Lauren McIver
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9daea4b |
| git_last_commit_date: 2021-05-19 12:45:06 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the Maaslin2 package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1013/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.6.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Maaslin2 |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Maaslin2_1.6.0.tar.gz |
| StartedAt: 2021-10-15 01:15:45 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:20:35 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 290.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Maaslin2_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Maaslin2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.6.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'::' or ':::' import not declared from: 'lme4'
Namespace in Imports field not imported from: 'MuMIn'
All declared Imports should be used.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Maaslin2 79.37 4.02 83.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Maaslin2 77.16 3.85 81.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.
Maaslin2.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Maaslin2_1.6.0.tar.gz && rm -rf Maaslin2.buildbin-libdir && mkdir Maaslin2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Maaslin2.buildbin-libdir Maaslin2_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Maaslin2_1.6.0.zip && rm Maaslin2_1.6.0.tar.gz Maaslin2_1.6.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
4 324k 4 16227 0 0 133k 0 0:00:02 --:--:-- 0:00:02 133k
100 324k 100 324k 0 0 1062k 0 --:--:-- --:--:-- --:--:-- 1061k
install for i386
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
Package version inconsistency detected.
glmmTMB was built with TMB version 1.7.21
Current TMB version is 1.7.22
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
** help
*** installing help indices
converting help for package 'Maaslin2'
finding HTML links ... done
Maaslin2 html
** 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
install for x64
* installing *source* package 'Maaslin2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Maaslin2' as Maaslin2_1.6.0.zip
* DONE (Maaslin2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Maaslin2' successfully unpacked and MD5 sums checked
|
Maaslin2.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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"
2021-10-15 01:19:18 INFO::Writing function arguments to log file
2021-10-15 01:19:18 INFO::Verifying options selected are valid
2021-10-15 01:19:18 INFO::Determining format of input files
2021-10-15 01:19:18 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-15 01:19:18 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-15 01:19:18 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2021-10-15 01:19:18 INFO::Filter data based on min abundance and min prevalence
2021-10-15 01:19:18 INFO::Total samples in data: 1595
2021-10-15 01:19:18 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-15 01:19:18 INFO::Total filtered features: 0
2021-10-15 01:19:18 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-15 01:19:18 INFO::Total filtered features with variance filtering: 0
2021-10-15 01:19:18 INFO::Filtered feature names from variance filtering:
2021-10-15 01:19:18 INFO::Running selected normalization method: TSS
2021-10-15 01:19:19 INFO::Bypass z-score application to metadata
2021-10-15 01:19:19 INFO::Running selected transform method: AST
2021-10-15 01:19:19 INFO::Running selected analysis method: LM
2021-10-15 01:19:20 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-15 01:19:21 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-15 01:19:21 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-15 01:19:21 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-15 01:19:21 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-15 01:19:21 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-15 01:19:22 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-15 01:19:22 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-15 01:19:22 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-15 01:19:22 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-15 01:19:22 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-15 01:19:23 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-15 01:19:23 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-15 01:19:23 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-15 01:19:23 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-15 01:19:23 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-15 01:19:23 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-15 01:19:24 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-15 01:19:24 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-15 01:19:24 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-15 01:19:24 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-15 01:19:24 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-15 01:19:25 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-15 01:19:25 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-15 01:19:25 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-15 01:19:25 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-15 01:19:25 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-15 01:19:26 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-15 01:19:26 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-15 01:19:26 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-15 01:19:26 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-15 01:19:26 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-15 01:19:26 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-15 01:19:27 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-15 01:19:27 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-15 01:19:27 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-15 01:19:27 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-15 01:19:27 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-15 01:19:27 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-15 01:19:28 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-15 01:19:28 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-15 01:19:28 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-15 01:19:28 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-15 01:19:29 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-15 01:19:29 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-15 01:19:29 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-15 01:19:29 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-15 01:19:29 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-15 01:19:29 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-15 01:19:30 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-15 01:19:30 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-15 01:19:30 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-15 01:19:30 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-15 01:19:30 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-15 01:19:30 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-15 01:19:31 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-15 01:19:31 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-15 01:19:31 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-15 01:19:31 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-15 01:19:31 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-15 01:19:31 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-15 01:19:32 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-15 01:19:32 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-15 01:19:32 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-15 01:19:32 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-15 01:19:32 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-15 01:19:32 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-15 01:19:33 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-15 01:19:33 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-15 01:19:33 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-15 01:19:33 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-15 01:19:33 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-15 01:19:33 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-15 01:19:34 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-15 01:19:34 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-15 01:19:34 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-15 01:19:34 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-15 01:19:34 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-15 01:19:34 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-15 01:19:35 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-15 01:19:35 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-15 01:19:35 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-15 01:19:35 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-15 01:19:35 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-15 01:19:36 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-15 01:19:36 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-15 01:19:36 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-15 01:19:36 INFO::Counting total values for each feature
2021-10-15 01:19:36 INFO::Writing residuals to file output/residuals.rds
2021-10-15 01:19:36 INFO::Writing fitted values to file output/fitted.rds
2021-10-15 01:19:36 INFO::Writing extracted random effects to file output/ranef.rds
2021-10-15 01:19:36 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2021-10-15 01:19:36 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"
2021-10-15 01:19:36 INFO::Writing function arguments to log file
2021-10-15 01:19:36 INFO::Verifying options selected are valid
2021-10-15 01:19:36 INFO::Determining format of input files
2021-10-15 01:19:36 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-15 01:19:36 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-15 01:19:36 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2021-10-15 01:19:36 INFO::Filter data based on min abundance and min prevalence
2021-10-15 01:19:36 INFO::Total samples in data: 1595
2021-10-15 01:19:36 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-15 01:19:36 INFO::Total filtered features: 0
2021-10-15 01:19:36 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-15 01:19:36 INFO::Total filtered features with variance filtering: 0
2021-10-15 01:19:36 INFO::Filtered feature names from variance filtering:
2021-10-15 01:19:36 INFO::Running selected normalization method: NONE
2021-10-15 01:19:36 INFO::Bypass z-score application to metadata
2021-10-15 01:19:36 INFO::Running selected transform method: AST
2021-10-15 01:19:36 INFO::Running selected analysis method: LM
2021-10-15 01:19:36 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-15 01:19:36 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-15 01:19:37 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-15 01:19:37 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-15 01:19:37 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-15 01:19:37 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-15 01:19:37 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-15 01:19:37 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-15 01:19:38 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-15 01:19:38 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-15 01:19:38 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-15 01:19:38 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-15 01:19:38 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-15 01:19:39 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-15 01:19:39 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-15 01:19:39 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-15 01:19:39 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-15 01:19:39 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-15 01:19:40 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-15 01:19:40 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-15 01:19:40 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-15 01:19:40 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-15 01:19:40 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-15 01:19:40 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-15 01:19:41 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-15 01:19:41 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-15 01:19:41 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-15 01:19:41 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-15 01:19:41 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-15 01:19:41 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-15 01:19:42 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-15 01:19:42 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-15 01:19:42 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-15 01:19:42 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-15 01:19:42 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-15 01:19:42 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-15 01:19:43 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-15 01:19:43 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-15 01:19:43 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-15 01:19:43 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-15 01:19:43 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-15 01:19:44 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-15 01:19:44 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-15 01:19:44 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-15 01:19:44 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-15 01:19:44 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-15 01:19:44 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-15 01:19:45 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-15 01:19:45 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-15 01:19:45 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-15 01:19:45 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-15 01:19:45 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-15 01:19:45 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-15 01:19:46 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-15 01:19:46 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-15 01:19:46 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-15 01:19:46 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-15 01:19:46 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-15 01:19:47 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-15 01:19:47 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-15 01:19:47 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-15 01:19:47 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-15 01:19:47 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-15 01:19:47 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-15 01:19:48 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-15 01:19:48 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-15 01:19:48 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-15 01:19:48 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-15 01:19:48 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-15 01:19:48 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-15 01:19:49 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-15 01:19:49 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-15 01:19:49 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-15 01:19:49 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-15 01:19:49 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-15 01:19:49 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-15 01:19:50 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-15 01:19:50 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-15 01:19:50 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-15 01:19:50 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-15 01:19:50 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-15 01:19:50 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-15 01:19:51 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-15 01:19:51 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-15 01:19:51 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-15 01:19:51 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-15 01:19:51 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-15 01:19:52 INFO::Counting total values for each feature
2021-10-15 01:19:52 INFO::Writing residuals to file output2/residuals.rds
2021-10-15 01:19:52 INFO::Writing fitted values to file output2/fitted.rds
2021-10-15 01:19:52 INFO::Writing extracted random effects to file output2/ranef.rds
2021-10-15 01:19:52 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2021-10-15 01:19:52 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 ]
>
>
> proc.time()
user system elapsed
35.25 0.62 35.86
|
Maaslin2.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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"
2021-10-15 01:19:54 INFO::Writing function arguments to log file
2021-10-15 01:19:54 INFO::Verifying options selected are valid
2021-10-15 01:19:54 INFO::Determining format of input files
2021-10-15 01:19:54 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-15 01:19:54 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-15 01:19:54 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2021-10-15 01:19:54 INFO::Filter data based on min abundance and min prevalence
2021-10-15 01:19:54 INFO::Total samples in data: 1595
2021-10-15 01:19:54 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-15 01:19:54 INFO::Total filtered features: 0
2021-10-15 01:19:54 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-15 01:19:54 INFO::Total filtered features with variance filtering: 0
2021-10-15 01:19:54 INFO::Filtered feature names from variance filtering:
2021-10-15 01:19:54 INFO::Running selected normalization method: TSS
2021-10-15 01:19:55 INFO::Bypass z-score application to metadata
2021-10-15 01:19:55 INFO::Running selected transform method: AST
2021-10-15 01:19:55 INFO::Running selected analysis method: LM
2021-10-15 01:19:55 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-15 01:19:56 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-15 01:19:56 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-15 01:19:56 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-15 01:19:56 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-15 01:19:57 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-15 01:19:57 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-15 01:19:57 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-15 01:19:57 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-15 01:19:57 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-15 01:19:58 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-15 01:19:58 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-15 01:19:58 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-15 01:19:58 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-15 01:19:58 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-15 01:19:59 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-15 01:19:59 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-15 01:19:59 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-15 01:19:59 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-15 01:19:59 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-15 01:20:00 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-15 01:20:00 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-15 01:20:00 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-15 01:20:00 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-15 01:20:00 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-15 01:20:00 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-15 01:20:01 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-15 01:20:01 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-15 01:20:01 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-15 01:20:01 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-15 01:20:01 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-15 01:20:01 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-15 01:20:02 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-15 01:20:02 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-15 01:20:02 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-15 01:20:02 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-15 01:20:03 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-15 01:20:03 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-15 01:20:03 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-15 01:20:03 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-15 01:20:03 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-15 01:20:03 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-15 01:20:04 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-15 01:20:04 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-15 01:20:04 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-15 01:20:04 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-15 01:20:04 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-15 01:20:04 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-15 01:20:05 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-15 01:20:05 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-15 01:20:05 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-15 01:20:05 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-15 01:20:05 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-15 01:20:05 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-15 01:20:06 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-15 01:20:06 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-15 01:20:06 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-15 01:20:06 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-15 01:20:06 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-15 01:20:07 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-15 01:20:07 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-15 01:20:07 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-15 01:20:07 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-15 01:20:07 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-15 01:20:08 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-15 01:20:08 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-15 01:20:08 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-15 01:20:08 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-15 01:20:08 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-15 01:20:08 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-15 01:20:09 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-15 01:20:09 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-15 01:20:09 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-15 01:20:09 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-15 01:20:09 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-15 01:20:09 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-15 01:20:10 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-15 01:20:10 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-15 01:20:10 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-15 01:20:10 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-15 01:20:10 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-15 01:20:11 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-15 01:20:11 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-15 01:20:11 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-15 01:20:11 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-15 01:20:11 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-15 01:20:12 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-15 01:20:12 INFO::Counting total values for each feature
2021-10-15 01:20:12 INFO::Writing residuals to file output/residuals.rds
2021-10-15 01:20:12 INFO::Writing fitted values to file output/fitted.rds
2021-10-15 01:20:12 INFO::Writing extracted random effects to file output/ranef.rds
2021-10-15 01:20:12 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2021-10-15 01:20:12 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"
2021-10-15 01:20:12 INFO::Writing function arguments to log file
2021-10-15 01:20:12 INFO::Verifying options selected are valid
2021-10-15 01:20:12 INFO::Determining format of input files
2021-10-15 01:20:12 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-15 01:20:12 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-15 01:20:12 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2021-10-15 01:20:12 INFO::Filter data based on min abundance and min prevalence
2021-10-15 01:20:12 INFO::Total samples in data: 1595
2021-10-15 01:20:12 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-15 01:20:12 INFO::Total filtered features: 0
2021-10-15 01:20:12 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-15 01:20:12 INFO::Total filtered features with variance filtering: 0
2021-10-15 01:20:12 INFO::Filtered feature names from variance filtering:
2021-10-15 01:20:12 INFO::Running selected normalization method: NONE
2021-10-15 01:20:12 INFO::Bypass z-score application to metadata
2021-10-15 01:20:12 INFO::Running selected transform method: AST
2021-10-15 01:20:12 INFO::Running selected analysis method: LM
2021-10-15 01:20:12 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-15 01:20:12 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-15 01:20:13 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-15 01:20:13 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-15 01:20:13 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-15 01:20:13 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-15 01:20:14 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-15 01:20:14 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-15 01:20:14 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-15 01:20:14 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-15 01:20:14 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-15 01:20:15 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-15 01:20:15 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-15 01:20:15 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-15 01:20:15 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-15 01:20:16 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-15 01:20:16 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-15 01:20:16 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-15 01:20:16 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-15 01:20:16 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-15 01:20:16 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-15 01:20:17 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-15 01:20:17 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-15 01:20:17 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-15 01:20:17 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-15 01:20:17 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-15 01:20:18 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-15 01:20:18 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-15 01:20:18 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-15 01:20:18 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-15 01:20:18 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-15 01:20:18 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-15 01:20:19 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-15 01:20:19 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-15 01:20:19 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-15 01:20:19 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-15 01:20:19 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-15 01:20:19 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-15 01:20:20 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-15 01:20:20 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-15 01:20:20 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-15 01:20:20 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-15 01:20:20 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-15 01:20:20 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-15 01:20:21 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-15 01:20:21 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-15 01:20:21 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-15 01:20:21 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-15 01:20:21 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-15 01:20:21 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-15 01:20:21 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-15 01:20:22 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-15 01:20:22 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-15 01:20:22 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-15 01:20:22 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-15 01:20:22 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-15 01:20:22 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-15 01:20:23 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-15 01:20:23 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-15 01:20:23 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-15 01:20:23 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-15 01:20:23 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-15 01:20:23 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-15 01:20:24 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-15 01:20:24 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-15 01:20:24 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-15 01:20:24 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-15 01:20:24 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-15 01:20:24 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-15 01:20:24 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-15 01:20:25 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-15 01:20:25 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-15 01:20:25 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-15 01:20:25 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-15 01:20:25 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-15 01:20:25 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-15 01:20:26 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-15 01:20:26 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-15 01:20:26 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-15 01:20:26 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-15 01:20:26 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-15 01:20:26 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-15 01:20:27 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-15 01:20:27 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-15 01:20:27 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-15 01:20:27 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-15 01:20:27 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-15 01:20:27 INFO::Counting total values for each feature
2021-10-15 01:20:27 INFO::Writing residuals to file output2/residuals.rds
2021-10-15 01:20:28 INFO::Writing fitted values to file output2/fitted.rds
2021-10-15 01:20:28 INFO::Writing extracted random effects to file output2/ranef.rds
2021-10-15 01:20:28 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2021-10-15 01:20:28 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 6 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
35.29 0.29 35.59
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Maaslin2.Rcheck/examples_i386/Maaslin2-Ex.timings
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Maaslin2.Rcheck/examples_x64/Maaslin2-Ex.timings
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