Lauren McIver
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:38 -0400 (Fri, 18 Oct 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" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 12.7.5 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: 1.18.0 |
| 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: 2024-10-17 01:56:56 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 02:00:59 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 243.5 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 22.04.5 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 84.88 0.804 85.626
* 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"
2024-10-17 01:58:52.168466 INFO::Writing function arguments to log file
2024-10-17 01:58:52.20701 INFO::Verifying options selected are valid
2024-10-17 01:58:52.242687 INFO::Determining format of input files
2024-10-17 01:58:52.244135 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-17 01:58:52.248899 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-17 01:58:52.250182 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-10-17 01:58:52.252548 INFO::Filter data based on min abundance and min prevalence
2024-10-17 01:58:52.253415 INFO::Total samples in data: 1595
2024-10-17 01:58:52.254234 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-17 01:58:52.258017 INFO::Total filtered features: 0
2024-10-17 01:58:52.259047 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-17 01:58:52.272734 INFO::Total filtered features with variance filtering: 0
2024-10-17 01:58:52.273718 INFO::Filtered feature names from variance filtering:
2024-10-17 01:58:52.274606 INFO::Running selected normalization method: TSS
2024-10-17 01:58:53.427925 INFO::Bypass z-score application to metadata
2024-10-17 01:58:53.429181 INFO::Running selected transform method: AST
2024-10-17 01:58:53.445215 INFO::Running selected analysis method: LM
2024-10-17 01:58:53.917423 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-17 01:58:54.267646 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-17 01:58:54.411326 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-17 01:58:54.555801 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-17 01:58:54.707178 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-17 01:58:54.848022 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-17 01:58:54.98958 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-17 01:58:55.132896 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-17 01:58:55.250794 WARNING::Fitting problem for feature 8 a warning was issued
2024-10-17 01:58:55.397545 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-17 01:58:55.507469 WARNING::Fitting problem for feature 9 a warning was issued
2024-10-17 01:58:55.661983 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-17 01:58:55.798034 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-17 01:58:55.935149 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-17 01:58:56.097035 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-17 01:58:56.211759 WARNING::Fitting problem for feature 13 a warning was issued
2024-10-17 01:58:56.356122 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-17 01:58:56.491307 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-17 01:58:56.636004 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-17 01:58:56.772143 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-17 01:58:56.911309 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-17 01:58:57.058582 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-17 01:58:57.189035 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-17 01:58:57.340778 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-17 01:58:57.487615 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-17 01:58:57.648838 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-17 01:58:57.788347 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-17 01:58:57.928575 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-17 01:58:58.076273 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-17 01:58:58.214741 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-17 01:58:58.357715 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-17 01:58:58.766837 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-17 01:58:58.907485 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-17 01:58:59.049595 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-17 01:58:59.207674 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-17 01:58:59.348558 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-17 01:58:59.495796 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-17 01:58:59.632046 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-17 01:58:59.780111 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-17 01:58:59.918761 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-17 01:59:00.057915 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-17 01:59:00.196868 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-17 01:59:00.333164 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-17 01:59:00.474623 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-17 01:59:00.617319 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-17 01:59:00.762894 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-17 01:59:00.903911 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-17 01:59:01.043438 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-17 01:59:01.181627 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-17 01:59:01.321896 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-17 01:59:01.475143 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-17 01:59:01.613293 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-17 01:59:01.755397 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-17 01:59:01.899798 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-17 01:59:02.05305 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-17 01:59:02.209916 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-17 01:59:02.376014 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-17 01:59:02.519417 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-17 01:59:02.673663 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-17 01:59:02.825372 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-17 01:59:02.965632 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-17 01:59:03.119781 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-17 01:59:03.259415 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-17 01:59:03.409133 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-17 01:59:03.553863 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-17 01:59:03.698882 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-17 01:59:03.836313 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-17 01:59:03.976144 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-17 01:59:04.106856 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-17 01:59:04.247542 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-17 01:59:04.374594 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-17 01:59:04.517689 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-17 01:59:04.659625 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-17 01:59:05.046654 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-17 01:59:05.180714 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-17 01:59:05.314917 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-17 01:59:05.452606 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-17 01:59:05.585312 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-17 01:59:05.720508 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-17 01:59:05.866515 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-17 01:59:06.002517 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-17 01:59:06.145928 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-17 01:59:06.292219 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-17 01:59:06.432735 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-17 01:59:06.571972 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-17 01:59:06.710732 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-17 01:59:06.845369 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-17 01:59:06.980201 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-17 01:59:07.114379 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-17 01:59:07.447572 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-17 01:59:07.619619 INFO::Counting total values for each feature
2024-10-17 01:59:07.650138 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-10-17 01:59:07.796436 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-10-17 01:59:07.947664 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-10-17 01:59:08.104626 INFO::Writing residuals to file output/fits/residuals.rds
2024-10-17 01:59:08.163657 INFO::Writing fitted values to file output/fits/fitted.rds
2024-10-17 01:59:08.196336 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-10-17 01:59:08.202298 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-10-17 01:59:08.209741 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"
2024-10-17 01:59:08.22586 INFO::Writing function arguments to log file
2024-10-17 01:59:08.232198 INFO::Verifying options selected are valid
2024-10-17 01:59:08.233318 INFO::Determining format of input files
2024-10-17 01:59:08.234513 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-17 01:59:08.239957 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-17 01:59:08.241132 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-10-17 01:59:08.242847 INFO::Filter data based on min abundance and min prevalence
2024-10-17 01:59:08.243765 INFO::Total samples in data: 1595
2024-10-17 01:59:08.244674 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-17 01:59:08.248664 INFO::Total filtered features: 0
2024-10-17 01:59:08.249705 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-17 01:59:08.257554 INFO::Total filtered features with variance filtering: 0
2024-10-17 01:59:08.258633 INFO::Filtered feature names from variance filtering:
2024-10-17 01:59:08.259564 INFO::Running selected normalization method: NONE
2024-10-17 01:59:08.260502 INFO::Bypass z-score application to metadata
2024-10-17 01:59:08.2614 INFO::Running selected transform method: AST
2024-10-17 01:59:08.29445 INFO::Running selected analysis method: LM
2024-10-17 01:59:08.296072 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-17 01:59:08.432916 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-17 01:59:08.567505 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-17 01:59:08.701061 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-17 01:59:08.844405 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-17 01:59:08.973573 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-17 01:59:09.108458 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-17 01:59:09.241396 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-17 01:59:09.382857 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-17 01:59:09.514721 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-17 01:59:09.647704 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-17 01:59:09.758788 WARNING::Fitting problem for feature 11 a warning was issued
2024-10-17 01:59:09.909214 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-17 01:59:10.037057 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-17 01:59:10.169769 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-17 01:59:10.303506 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-17 01:59:10.448245 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-17 01:59:10.554374 WARNING::Fitting problem for feature 16 a warning was issued
2024-10-17 01:59:10.686567 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-17 01:59:10.819796 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-17 01:59:10.959308 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-17 01:59:11.086595 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-17 01:59:11.223664 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-17 01:59:11.362663 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-17 01:59:11.49788 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-17 01:59:11.627502 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-17 01:59:11.761173 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-17 01:59:11.903574 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-17 01:59:12.036934 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-17 01:59:12.171113 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-17 01:59:12.540808 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-17 01:59:12.666444 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-17 01:59:12.80149 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-17 01:59:12.934201 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-17 01:59:13.077054 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-17 01:59:13.204294 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-17 01:59:13.337566 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-17 01:59:13.46651 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-17 01:59:13.599982 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-17 01:59:13.740554 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-17 01:59:13.872665 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-17 01:59:13.99969 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-17 01:59:14.127814 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-17 01:59:14.270223 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-17 01:59:14.402822 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-17 01:59:14.538112 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-17 01:59:14.672169 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-17 01:59:14.806046 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-17 01:59:14.952055 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-17 01:59:15.078603 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-17 01:59:15.211027 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-17 01:59:15.341671 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-17 01:59:15.470554 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-17 01:59:15.602607 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-17 01:59:15.723245 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-17 01:59:15.843434 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-17 01:59:15.985426 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-17 01:59:16.13536 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-17 01:59:16.278731 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-17 01:59:16.417449 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-17 01:59:16.553604 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-17 01:59:16.692247 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-17 01:59:16.81857 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-17 01:59:16.946424 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-17 01:59:17.075446 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-17 01:59:17.20682 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-17 01:59:17.345096 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-17 01:59:17.474728 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-17 01:59:17.603282 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-17 01:59:17.716288 WARNING::Fitting problem for feature 67 a warning was issued
2024-10-17 01:59:17.867211 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-17 01:59:17.998817 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-17 01:59:18.138479 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-17 01:59:18.275822 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-17 01:59:18.409048 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-17 01:59:18.462775 WARNING::Fitting problem for feature 72 a warning was issued
2024-10-17 01:59:18.599437 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-17 01:59:18.731663 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-17 01:59:18.864841 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-17 01:59:18.995837 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-17 01:59:19.38183 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-17 01:59:19.510854 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-17 01:59:19.645093 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-17 01:59:19.782342 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-17 01:59:19.921588 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-17 01:59:20.060136 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-17 01:59:20.190673 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-17 01:59:20.319207 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-17 01:59:20.451706 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-17 01:59:20.59919 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-17 01:59:20.742789 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-17 01:59:20.905641 INFO::Counting total values for each feature
2024-10-17 01:59:20.928701 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-10-17 01:59:21.073896 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-10-17 01:59:21.219117 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-10-17 01:59:21.375113 INFO::Writing residuals to file output2/fits/residuals.rds
2024-10-17 01:59:21.451054 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-10-17 01:59:21.524256 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-10-17 01:59:21.530173 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-10-17 01:59:21.535894 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
29.952 0.532 30.474
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 84.880 | 0.804 | 85.626 | |