Lauren McIver
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 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 2025-01-02 12:03 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.20.0 |
| 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: 2024-12-30 23:21:46 -0500 (Mon, 30 Dec 2024) |
| EndedAt: 2024-12-30 23:25:47 -0500 (Mon, 30 Dec 2024) |
| EllapsedTime: 241.3 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 ‘/home/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 87.208 0.819 88.021
* 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
‘/home/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 ‘/home/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"
2024-12-30 23:23:42.448374 INFO::Writing function arguments to log file
2024-12-30 23:23:42.486536 INFO::Verifying options selected are valid
2024-12-30 23:23:42.517847 INFO::Determining format of input files
2024-12-30 23:23:42.51936 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-30 23:23:42.524275 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-30 23:23:42.525683 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-30 23:23:42.527992 INFO::Filter data based on min abundance and min prevalence
2024-12-30 23:23:42.528866 INFO::Total samples in data: 1595
2024-12-30 23:23:42.529673 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-30 23:23:42.533259 INFO::Total filtered features: 0
2024-12-30 23:23:42.534271 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-30 23:23:42.541579 INFO::Total filtered features with variance filtering: 0
2024-12-30 23:23:42.542665 INFO::Filtered feature names from variance filtering:
2024-12-30 23:23:42.543525 INFO::Running selected normalization method: TSS
2024-12-30 23:23:43.615475 INFO::Bypass z-score application to metadata
2024-12-30 23:23:43.616691 INFO::Running selected transform method: AST
2024-12-30 23:23:43.633667 INFO::Running selected analysis method: LM
2024-12-30 23:23:44.110216 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-30 23:23:44.426646 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-30 23:23:44.583131 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-30 23:23:44.722252 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-30 23:23:44.868406 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-30 23:23:45.007182 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-30 23:23:45.144441 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-30 23:23:45.287431 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-30 23:23:45.394913 WARNING::Fitting problem for feature 8 a warning was issued
2024-12-30 23:23:45.543844 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-30 23:23:45.654262 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-30 23:23:45.834961 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-30 23:23:45.98856 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-30 23:23:46.178002 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-30 23:23:46.320697 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-30 23:23:46.43576 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-30 23:23:46.586087 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-30 23:23:46.723793 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-30 23:23:46.866534 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-30 23:23:47.001445 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-30 23:23:47.147323 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-30 23:23:47.287211 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-30 23:23:47.64697 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-30 23:23:47.777677 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-30 23:23:47.919324 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-30 23:23:48.069724 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-30 23:23:48.201607 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-30 23:23:48.336538 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-30 23:23:48.475261 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-30 23:23:48.611425 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-30 23:23:48.749675 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-30 23:23:48.88678 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-30 23:23:49.028072 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-30 23:23:49.156502 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-30 23:23:49.320069 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-30 23:23:49.467698 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-30 23:23:49.628947 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-30 23:23:49.766824 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-30 23:23:49.90429 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-30 23:23:50.051492 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-30 23:23:50.191056 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-30 23:23:50.325007 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-30 23:23:50.461712 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-30 23:23:50.601829 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-30 23:23:50.737602 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-30 23:23:50.88102 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-30 23:23:51.011399 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-30 23:23:51.149257 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-30 23:23:51.297956 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-30 23:23:51.437273 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-30 23:23:51.581944 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-30 23:23:51.718826 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-30 23:23:51.851554 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-30 23:23:51.990401 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-30 23:23:52.125267 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-30 23:23:52.264457 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-30 23:23:52.411234 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-30 23:23:52.539141 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-30 23:23:52.683483 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-30 23:23:52.825649 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-30 23:23:52.953692 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-30 23:23:53.099244 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-30 23:23:53.230605 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-30 23:23:53.368058 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-30 23:23:53.498634 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-30 23:23:53.64105 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-30 23:23:53.775293 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-30 23:23:53.910407 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-30 23:23:54.040699 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-30 23:23:54.181616 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-30 23:23:54.306541 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-30 23:23:54.698613 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-30 23:23:54.850995 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-30 23:23:55.00552 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-30 23:23:55.159063 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-30 23:23:55.295726 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-30 23:23:55.435483 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-30 23:23:55.579983 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-30 23:23:55.715394 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-30 23:23:55.850216 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-30 23:23:55.991313 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-30 23:23:56.134673 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-30 23:23:56.278469 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-30 23:23:56.418352 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-30 23:23:56.556649 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-30 23:23:56.69505 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-30 23:23:56.835301 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-30 23:23:56.965831 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-30 23:23:57.103322 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-30 23:23:57.247362 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-30 23:23:57.426956 INFO::Counting total values for each feature
2024-12-30 23:23:57.465468 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-30 23:23:57.559769 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-30 23:23:57.655302 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-30 23:23:57.753214 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-30 23:23:57.800688 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-30 23:23:57.827119 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-30 23:23:57.832346 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-30 23:23:57.837396 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"
2024-12-30 23:23:57.849205 INFO::Writing function arguments to log file
2024-12-30 23:23:57.854625 INFO::Verifying options selected are valid
2024-12-30 23:23:57.855536 INFO::Determining format of input files
2024-12-30 23:23:57.856568 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-30 23:23:57.861217 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-30 23:23:57.862171 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-12-30 23:23:57.863704 INFO::Filter data based on min abundance and min prevalence
2024-12-30 23:23:57.864506 INFO::Total samples in data: 1595
2024-12-30 23:23:57.865296 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-30 23:23:57.869578 INFO::Total filtered features: 0
2024-12-30 23:23:57.870528 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-30 23:23:57.877622 INFO::Total filtered features with variance filtering: 0
2024-12-30 23:23:57.878659 INFO::Filtered feature names from variance filtering:
2024-12-30 23:23:57.879464 INFO::Running selected normalization method: NONE
2024-12-30 23:23:57.880225 INFO::Bypass z-score application to metadata
2024-12-30 23:23:57.881001 INFO::Running selected transform method: AST
2024-12-30 23:23:57.900678 INFO::Running selected analysis method: LM
2024-12-30 23:23:57.902309 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-30 23:23:58.033225 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-30 23:23:58.169644 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-30 23:23:58.302384 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-30 23:23:58.431915 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-30 23:23:58.573303 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-30 23:23:58.705305 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-30 23:23:58.838197 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-30 23:23:58.973874 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-30 23:23:59.10369 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-30 23:23:59.235758 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-30 23:23:59.349844 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-30 23:23:59.486254 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-30 23:23:59.613724 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-30 23:23:59.750499 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-30 23:23:59.879052 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-30 23:24:00.028059 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-30 23:24:00.192748 WARNING::Fitting problem for feature 16 a warning was issued
2024-12-30 23:24:00.322482 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-30 23:24:00.460484 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-30 23:24:00.589258 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-30 23:24:00.713641 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-30 23:24:00.854901 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-30 23:24:00.985161 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-30 23:24:01.121381 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-30 23:24:01.24326 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-30 23:24:01.381464 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-30 23:24:01.534375 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-30 23:24:01.688007 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-30 23:24:01.822817 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-30 23:24:01.954175 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-30 23:24:02.078654 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-30 23:24:02.229071 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-30 23:24:02.357554 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-30 23:24:02.500726 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-30 23:24:02.635083 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-30 23:24:02.76372 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-30 23:24:02.893318 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-30 23:24:03.034216 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-30 23:24:03.164382 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-30 23:24:03.2935 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-30 23:24:03.426316 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-30 23:24:03.552168 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-30 23:24:03.689179 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-30 23:24:03.817749 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-30 23:24:03.950246 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-30 23:24:04.08959 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-30 23:24:04.219771 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-30 23:24:04.357236 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-30 23:24:04.499726 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-30 23:24:04.636809 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-30 23:24:04.78055 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-30 23:24:04.906592 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-30 23:24:05.054241 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-30 23:24:05.175416 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-30 23:24:05.305293 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-30 23:24:05.434997 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-30 23:24:05.563643 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-30 23:24:05.704228 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-30 23:24:05.833644 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-30 23:24:05.973523 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-30 23:24:06.107504 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-30 23:24:06.244046 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-30 23:24:06.381773 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-30 23:24:06.512267 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-30 23:24:06.65399 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-30 23:24:06.781835 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-30 23:24:06.925101 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-30 23:24:07.051906 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-30 23:24:07.160891 WARNING::Fitting problem for feature 67 a warning was issued
2024-12-30 23:24:07.311541 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-30 23:24:07.442121 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-30 23:24:07.577459 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-30 23:24:07.725181 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-30 23:24:07.852255 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-30 23:24:07.897421 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-30 23:24:08.038244 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-30 23:24:08.16855 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-30 23:24:08.314266 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-30 23:24:08.44474 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-30 23:24:08.587523 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-30 23:24:08.729577 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-30 23:24:08.862357 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-30 23:24:09.006492 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-30 23:24:09.133752 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-30 23:24:09.281292 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-30 23:24:09.409721 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-30 23:24:09.539255 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-30 23:24:09.675727 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-30 23:24:09.805825 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-30 23:24:09.94937 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-30 23:24:10.104127 INFO::Counting total values for each feature
2024-12-30 23:24:10.12625 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-30 23:24:10.220195 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-30 23:24:10.313656 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-30 23:24:10.419773 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-30 23:24:10.483306 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-30 23:24:10.544684 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-30 23:24:10.55014 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-30 23:24:10.554788 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
28.654 0.529 29.175
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 87.208 | 0.819 | 88.021 | |