Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-09 12:07 -0500 (Mon, 09 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 1130/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.20.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz |
StartedAt: 2024-12-06 23:31:41 -0500 (Fri, 06 Dec 2024) |
EndedAt: 2024-12-06 23:34:31 -0500 (Fri, 06 Dec 2024) |
EllapsedTime: 170.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.20.0’ * 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 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 91.67 1.693 93.556 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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" 2024-12-06 23:33:47.584201 INFO::Writing function arguments to log file 2024-12-06 23:33:47.631612 INFO::Verifying options selected are valid 2024-12-06 23:33:47.673669 INFO::Determining format of input files 2024-12-06 23:33:47.675599 INFO::Input format is data samples as rows and metadata samples as rows 2024-12-06 23:33:47.682197 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-12-06 23:33:47.683944 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2024-12-06 23:33:47.686522 INFO::Filter data based on min abundance and min prevalence 2024-12-06 23:33:47.687544 INFO::Total samples in data: 1595 2024-12-06 23:33:47.688392 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-12-06 23:33:47.701399 INFO::Total filtered features: 0 2024-12-06 23:33:47.702859 INFO::Filtered feature names from abundance and prevalence filtering: 2024-12-06 23:33:47.712736 INFO::Total filtered features with variance filtering: 0 2024-12-06 23:33:47.714563 INFO::Filtered feature names from variance filtering: 2024-12-06 23:33:47.715738 INFO::Running selected normalization method: TSS 2024-12-06 23:33:49.003491 INFO::Bypass z-score application to metadata 2024-12-06 23:33:49.005229 INFO::Running selected transform method: AST 2024-12-06 23:33:49.023614 INFO::Running selected analysis method: LM 2024-12-06 23:33:49.580338 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-12-06 23:33:49.993601 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-12-06 23:33:50.188414 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-12-06 23:33:50.367561 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-12-06 23:33:50.554185 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-12-06 23:33:50.725706 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-12-06 23:33:50.8994 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-12-06 23:33:51.085989 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-12-06 23:33:51.264509 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-12-06 23:33:51.446957 WARNING::Fitting problem for feature 9 a warning was issued 2024-12-06 23:33:51.620931 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-12-06 23:33:51.793938 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-12-06 23:33:51.960774 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-12-06 23:33:52.127816 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-12-06 23:33:52.306767 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-12-06 23:33:52.487501 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-12-06 23:33:52.662333 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-12-06 23:33:52.842434 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-12-06 23:33:53.023095 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-12-06 23:33:53.200986 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-12-06 23:33:53.356746 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-12-06 23:33:53.544397 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-12-06 23:33:53.726069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-12-06 23:33:53.900122 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-12-06 23:33:54.076455 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-12-06 23:33:54.257539 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-12-06 23:33:54.440513 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-12-06 23:33:54.634738 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-12-06 23:33:54.811288 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-12-06 23:33:54.984989 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-12-06 23:33:55.172086 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-12-06 23:33:55.337815 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-12-06 23:33:55.532126 INFO::Fitting model to feature number 32, Prevotella.copri 2024-12-06 23:33:55.709293 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-12-06 23:33:55.897163 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-12-06 23:33:56.058955 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-12-06 23:33:56.238107 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-12-06 23:33:56.403379 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-12-06 23:33:56.579732 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-12-06 23:33:56.735623 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-12-06 23:33:56.904228 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-12-06 23:33:57.084428 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-12-06 23:33:57.256289 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-12-06 23:33:57.440083 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-12-06 23:33:57.621103 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-12-06 23:33:57.78268 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-12-06 23:33:57.973016 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-12-06 23:33:58.431989 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-12-06 23:33:58.605869 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-12-06 23:33:58.770608 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-12-06 23:33:59.246689 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-12-06 23:33:59.413026 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-12-06 23:33:59.591233 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-12-06 23:33:59.768477 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-12-06 23:33:59.958453 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-12-06 23:34:00.120711 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-12-06 23:34:00.298788 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-12-06 23:34:00.488741 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-12-06 23:34:00.647888 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-12-06 23:34:00.826795 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-12-06 23:34:01.003585 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-12-06 23:34:01.166398 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-12-06 23:34:01.336107 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-12-06 23:34:01.52063 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-12-06 23:34:01.686929 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-12-06 23:34:01.850301 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-12-06 23:34:02.015975 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-12-06 23:34:02.130178 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-12-06 23:34:02.289294 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-12-06 23:34:02.469827 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-12-06 23:34:02.640656 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-12-06 23:34:02.811897 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-12-06 23:34:02.97888 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-12-06 23:34:03.141666 INFO::Fitting model to feature number 73, Dialister.invisus 2024-12-06 23:34:03.315059 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-12-06 23:34:03.480848 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-12-06 23:34:03.651894 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-12-06 23:34:03.832537 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-12-06 23:34:04.005525 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-12-06 23:34:04.195974 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-12-06 23:34:04.36767 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-12-06 23:34:04.548636 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-12-06 23:34:04.62594 INFO::Fitting model to feature number 82, Escherichia.coli 2024-12-06 23:34:04.713774 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-12-06 23:34:04.823321 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-12-06 23:34:04.937154 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-12-06 23:34:05.042598 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-12-06 23:34:05.207896 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-12-06 23:34:05.327462 INFO::Counting total values for each feature 2024-12-06 23:34:05.353849 INFO::Writing filtered data to file output/features/filtered_data.tsv 2024-12-06 23:34:05.502288 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2024-12-06 23:34:05.675444 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2024-12-06 23:34:05.853643 INFO::Writing residuals to file output/fits/residuals.rds 2024-12-06 23:34:05.940453 INFO::Writing fitted values to file output/fits/fitted.rds 2024-12-06 23:34:05.989696 INFO::Writing extracted random effects to file output/fits/ranef.rds 2024-12-06 23:34:05.999119 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2024-12-06 23:34:06.00852 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" 2024-12-06 23:34:06.025774 INFO::Writing function arguments to log file 2024-12-06 23:34:06.03288 INFO::Verifying options selected are valid 2024-12-06 23:34:06.034015 INFO::Determining format of input files 2024-12-06 23:34:06.035181 INFO::Input format is data samples as rows and metadata samples as rows 2024-12-06 23:34:06.041021 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-12-06 23:34:06.042345 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2024-12-06 23:34:06.04414 INFO::Filter data based on min abundance and min prevalence 2024-12-06 23:34:06.045493 INFO::Total samples in data: 1595 2024-12-06 23:34:06.046468 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-12-06 23:34:06.051492 INFO::Total filtered features: 0 2024-12-06 23:34:06.052818 INFO::Filtered feature names from abundance and prevalence filtering: 2024-12-06 23:34:06.069961 INFO::Total filtered features with variance filtering: 0 2024-12-06 23:34:06.071594 INFO::Filtered feature names from variance filtering: 2024-12-06 23:34:06.072462 INFO::Running selected normalization method: NONE 2024-12-06 23:34:06.073261 INFO::Bypass z-score application to metadata 2024-12-06 23:34:06.074059 INFO::Running selected transform method: AST 2024-12-06 23:34:06.113756 INFO::Running selected analysis method: LM 2024-12-06 23:34:06.116926 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-12-06 23:34:06.281965 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-12-06 23:34:06.444264 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-12-06 23:34:06.618517 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-12-06 23:34:06.781213 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-12-06 23:34:06.952183 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-12-06 23:34:07.12094 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-12-06 23:34:07.28234 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-12-06 23:34:07.450215 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-12-06 23:34:07.609794 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-12-06 23:34:07.786858 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-12-06 23:34:07.923527 WARNING::Fitting problem for feature 11 a warning was issued 2024-12-06 23:34:08.136431 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-12-06 23:34:08.301561 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-12-06 23:34:08.436768 WARNING::Fitting problem for feature 13 a warning was issued 2024-12-06 23:34:08.625603 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-12-06 23:34:08.785993 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-12-06 23:34:08.953851 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-12-06 23:34:09.126914 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-12-06 23:34:09.291901 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-12-06 23:34:09.45623 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-12-06 23:34:09.628165 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-12-06 23:34:09.787271 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-12-06 23:34:09.958069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-12-06 23:34:10.136749 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-12-06 23:34:10.291978 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-12-06 23:34:10.467874 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-12-06 23:34:10.626049 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-12-06 23:34:10.783957 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-12-06 23:34:10.961412 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-12-06 23:34:11.117223 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-12-06 23:34:11.283704 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-12-06 23:34:11.442302 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-12-06 23:34:11.613918 INFO::Fitting model to feature number 32, Prevotella.copri 2024-12-06 23:34:11.780327 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-12-06 23:34:11.952194 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-12-06 23:34:12.120428 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-12-06 23:34:12.296413 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-12-06 23:34:12.462537 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-12-06 23:34:12.647273 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-12-06 23:34:12.807802 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-12-06 23:34:12.97177 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-12-06 23:34:13.140811 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-12-06 23:34:13.298202 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-12-06 23:34:13.477613 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-12-06 23:34:13.640796 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-12-06 23:34:13.805683 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-12-06 23:34:13.986261 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-12-06 23:34:14.149813 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-12-06 23:34:14.310792 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-12-06 23:34:14.486586 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-12-06 23:34:14.643667 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-12-06 23:34:14.79159 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-12-06 23:34:14.966885 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-12-06 23:34:15.112451 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-12-06 23:34:15.274642 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-12-06 23:34:15.430673 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-12-06 23:34:15.590518 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-12-06 23:34:15.772039 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-12-06 23:34:15.930341 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-12-06 23:34:16.105064 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-12-06 23:34:16.27157 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-12-06 23:34:16.423304 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-12-06 23:34:16.592715 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-12-06 23:34:16.744586 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-12-06 23:34:16.91601 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-12-06 23:34:17.073426 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-12-06 23:34:17.254871 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-12-06 23:34:17.413833 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-12-06 23:34:17.576585 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-12-06 23:34:17.749559 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-12-06 23:34:17.916143 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-12-06 23:34:18.090242 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-12-06 23:34:18.268164 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-12-06 23:34:18.325698 WARNING::Fitting problem for feature 72 a warning was issued 2024-12-06 23:34:18.485099 INFO::Fitting model to feature number 73, Dialister.invisus 2024-12-06 23:34:18.660768 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-12-06 23:34:18.821281 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-12-06 23:34:18.999707 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-12-06 23:34:19.166561 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-12-06 23:34:19.323418 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-12-06 23:34:19.497483 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-12-06 23:34:19.66292 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-12-06 23:34:19.834699 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-12-06 23:34:20.003673 INFO::Fitting model to feature number 82, Escherichia.coli 2024-12-06 23:34:20.174259 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-12-06 23:34:20.325938 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-12-06 23:34:20.497505 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-12-06 23:34:20.654101 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-12-06 23:34:20.834952 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-12-06 23:34:21.033449 INFO::Counting total values for each feature 2024-12-06 23:34:21.059982 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2024-12-06 23:34:21.205283 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2024-12-06 23:34:21.352225 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2024-12-06 23:34:21.525991 INFO::Writing residuals to file output2/fits/residuals.rds 2024-12-06 23:34:21.636584 INFO::Writing fitted values to file output2/fits/fitted.rds 2024-12-06 23:34:22.034643 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2024-12-06 23:34:22.045313 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2024-12-06 23:34:22.052 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 4 | SKIP 0 | PASS 12 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 35.038 0.795 35.874
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 91.670 | 1.693 | 93.556 | |