Lauren McIver
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 2f9ea7a |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-23 11:38 -0400 (Tue, 23 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 1111/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.19.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2024-07-23 00:45:09 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 00:49:12 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 243.5 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-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 ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 85.141 0.881 86.006
* 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 4.4.1 (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"
2024-07-23 00:47:05.682729 INFO::Writing function arguments to log file
2024-07-23 00:47:05.721245 INFO::Verifying options selected are valid
2024-07-23 00:47:05.757654 INFO::Determining format of input files
2024-07-23 00:47:05.759019 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-23 00:47:05.763662 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-23 00:47:05.765001 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-23 00:47:05.767361 INFO::Filter data based on min abundance and min prevalence
2024-07-23 00:47:05.768276 INFO::Total samples in data: 1595
2024-07-23 00:47:05.769074 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-23 00:47:05.772867 INFO::Total filtered features: 0
2024-07-23 00:47:05.773819 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-23 00:47:05.787436 INFO::Total filtered features with variance filtering: 0
2024-07-23 00:47:05.788519 INFO::Filtered feature names from variance filtering:
2024-07-23 00:47:05.789331 INFO::Running selected normalization method: TSS
2024-07-23 00:47:06.988529 INFO::Bypass z-score application to metadata
2024-07-23 00:47:06.989748 INFO::Running selected transform method: AST
2024-07-23 00:47:07.006211 INFO::Running selected analysis method: LM
2024-07-23 00:47:07.525254 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-23 00:47:07.90235 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-23 00:47:08.050322 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-23 00:47:08.200397 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-23 00:47:08.358129 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-23 00:47:08.507408 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-23 00:47:08.655381 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-23 00:47:08.815939 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-23 00:47:08.935551 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-23 00:47:09.091187 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-23 00:47:09.200459 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-23 00:47:09.357352 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-23 00:47:09.49419 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-23 00:47:09.633943 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-23 00:47:09.797953 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-23 00:47:09.918108 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-23 00:47:10.07097 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-23 00:47:10.214659 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-23 00:47:10.36215 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-23 00:47:10.497381 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-23 00:47:10.654831 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-23 00:47:10.821851 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-23 00:47:10.967099 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-23 00:47:11.111844 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-23 00:47:11.26627 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-23 00:47:11.405859 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-23 00:47:11.545919 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-23 00:47:11.691441 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-23 00:47:11.84104 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-23 00:47:11.98277 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-23 00:47:12.133927 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-23 00:47:12.296882 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-23 00:47:12.449306 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-23 00:47:12.587842 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-23 00:47:12.742969 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-23 00:47:12.886809 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-23 00:47:13.033116 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-23 00:47:13.180109 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-23 00:47:13.327053 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-23 00:47:13.475402 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-23 00:47:13.654371 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-23 00:47:13.79615 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-23 00:47:13.949083 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-23 00:47:14.112208 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-23 00:47:14.261746 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-23 00:47:14.415217 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-23 00:47:14.566641 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-23 00:47:14.70453 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-23 00:47:14.848428 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-23 00:47:14.99195 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-23 00:47:15.147497 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-23 00:47:15.287199 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-23 00:47:15.446393 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-23 00:47:15.607828 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-23 00:47:15.752779 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-23 00:47:15.897188 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-23 00:47:16.052832 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-23 00:47:16.193432 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-23 00:47:16.341505 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-23 00:47:16.500583 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-23 00:47:16.641564 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-23 00:47:16.788165 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-23 00:47:16.93802 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-23 00:47:17.086604 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-23 00:47:17.237497 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-23 00:47:17.382995 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-23 00:47:17.525451 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-23 00:47:17.675165 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-23 00:47:17.816845 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-23 00:47:17.961949 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-23 00:47:18.10884 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-23 00:47:18.256146 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-23 00:47:18.413639 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-23 00:47:18.563617 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-23 00:47:19.013379 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-23 00:47:19.153247 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-23 00:47:19.290618 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-23 00:47:19.434009 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-23 00:47:19.596243 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-23 00:47:19.733812 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-23 00:47:19.871505 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-23 00:47:20.027179 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-23 00:47:20.176177 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-23 00:47:20.33047 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-23 00:47:20.477669 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-23 00:47:20.616925 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-23 00:47:20.753389 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-23 00:47:21.112787 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-23 00:47:21.252399 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-23 00:47:21.418895 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-23 00:47:21.617621 INFO::Counting total values for each feature
2024-07-23 00:47:21.664475 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-23 00:47:21.810234 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-23 00:47:21.961786 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-23 00:47:22.114097 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-23 00:47:22.171206 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-23 00:47:22.203753 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-23 00:47:22.209506 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-23 00:47:22.216186 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"
2024-07-23 00:47:22.229699 INFO::Writing function arguments to log file
2024-07-23 00:47:22.235506 INFO::Verifying options selected are valid
2024-07-23 00:47:22.236584 INFO::Determining format of input files
2024-07-23 00:47:22.237745 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-23 00:47:22.242914 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-23 00:47:22.244178 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-07-23 00:47:22.245923 INFO::Filter data based on min abundance and min prevalence
2024-07-23 00:47:22.246848 INFO::Total samples in data: 1595
2024-07-23 00:47:22.247729 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-23 00:47:22.251395 INFO::Total filtered features: 0
2024-07-23 00:47:22.25235 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-23 00:47:22.259686 INFO::Total filtered features with variance filtering: 0
2024-07-23 00:47:22.260714 INFO::Filtered feature names from variance filtering:
2024-07-23 00:47:22.261542 INFO::Running selected normalization method: NONE
2024-07-23 00:47:22.26233 INFO::Bypass z-score application to metadata
2024-07-23 00:47:22.263129 INFO::Running selected transform method: AST
2024-07-23 00:47:22.277361 INFO::Running selected analysis method: LM
2024-07-23 00:47:22.279011 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-23 00:47:22.420505 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-23 00:47:22.568872 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-23 00:47:22.701976 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-23 00:47:22.840857 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-23 00:47:22.979076 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-23 00:47:23.130458 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-23 00:47:23.266774 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-23 00:47:23.404445 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-23 00:47:23.546324 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-23 00:47:23.70009 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-23 00:47:23.814267 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-23 00:47:23.955506 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-23 00:47:24.087235 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-23 00:47:24.22263 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-23 00:47:24.362328 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-23 00:47:24.501991 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-23 00:47:24.61373 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-23 00:47:24.757573 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-23 00:47:24.911731 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-23 00:47:25.047252 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-23 00:47:25.176788 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-23 00:47:25.31881 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-23 00:47:25.465216 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-23 00:47:25.597065 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-23 00:47:25.72802 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-23 00:47:25.867526 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-23 00:47:26.009001 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-23 00:47:26.145703 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-23 00:47:26.281521 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-23 00:47:26.419052 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-23 00:47:26.546474 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-23 00:47:26.679829 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-23 00:47:26.818602 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-23 00:47:26.961602 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-23 00:47:27.089343 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-23 00:47:27.222037 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-23 00:47:27.355291 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-23 00:47:27.499444 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-23 00:47:27.632465 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-23 00:47:27.770743 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-23 00:47:27.911872 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-23 00:47:28.041791 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-23 00:47:28.175737 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-23 00:47:28.311466 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-23 00:47:28.446147 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-23 00:47:28.580909 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-23 00:47:28.725508 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-23 00:47:28.865478 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-23 00:47:28.992758 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-23 00:47:29.128838 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-23 00:47:29.274421 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-23 00:47:29.407512 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-23 00:47:29.548727 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-23 00:47:29.698365 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-23 00:47:29.823257 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-23 00:47:29.959337 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-23 00:47:30.097022 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-23 00:47:30.240562 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-23 00:47:30.369331 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-23 00:47:30.500984 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-23 00:47:30.636029 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-23 00:47:30.770561 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-23 00:47:30.899346 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-23 00:47:31.028232 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-23 00:47:31.164135 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-23 00:47:31.297007 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-23 00:47:31.439754 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-23 00:47:31.57094 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-23 00:47:31.680229 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-23 00:47:31.819167 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-23 00:47:31.95544 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-23 00:47:32.092288 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-23 00:47:32.230166 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-23 00:47:32.361103 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-23 00:47:32.407097 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-23 00:47:32.545841 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-23 00:47:32.67683 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-23 00:47:32.809466 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-23 00:47:32.941658 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-23 00:47:33.098728 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-23 00:47:33.229131 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-23 00:47:33.373582 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-23 00:47:33.519911 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-23 00:47:33.674063 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-23 00:47:33.819238 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-23 00:47:33.953445 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-23 00:47:34.088272 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-23 00:47:34.232614 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-23 00:47:34.363056 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-23 00:47:34.50218 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-23 00:47:34.663077 INFO::Counting total values for each feature
2024-07-23 00:47:34.694334 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-23 00:47:34.839434 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-23 00:47:34.984141 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-23 00:47:35.13648 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-23 00:47:35.210998 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-23 00:47:35.284057 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-23 00:47:35.289994 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-23 00:47:35.295675 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
30.315 0.467 30.774
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 85.141 | 0.881 | 86.006 | |