Lauren McIver
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 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 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 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: 1.18.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz |
| StartedAt: 2024-07-11 00:28:45 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 00:32:47 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 241.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 83.145 0.855 83.944
* 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-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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"
2024-07-11 00:30:38.919561 INFO::Writing function arguments to log file
2024-07-11 00:30:38.95804 INFO::Verifying options selected are valid
2024-07-11 00:30:38.994015 INFO::Determining format of input files
2024-07-11 00:30:38.995516 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-11 00:30:39.000371 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-11 00:30:39.001659 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-11 00:30:39.004028 INFO::Filter data based on min abundance and min prevalence
2024-07-11 00:30:39.00489 INFO::Total samples in data: 1595
2024-07-11 00:30:39.005697 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-11 00:30:39.009446 INFO::Total filtered features: 0
2024-07-11 00:30:39.010408 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-11 00:30:39.02403 INFO::Total filtered features with variance filtering: 0
2024-07-11 00:30:39.025079 INFO::Filtered feature names from variance filtering:
2024-07-11 00:30:39.025941 INFO::Running selected normalization method: TSS
2024-07-11 00:30:40.254002 INFO::Bypass z-score application to metadata
2024-07-11 00:30:40.255681 INFO::Running selected transform method: AST
2024-07-11 00:30:40.273198 INFO::Running selected analysis method: LM
2024-07-11 00:30:40.868305 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-11 00:30:41.235947 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-11 00:30:41.387159 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-11 00:30:41.54655 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-11 00:30:41.719022 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-11 00:30:41.872641 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-11 00:30:42.035641 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-11 00:30:42.181535 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-11 00:30:42.303103 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-11 00:30:42.463868 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-11 00:30:42.584404 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-11 00:30:42.773342 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-11 00:30:42.910661 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-11 00:30:43.049957 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-11 00:30:43.193372 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-11 00:30:43.313683 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-11 00:30:43.472522 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-11 00:30:43.625587 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-11 00:30:43.81014 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-11 00:30:43.974852 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-11 00:30:44.143451 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-11 00:30:44.320706 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-11 00:30:44.469034 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-11 00:30:44.622035 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-11 00:30:44.774595 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-11 00:30:44.926478 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-11 00:30:45.075608 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-11 00:30:45.226807 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-11 00:30:45.385802 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-11 00:30:45.536345 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-11 00:30:45.685813 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-11 00:30:45.830417 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-11 00:30:45.984851 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-11 00:30:46.135537 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-11 00:30:46.29839 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-11 00:30:46.463464 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-11 00:30:46.614946 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-11 00:30:46.760648 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-11 00:30:46.924713 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-11 00:30:47.068674 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-11 00:30:47.211771 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-11 00:30:47.3559 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-11 00:30:47.496019 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-11 00:30:47.653064 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-11 00:30:47.808834 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-11 00:30:47.962494 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-11 00:30:48.104264 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-11 00:30:48.246894 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-11 00:30:48.394296 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-11 00:30:48.550132 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-11 00:30:48.710671 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-11 00:30:48.868867 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-11 00:30:49.043725 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-11 00:30:49.191322 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-11 00:30:49.341836 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-11 00:30:49.487539 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-11 00:30:49.637996 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-11 00:30:49.77932 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-11 00:30:49.928653 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-11 00:30:50.100839 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-11 00:30:50.241204 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-11 00:30:50.391679 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-11 00:30:50.528684 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-11 00:30:50.664652 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-11 00:30:50.813662 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-11 00:30:50.960822 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-11 00:30:51.118357 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-11 00:30:51.266869 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-11 00:30:51.432178 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-11 00:30:51.575572 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-11 00:30:51.72032 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-11 00:30:51.877886 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-11 00:30:52.031343 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-11 00:30:52.498825 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-11 00:30:52.63694 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-11 00:30:52.779311 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-11 00:30:52.933408 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-11 00:30:53.076959 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-11 00:30:53.217569 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-11 00:30:53.363959 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-11 00:30:53.515605 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-11 00:30:53.671569 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-11 00:30:53.814988 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-11 00:30:53.96794 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-11 00:30:54.11304 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-11 00:30:54.253686 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-11 00:30:54.393108 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-11 00:30:54.530479 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-11 00:30:54.670581 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-11 00:30:54.831889 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-11 00:30:55.031864 INFO::Counting total values for each feature
2024-07-11 00:30:55.083647 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-11 00:30:55.231386 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-11 00:30:55.384154 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-11 00:30:55.537622 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-11 00:30:55.59525 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-11 00:30:55.628122 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-11 00:30:55.634115 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-11 00:30:55.641081 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"
2024-07-11 00:30:55.65555 INFO::Writing function arguments to log file
2024-07-11 00:30:55.662033 INFO::Verifying options selected are valid
2024-07-11 00:30:55.663088 INFO::Determining format of input files
2024-07-11 00:30:55.664241 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-11 00:30:55.669314 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-11 00:30:55.670396 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-07-11 00:30:55.672004 INFO::Filter data based on min abundance and min prevalence
2024-07-11 00:30:55.672872 INFO::Total samples in data: 1595
2024-07-11 00:30:55.673721 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-11 00:30:55.677797 INFO::Total filtered features: 0
2024-07-11 00:30:55.678742 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-11 00:30:55.686613 INFO::Total filtered features with variance filtering: 0
2024-07-11 00:30:55.687844 INFO::Filtered feature names from variance filtering:
2024-07-11 00:30:55.688742 INFO::Running selected normalization method: NONE
2024-07-11 00:30:55.689725 INFO::Bypass z-score application to metadata
2024-07-11 00:30:55.690577 INFO::Running selected transform method: AST
2024-07-11 00:30:55.716342 INFO::Running selected analysis method: LM
2024-07-11 00:30:55.718513 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-11 00:30:55.857096 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-11 00:30:56.000143 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-11 00:30:56.129217 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-11 00:30:56.580926 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-11 00:30:56.715973 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-11 00:30:56.864633 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-11 00:30:57.008841 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-11 00:30:57.162505 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-11 00:30:57.300592 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-11 00:30:57.443464 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-11 00:30:57.566817 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-11 00:30:57.732775 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-11 00:30:57.868847 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-11 00:30:58.002017 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-11 00:30:58.154789 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-11 00:30:58.295546 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-11 00:30:58.407814 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-11 00:30:58.549317 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-11 00:30:58.691221 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-11 00:30:58.821326 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-11 00:30:58.948703 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-11 00:30:59.094529 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-11 00:30:59.233208 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-11 00:30:59.371626 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-11 00:30:59.510366 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-11 00:30:59.656426 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-11 00:30:59.79134 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-11 00:30:59.926028 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-11 00:31:00.072696 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-11 00:31:00.207516 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-11 00:31:00.339122 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-11 00:31:00.480439 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-11 00:31:00.612627 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-11 00:31:00.755116 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-11 00:31:00.89609 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-11 00:31:01.028816 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-11 00:31:01.161107 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-11 00:31:01.310333 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-11 00:31:01.452099 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-11 00:31:01.598463 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-11 00:31:01.745141 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-11 00:31:01.878877 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-11 00:31:02.021323 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-11 00:31:02.157331 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-11 00:31:02.290115 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-11 00:31:02.437866 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-11 00:31:02.592659 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-11 00:31:02.745966 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-11 00:31:02.887711 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-11 00:31:03.050372 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-11 00:31:03.189078 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-11 00:31:03.323856 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-11 00:31:03.484024 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-11 00:31:03.617364 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-11 00:31:03.746978 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-11 00:31:03.883626 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-11 00:31:04.02341 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-11 00:31:04.162579 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-11 00:31:04.295745 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-11 00:31:04.455063 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-11 00:31:04.598666 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-11 00:31:04.731098 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-11 00:31:04.873048 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-11 00:31:05.02732 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-11 00:31:05.171612 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-11 00:31:05.324557 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-11 00:31:05.494086 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-11 00:31:05.630961 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-11 00:31:05.748005 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-11 00:31:05.897933 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-11 00:31:06.044527 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-11 00:31:06.188212 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-11 00:31:06.332211 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-11 00:31:06.474428 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-11 00:31:06.523098 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-11 00:31:06.659536 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-11 00:31:06.804791 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-11 00:31:06.965083 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-11 00:31:07.11976 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-11 00:31:07.267221 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-11 00:31:07.407938 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-11 00:31:07.561974 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-11 00:31:07.709084 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-11 00:31:07.84547 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-11 00:31:08.0066 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-11 00:31:08.146402 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-11 00:31:08.286287 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-11 00:31:08.436216 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-11 00:31:08.570137 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-11 00:31:08.717595 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-11 00:31:08.900037 INFO::Counting total values for each feature
2024-07-11 00:31:08.92518 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-11 00:31:09.071917 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-11 00:31:09.217432 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-11 00:31:09.369709 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-11 00:31:09.445077 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-11 00:31:09.518091 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-11 00:31:09.524091 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-11 00:31:09.529687 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
31.167 0.597 31.755
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 83.145 | 0.855 | 83.944 | |