Lauren McIver
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 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 2024-06-14 14:38 -0400 (Fri, 14 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 |
| 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 | | ||||||||
|
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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz |
| StartedAt: 2024-06-13 05:50:28 -0400 (Thu, 13 Jun 2024) |
| EndedAt: 2024-06-13 05:55:35 -0400 (Thu, 13 Jun 2024) |
| EllapsedTime: 306.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 97.7 8.08 106.23
* 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
'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'Maaslin2' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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"
2024-06-13 05:54:42.28246 INFO::Writing function arguments to log file
2024-06-13 05:54:42.337263 INFO::Verifying options selected are valid
2024-06-13 05:54:42.372774 INFO::Determining format of input files
2024-06-13 05:54:42.3753 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-13 05:54:42.389242 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-13 05:54:42.391631 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-13 05:54:42.395526 INFO::Filter data based on min abundance and min prevalence
2024-06-13 05:54:42.398553 INFO::Total samples in data: 1595
2024-06-13 05:54:42.4013 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-13 05:54:42.409277 INFO::Total filtered features: 0
2024-06-13 05:54:42.412491 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-13 05:54:42.426369 INFO::Total filtered features with variance filtering: 0
2024-06-13 05:54:42.429609 INFO::Filtered feature names from variance filtering:
2024-06-13 05:54:42.432515 INFO::Running selected normalization method: TSS
2024-06-13 05:54:44.61428 INFO::Bypass z-score application to metadata
2024-06-13 05:54:44.617685 INFO::Running selected transform method: AST
2024-06-13 05:54:44.645562 INFO::Running selected analysis method: LM
2024-06-13 05:54:45.163125 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-13 05:54:45.870036 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-13 05:54:46.00874 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-13 05:54:46.151527 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-13 05:54:46.284176 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-13 05:54:46.422868 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-13 05:54:46.550498 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-13 05:54:46.715961 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-13 05:54:46.841788 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-13 05:54:46.976166 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-13 05:54:47.18097 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-13 05:54:47.335294 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-13 05:54:47.474219 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-13 05:54:47.611711 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-13 05:54:47.827526 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-13 05:54:47.957807 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-13 05:54:48.106518 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-13 05:54:48.230337 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-13 05:54:48.369821 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-13 05:54:48.506015 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-13 05:54:48.648538 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-13 05:54:48.78723 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-13 05:54:48.919467 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-13 05:54:49.09336 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-13 05:54:49.224586 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-13 05:54:49.353122 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-13 05:54:49.487896 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-13 05:54:49.62578 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-13 05:54:49.763639 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-13 05:54:49.935612 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-13 05:54:50.10668 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-13 05:54:50.555142 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-13 05:54:50.768283 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-13 05:54:50.990186 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-13 05:54:51.155437 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-13 05:54:51.316379 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-13 05:54:51.451572 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-13 05:54:51.585686 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-13 05:54:51.733865 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-13 05:54:51.926668 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-13 05:54:52.130383 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-13 05:54:52.356307 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-13 05:54:52.534108 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-13 05:54:52.709508 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-13 05:54:52.875792 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-13 05:54:53.038245 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-13 05:54:53.224132 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-13 05:54:53.38511 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-13 05:54:53.531913 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-13 05:54:53.711437 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-13 05:54:53.88773 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-13 05:54:54.044237 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-13 05:54:54.183248 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-13 05:54:54.318548 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-13 05:54:54.464551 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-13 05:54:54.605277 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-13 05:54:54.838951 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-13 05:54:55.061782 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-13 05:54:55.269715 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-13 05:54:55.759112 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-13 05:54:55.97227 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-13 05:54:56.158815 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-13 05:54:56.317779 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-13 05:54:56.454178 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-13 05:54:56.588855 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-13 05:54:56.714233 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-13 05:54:56.846504 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-13 05:54:56.979005 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-13 05:54:57.103607 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-13 05:54:57.257775 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-13 05:54:57.478628 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-13 05:54:57.704083 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-13 05:54:57.904506 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-13 05:54:58.084717 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-13 05:54:58.265776 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-13 05:54:58.455199 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-13 05:54:58.634994 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-13 05:54:58.828299 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-13 05:54:59.04852 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-13 05:54:59.26588 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-13 05:54:59.48021 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-13 05:54:59.672528 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-13 05:54:59.884767 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-13 05:55:00.080929 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-13 05:55:00.277401 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-13 05:55:00.491804 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-13 05:55:00.694283 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-13 05:55:00.916983 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-13 05:55:01.182125 INFO::Counting total values for each feature
2024-06-13 05:55:01.242015 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-13 05:55:01.683149 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-13 05:55:02.189142 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-13 05:55:02.639989 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-13 05:55:02.693828 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-13 05:55:02.725544 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-13 05:55:02.734247 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-13 05:55:02.757381 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"
2024-06-13 05:55:02.796362 INFO::Writing function arguments to log file
2024-06-13 05:55:02.817199 INFO::Verifying options selected are valid
2024-06-13 05:55:02.820293 INFO::Determining format of input files
2024-06-13 05:55:02.823662 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-13 05:55:02.832535 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-13 05:55:02.835577 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-06-13 05:55:02.838509 INFO::Filter data based on min abundance and min prevalence
2024-06-13 05:55:02.840522 INFO::Total samples in data: 1595
2024-06-13 05:55:02.843463 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-13 05:55:02.850959 INFO::Total filtered features: 0
2024-06-13 05:55:02.853931 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-13 05:55:02.86539 INFO::Total filtered features with variance filtering: 0
2024-06-13 05:55:02.868676 INFO::Filtered feature names from variance filtering:
2024-06-13 05:55:02.871488 INFO::Running selected normalization method: NONE
2024-06-13 05:55:02.874131 INFO::Bypass z-score application to metadata
2024-06-13 05:55:02.876801 INFO::Running selected transform method: AST
2024-06-13 05:55:02.899329 INFO::Running selected analysis method: LM
2024-06-13 05:55:02.903143 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-13 05:55:03.085556 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-13 05:55:03.285581 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-13 05:55:03.504408 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-13 05:55:03.712718 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-13 05:55:03.918271 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-13 05:55:04.136018 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-13 05:55:04.33636 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-13 05:55:04.542748 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-13 05:55:04.658704 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-13 05:55:04.868884 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-13 05:55:05.011598 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-13 05:55:05.131029 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-13 05:55:05.270896 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-13 05:55:05.435523 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-13 05:55:05.575496 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-13 05:55:05.71456 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-13 05:55:05.861843 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-13 05:55:05.96314 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-13 05:55:06.129505 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-13 05:55:06.263642 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-13 05:55:06.442093 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-13 05:55:06.937709 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-13 05:55:07.162472 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-13 05:55:07.366667 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-13 05:55:07.558072 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-13 05:55:07.751311 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-13 05:55:07.922507 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-13 05:55:08.126559 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-13 05:55:08.294893 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-13 05:55:08.425626 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-13 05:55:08.545624 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-13 05:55:08.703399 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-13 05:55:08.870569 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-13 05:55:09.019136 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-13 05:55:09.156991 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-13 05:55:09.31003 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-13 05:55:09.447962 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-13 05:55:09.574016 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-13 05:55:09.701371 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-13 05:55:09.899447 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-13 05:55:10.088742 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-13 05:55:10.272519 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-13 05:55:10.460663 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-13 05:55:10.667841 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-13 05:55:10.85768 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-13 05:55:10.99106 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-13 05:55:11.134121 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-13 05:55:11.273596 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-13 05:55:11.402183 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-13 05:55:11.52563 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-13 05:55:11.660708 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-13 05:55:11.790921 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-13 05:55:11.913435 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-13 05:55:12.079145 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-13 05:55:12.220447 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-13 05:55:12.362848 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-13 05:55:12.547952 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-13 05:55:12.66319 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-13 05:55:12.781765 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-13 05:55:12.905625 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-13 05:55:13.030821 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-13 05:55:13.152069 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-13 05:55:13.275135 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-13 05:55:13.400472 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-13 05:55:13.525155 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-13 05:55:13.650331 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-13 05:55:13.768118 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-13 05:55:13.895227 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-13 05:55:14.066063 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-13 05:55:14.226225 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-13 05:55:14.352286 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-13 05:55:14.480292 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-13 05:55:14.620748 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-13 05:55:14.742908 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-13 05:55:14.787322 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-13 05:55:14.987911 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-13 05:55:15.128808 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-13 05:55:15.338521 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-13 05:55:15.532628 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-13 05:55:15.744705 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-13 05:55:15.945232 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-13 05:55:16.155564 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-13 05:55:16.371462 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-13 05:55:16.542806 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-13 05:55:16.721877 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-13 05:55:16.927581 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-13 05:55:17.132652 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-13 05:55:17.28084 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-13 05:55:17.42729 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-13 05:55:17.56822 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-13 05:55:17.733542 INFO::Counting total values for each feature
2024-06-13 05:55:17.776912 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-13 05:55:18.261292 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-13 05:55:18.75172 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-13 05:55:19.091339 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-13 05:55:19.157568 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-13 05:55:19.212033 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-13 05:55:19.220872 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-13 05:55:19.240699 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 5 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
35.79 5.89 41.65
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 97.70 | 8.08 | 106.23 | |