05:47.666387 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 22:05:47.668432 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 22:05:47.668781 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-06-27 22:05:47.669333 INFO::Filter data based on min abundance and min prevalence
2024-06-27 22:05:47.669611 INFO::Total samples in data: 1595
2024-06-27 22:05:47.669873 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 22:05:47.675545 INFO::Total filtered features: 0
2024-06-27 22:05:47.675945 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 22:05:47.678899 INFO::Total filtered features with variance filtering: 0
2024-06-27 22:05:47.679229 INFO::Filtered feature names from variance filtering:
2024-06-27 22:05:47.679502 INFO::Running selected normalization method: NONE
2024-06-27 22:05:47.679762 INFO::Bypass z-score application to metadata
2024-06-27 22:05:47.680017 INFO::Running selected transform method: AST
2024-06-27 22:05:47.685711 INFO::Running selected analysis method: LM
2024-06-27 22:05:47.686246 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 22:05:47.737916 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 22:05:47.788935 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 22:05:47.842679 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 22:05:47.894042 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 22:05:47.944116 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 22:05:47.998882 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 22:05:48.054611 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 22:05:48.105228 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 22:05:48.155487 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 22:05:48.205843 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 22:05:48.249835 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-27 22:05:48.312234 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 22:05:48.362302 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 22:05:48.405607 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-27 22:05:48.459685 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 22:05:48.514306 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 22:05:48.567234 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 22:05:48.615575 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 22:05:48.667708 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 22:05:48.723634 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 22:05:48.772811 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 22:05:48.823964 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 22:05:48.87691 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 22:05:48.934146 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 22:05:48.98335 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 22:05:49.035898 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 22:05:49.091552 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 22:05:49.14312 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 22:05:49.195356 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 22:05:49.244644 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 22:05:49.297279 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 22:05:49.346954 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 22:05:49.397123 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 22:05:49.449619 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 22:05:49.504343 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 22:05:49.555202 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 22:05:49.607289 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 22:05:49.660011 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 22:05:49.715252 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 22:05:49.766372 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 22:05:49.814879 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 22:05:49.866884 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 22:05:49.916336 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 22:05:49.965789 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 22:05:50.022876 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 22:05:50.076919 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 22:05:50.127817 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 22:05:50.191047 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 22:05:50.239523 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 22:05:50.291206 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 22:05:50.341923 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 22:05:50.395325 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 22:05:50.44782 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 22:05:50.495786 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 22:05:50.542046 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 22:05:50.589962 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 22:05:50.642473 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 22:05:50.691891 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 22:05:50.740483 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 22:05:50.78931 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 22:05:50.847497 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 22:05:50.896377 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 22:05:50.946063 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 22:05:50.996392 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 22:05:51.052498 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 22:05:51.102079 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 22:05:51.15374 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 22:05:51.205978 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 22:05:51.26261 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 22:05:51.310855 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 22:05:51.360318 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 22:05:51.411279 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 22:05:51.474945 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 22:05:51.492764 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-27 22:05:51.540092 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 22:05:51.593552 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 22:05:51.646836 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 22:05:51.699272 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 22:05:51.748515 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 22:05:51.798404 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 22:05:51.849512 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 22:05:51.907564 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 22:05:51.957914 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 22:05:52.012058 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 22:05:52.061299 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 22:05:52.114496 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 22:05:52.162373 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 22:05:52.212255 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 22:05:52.26615 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 22:05:52.330006 INFO::Counting total values for each feature
2024-06-27 22:05:52.338743 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-27 22:05:52.385239 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-27 22:05:52.431841 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-27 22:05:52.486761 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-27 22:05:52.522683 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-27 22:05:52.556993 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-27 22:05:52.559963 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-27 22:05:52.56216 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
11.276 0.260 11.534
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 28.718 | 0.560 | 29.304 | |