Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:42 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1138/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.18.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: Maaslin2 |
Version: 1.18.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Maaslin2_1.18.0.tar.gz |
StartedAt: 2024-05-04 08:59:44 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 09:03:15 -0000 (Sat, 04 May 2024) |
EllapsedTime: 211.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Maaslin2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.18.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Maaslin2’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE maaslin2_association_plots: no visible binding for global variable ‘xnames’ Undefined global functions or variables: xnames * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Maaslin2 120.533 1.022 121.798 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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" 2024-05-04 09:02:24.563232 INFO::Writing function arguments to log file 2024-05-04 09:02:24.621368 INFO::Verifying options selected are valid 2024-05-04 09:02:24.669118 INFO::Determining format of input files 2024-05-04 09:02:24.671202 INFO::Input format is data samples as rows and metadata samples as rows 2024-05-04 09:02:24.679457 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-05-04 09:02:24.681532 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2024-05-04 09:02:24.685403 INFO::Filter data based on min abundance and min prevalence 2024-05-04 09:02:24.686901 INFO::Total samples in data: 1595 2024-05-04 09:02:24.688364 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-05-04 09:02:24.700059 INFO::Total filtered features: 0 2024-05-04 09:02:24.701824 INFO::Filtered feature names from abundance and prevalence filtering: 2024-05-04 09:02:24.745654 INFO::Total filtered features with variance filtering: 0 2024-05-04 09:02:24.747441 INFO::Filtered feature names from variance filtering: 2024-05-04 09:02:24.749027 INFO::Running selected normalization method: TSS 2024-05-04 09:02:26.333635 INFO::Bypass z-score application to metadata 2024-05-04 09:02:26.335254 INFO::Running selected transform method: AST 2024-05-04 09:02:26.360751 INFO::Running selected analysis method: LM 2024-05-04 09:02:27.014241 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-05-04 09:02:27.534368 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-05-04 09:02:27.787664 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-05-04 09:02:28.039517 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-05-04 09:02:28.69689 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-05-04 09:02:29.019024 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-05-04 09:02:29.301363 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-05-04 09:02:29.562304 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-05-04 09:02:29.784803 WARNING::Fitting problem for feature 8 a warning was issued 2024-05-04 09:02:30.156386 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-05-04 09:02:30.371772 WARNING::Fitting problem for feature 9 a warning was issued 2024-05-04 09:02:30.65863 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-05-04 09:02:30.895089 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-05-04 09:02:31.133181 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-05-04 09:02:31.397411 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-05-04 09:02:31.602913 WARNING::Fitting problem for feature 13 a warning was issued 2024-05-04 09:02:31.858848 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-05-04 09:02:32.10394 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-05-04 09:02:32.380121 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-05-04 09:02:32.622991 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-05-04 09:02:32.888067 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-05-04 09:02:33.150475 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-05-04 09:02:33.389702 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-05-04 09:02:33.649612 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-05-04 09:02:33.911869 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-05-04 09:02:34.482216 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-05-04 09:02:34.733394 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-05-04 09:02:34.991633 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-05-04 09:02:35.254581 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-05-04 09:02:35.497226 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-05-04 09:02:35.745163 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-05-04 09:02:36.008234 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-05-04 09:02:36.287221 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-05-04 09:02:36.531 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-05-04 09:02:36.800168 INFO::Fitting model to feature number 32, Prevotella.copri 2024-05-04 09:02:37.060793 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-05-04 09:02:37.321029 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-05-04 09:02:37.567177 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-05-04 09:02:37.794392 WARNING::Fitting problem for feature 35 a warning was issued 2024-05-04 09:02:38.050958 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-05-04 09:02:38.298105 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-05-04 09:02:38.555239 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-05-04 09:02:38.79126 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-05-04 09:02:39.027874 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-05-04 09:02:39.299271 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-05-04 09:02:39.56158 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-05-04 09:02:39.814941 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-05-04 09:02:40.069058 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-05-04 09:02:40.299342 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-05-04 09:02:40.537793 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-05-04 09:02:40.794564 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-05-04 09:02:41.052662 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-05-04 09:02:41.308836 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-05-04 09:02:41.563123 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-05-04 09:02:41.810491 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-05-04 09:02:42.062447 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-05-04 09:02:42.318364 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-05-04 09:02:42.584651 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-05-04 09:02:42.819823 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-05-04 09:02:43.089675 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-05-04 09:02:43.357013 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-05-04 09:02:43.609621 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-05-04 09:02:43.885952 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-05-04 09:02:44.142948 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-05-04 09:02:44.374487 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-05-04 09:02:44.619233 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-05-04 09:02:44.864988 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-05-04 09:02:45.121029 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-05-04 09:02:45.359448 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-05-04 09:02:45.605814 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-05-04 09:02:45.870098 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-05-04 09:02:46.101173 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-05-04 09:02:46.365035 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-05-04 09:02:46.652598 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-05-04 09:02:46.920819 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-05-04 09:02:47.165516 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-05-04 09:02:47.698002 INFO::Fitting model to feature number 73, Dialister.invisus 2024-05-04 09:02:47.935928 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-05-04 09:02:48.180398 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-05-04 09:02:48.438897 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-05-04 09:02:48.70591 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-05-04 09:02:48.958077 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-05-04 09:02:49.221647 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-05-04 09:02:49.782624 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-05-04 09:02:50.030822 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-05-04 09:02:50.298963 INFO::Fitting model to feature number 82, Escherichia.coli 2024-05-04 09:02:50.550933 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-05-04 09:02:50.783706 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-05-04 09:02:51.021106 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-05-04 09:02:51.265549 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-05-04 09:02:51.504432 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-05-04 09:02:51.817256 INFO::Counting total values for each feature 2024-05-04 09:02:51.878011 INFO::Writing filtered data to file output/features/filtered_data.tsv 2024-05-04 09:02:52.00472 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2024-05-04 09:02:52.133166 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2024-05-04 09:02:52.264161 INFO::Writing residuals to file output/fits/residuals.rds 2024-05-04 09:02:52.314031 INFO::Writing fitted values to file output/fits/fitted.rds 2024-05-04 09:02:52.341157 INFO::Writing extracted random effects to file output/fits/ranef.rds 2024-05-04 09:02:52.347329 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2024-05-04 09:02:52.354384 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" 2024-05-04 09:02:52.372397 INFO::Writing function arguments to log file 2024-05-04 09:02:52.380611 INFO::Verifying options selected are valid 2024-05-04 09:02:52.381948 INFO::Determining format of input files 2024-05-04 09:02:52.383443 INFO::Input format is data samples as rows and metadata samples as rows 2024-05-04 09:02:52.39068 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-05-04 09:02:52.39233 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2024-05-04 09:02:52.394616 INFO::Filter data based on min abundance and min prevalence 2024-05-04 09:02:52.395944 INFO::Total samples in data: 1595 2024-05-04 09:02:52.397155 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-05-04 09:02:52.40777 INFO::Total filtered features: 0 2024-05-04 09:02:52.409338 INFO::Filtered feature names from abundance and prevalence filtering: 2024-05-04 09:02:52.440566 INFO::Total filtered features with variance filtering: 0 2024-05-04 09:02:52.442082 INFO::Filtered feature names from variance filtering: 2024-05-04 09:02:52.44328 INFO::Running selected normalization method: NONE 2024-05-04 09:02:52.444423 INFO::Bypass z-score application to metadata 2024-05-04 09:02:52.445556 INFO::Running selected transform method: AST 2024-05-04 09:02:52.483405 INFO::Running selected analysis method: LM 2024-05-04 09:02:52.48614 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-05-04 09:02:52.718982 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-05-04 09:02:52.970952 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-05-04 09:02:53.207645 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-05-04 09:02:53.453055 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-05-04 09:02:53.685456 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-05-04 09:02:53.948007 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-05-04 09:02:54.181435 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-05-04 09:02:54.419841 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-05-04 09:02:54.648511 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-05-04 09:02:54.885031 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-05-04 09:02:55.140486 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-05-04 09:02:55.361782 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-05-04 09:02:55.589243 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-05-04 09:02:55.826781 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-05-04 09:02:56.059139 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-05-04 09:02:56.243618 WARNING::Fitting problem for feature 16 a warning was issued 2024-05-04 09:02:56.497797 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-05-04 09:02:56.750842 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-05-04 09:02:56.997983 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-05-04 09:02:57.246145 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-05-04 09:02:57.473143 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-05-04 09:02:57.709052 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-05-04 09:02:57.932239 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-05-04 09:02:58.143827 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-05-04 09:02:58.379288 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-05-04 09:02:58.60044 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-05-04 09:02:58.831282 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-05-04 09:02:59.05852 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-05-04 09:02:59.270446 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-05-04 09:02:59.491869 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-05-04 09:02:59.707952 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-05-04 09:02:59.936157 INFO::Fitting model to feature number 32, Prevotella.copri 2024-05-04 09:03:00.164601 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-05-04 09:03:00.389298 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-05-04 09:03:00.607744 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-05-04 09:03:00.846951 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-05-04 09:03:01.074704 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-05-04 09:03:01.316046 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-05-04 09:03:01.54051 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-05-04 09:03:01.778121 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-05-04 09:03:02.000386 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-05-04 09:03:02.226002 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-05-04 09:03:02.454745 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-05-04 09:03:02.679841 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-05-04 09:03:02.914919 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-05-04 09:03:03.138567 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-05-04 09:03:03.373246 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-05-04 09:03:03.600772 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-05-04 09:03:03.826543 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-05-04 09:03:04.049055 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-05-04 09:03:04.267815 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-05-04 09:03:04.486701 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-05-04 09:03:04.697916 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-05-04 09:03:04.899026 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-05-04 09:03:05.110977 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-05-04 09:03:05.336706 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-05-04 09:03:05.556548 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-05-04 09:03:05.784563 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-05-04 09:03:06.00049 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-05-04 09:03:06.253829 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-05-04 09:03:06.47522 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-05-04 09:03:06.699132 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-05-04 09:03:06.925464 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-05-04 09:03:07.143759 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-05-04 09:03:07.370996 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-05-04 09:03:07.583511 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-05-04 09:03:07.805132 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-05-04 09:03:07.986614 WARNING::Fitting problem for feature 67 a warning was issued 2024-05-04 09:03:08.231581 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-05-04 09:03:08.45249 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-05-04 09:03:08.684165 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-05-04 09:03:08.926576 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-05-04 09:03:09.146637 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-05-04 09:03:09.234055 WARNING::Fitting problem for feature 72 a warning was issued 2024-05-04 09:03:09.452557 INFO::Fitting model to feature number 73, Dialister.invisus 2024-05-04 09:03:09.6952 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-05-04 09:03:09.923838 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-05-04 09:03:10.148099 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-05-04 09:03:10.395314 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-05-04 09:03:10.629071 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-05-04 09:03:10.864593 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-05-04 09:03:11.092763 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-05-04 09:03:11.306287 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-05-04 09:03:11.548676 INFO::Fitting model to feature number 82, Escherichia.coli 2024-05-04 09:03:11.770862 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-05-04 09:03:12.003351 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-05-04 09:03:12.216878 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-05-04 09:03:12.438624 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-05-04 09:03:12.688386 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-05-04 09:03:12.954694 INFO::Counting total values for each feature 2024-05-04 09:03:13.010591 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2024-05-04 09:03:13.136366 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2024-05-04 09:03:13.263451 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2024-05-04 09:03:13.394955 INFO::Writing residuals to file output2/fits/residuals.rds 2024-05-04 09:03:13.461715 INFO::Writing fitted values to file output2/fits/fitted.rds 2024-05-04 09:03:13.527383 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2024-05-04 09:03:13.534044 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2024-05-04 09:03:13.540526 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 49.562 0.902 50.567
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 120.533 | 1.022 | 121.798 | |