Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1106/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.19.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 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: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2024-06-10 23:42:47 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 23:45:36 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 169.0 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.19.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Maaslin2’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 90.04 1.647 91.948 * 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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" 2024-06-10 23:44:52.607969 INFO::Writing function arguments to log file 2024-06-10 23:44:52.65507 INFO::Verifying options selected are valid 2024-06-10 23:44:52.696596 INFO::Determining format of input files 2024-06-10 23:44:52.698409 INFO::Input format is data samples as rows and metadata samples as rows 2024-06-10 23:44:52.704496 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-06-10 23:44:52.706035 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2024-06-10 23:44:52.708491 INFO::Filter data based on min abundance and min prevalence 2024-06-10 23:44:52.709472 INFO::Total samples in data: 1595 2024-06-10 23:44:52.710349 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-06-10 23:44:52.722994 INFO::Total filtered features: 0 2024-06-10 23:44:52.724423 INFO::Filtered feature names from abundance and prevalence filtering: 2024-06-10 23:44:52.733696 INFO::Total filtered features with variance filtering: 0 2024-06-10 23:44:52.735038 INFO::Filtered feature names from variance filtering: 2024-06-10 23:44:52.735903 INFO::Running selected normalization method: TSS 2024-06-10 23:44:54.031905 INFO::Bypass z-score application to metadata 2024-06-10 23:44:54.033615 INFO::Running selected transform method: AST 2024-06-10 23:44:54.052777 INFO::Running selected analysis method: LM 2024-06-10 23:44:54.620647 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-06-10 23:44:55.032498 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-06-10 23:44:55.221459 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-06-10 23:44:55.392834 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-06-10 23:44:55.584004 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-06-10 23:44:55.760657 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-06-10 23:44:55.929325 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-06-10 23:44:56.107481 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-06-10 23:44:56.286477 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-06-10 23:44:56.464613 WARNING::Fitting problem for feature 9 a warning was issued 2024-06-10 23:44:56.641886 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-06-10 23:44:56.816985 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-06-10 23:44:56.983179 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-06-10 23:44:57.156459 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-06-10 23:44:57.325173 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-06-10 23:44:57.501338 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-06-10 23:44:57.67008 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-06-10 23:44:57.846108 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-06-10 23:44:58.023001 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-06-10 23:44:58.211339 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-06-10 23:44:58.370225 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-06-10 23:44:58.55286 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-06-10 23:44:58.737225 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-06-10 23:44:58.916404 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-06-10 23:44:59.094433 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-06-10 23:44:59.279274 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-06-10 23:44:59.457737 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-06-10 23:44:59.659079 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-06-10 23:44:59.832597 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-06-10 23:45:00.004796 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-06-10 23:45:00.19147 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-06-10 23:45:00.351886 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-06-10 23:45:00.535711 INFO::Fitting model to feature number 32, Prevotella.copri 2024-06-10 23:45:00.707084 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-06-10 23:45:00.894977 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-06-10 23:45:01.059942 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-06-10 23:45:01.245352 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-06-10 23:45:01.411933 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-06-10 23:45:01.598925 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-06-10 23:45:01.761209 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-06-10 23:45:01.935315 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-06-10 23:45:02.102808 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-06-10 23:45:02.279827 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-06-10 23:45:02.420172 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-06-10 23:45:02.586627 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-06-10 23:45:02.756044 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-06-10 23:45:02.933581 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-06-10 23:45:03.105489 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-06-10 23:45:03.567192 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-06-10 23:45:03.736089 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-06-10 23:45:03.905159 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-06-10 23:45:04.082798 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-06-10 23:45:04.249553 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-06-10 23:45:04.418703 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-06-10 23:45:04.899927 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-06-10 23:45:05.062818 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-06-10 23:45:05.239825 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-06-10 23:45:05.430838 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-06-10 23:45:05.605813 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-06-10 23:45:05.779624 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-06-10 23:45:05.948532 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-06-10 23:45:06.126236 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-06-10 23:45:06.291637 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-06-10 23:45:06.464447 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-06-10 23:45:06.644066 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-06-10 23:45:06.810169 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-06-10 23:45:06.976543 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-06-10 23:45:07.155511 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-06-10 23:45:07.310613 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-06-10 23:45:07.476996 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-06-10 23:45:07.663291 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-06-10 23:45:07.835005 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-06-10 23:45:07.993631 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-06-10 23:45:08.159468 INFO::Fitting model to feature number 73, Dialister.invisus 2024-06-10 23:45:08.324685 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-06-10 23:45:08.505845 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-06-10 23:45:08.678689 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-06-10 23:45:08.860069 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-06-10 23:45:09.042692 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-06-10 23:45:09.220752 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-06-10 23:45:09.724145 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-06-10 23:45:09.887196 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-06-10 23:45:10.063242 INFO::Fitting model to feature number 82, Escherichia.coli 2024-06-10 23:45:10.234995 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-06-10 23:45:10.423246 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-06-10 23:45:10.592694 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-06-10 23:45:10.7564 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-06-10 23:45:10.91715 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-06-10 23:45:11.141692 INFO::Counting total values for each feature 2024-06-10 23:45:11.179526 INFO::Writing filtered data to file output/features/filtered_data.tsv 2024-06-10 23:45:11.326777 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2024-06-10 23:45:11.500208 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2024-06-10 23:45:11.671378 INFO::Writing residuals to file output/fits/residuals.rds 2024-06-10 23:45:11.753588 INFO::Writing fitted values to file output/fits/fitted.rds 2024-06-10 23:45:11.797596 INFO::Writing extracted random effects to file output/fits/ranef.rds 2024-06-10 23:45:11.806857 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2024-06-10 23:45:11.815428 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" 2024-06-10 23:45:11.831666 INFO::Writing function arguments to log file 2024-06-10 23:45:11.838261 INFO::Verifying options selected are valid 2024-06-10 23:45:11.839331 INFO::Determining format of input files 2024-06-10 23:45:11.840474 INFO::Input format is data samples as rows and metadata samples as rows 2024-06-10 23:45:11.846458 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2024-06-10 23:45:11.847745 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2024-06-10 23:45:11.849383 INFO::Filter data based on min abundance and min prevalence 2024-06-10 23:45:11.850286 INFO::Total samples in data: 1595 2024-06-10 23:45:11.85109 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2024-06-10 23:45:11.855717 INFO::Total filtered features: 0 2024-06-10 23:45:11.856956 INFO::Filtered feature names from abundance and prevalence filtering: 2024-06-10 23:45:11.865772 INFO::Total filtered features with variance filtering: 0 2024-06-10 23:45:11.867124 INFO::Filtered feature names from variance filtering: 2024-06-10 23:45:11.867932 INFO::Running selected normalization method: NONE 2024-06-10 23:45:11.868696 INFO::Bypass z-score application to metadata 2024-06-10 23:45:11.869491 INFO::Running selected transform method: AST 2024-06-10 23:45:11.887208 INFO::Running selected analysis method: LM 2024-06-10 23:45:11.889087 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2024-06-10 23:45:12.058804 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2024-06-10 23:45:12.216361 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2024-06-10 23:45:12.370244 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2024-06-10 23:45:12.533044 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2024-06-10 23:45:12.71247 INFO::Fitting model to feature number 6, Bacteroides.caccae 2024-06-10 23:45:12.87907 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2024-06-10 23:45:13.04327 INFO::Fitting model to feature number 8, Bacteroides.dorei 2024-06-10 23:45:13.199267 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2024-06-10 23:45:13.372956 INFO::Fitting model to feature number 10, Bacteroides.faecis 2024-06-10 23:45:13.538266 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2024-06-10 23:45:13.676233 WARNING::Fitting problem for feature 11 a warning was issued 2024-06-10 23:45:13.85935 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2024-06-10 23:45:14.03242 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2024-06-10 23:45:14.165832 WARNING::Fitting problem for feature 13 a warning was issued 2024-06-10 23:45:14.335117 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2024-06-10 23:45:14.514044 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2024-06-10 23:45:14.694091 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2024-06-10 23:45:14.862926 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2024-06-10 23:45:15.030756 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2024-06-10 23:45:15.152871 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2024-06-10 23:45:15.257535 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2024-06-10 23:45:15.430354 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2024-06-10 23:45:15.585722 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2024-06-10 23:45:15.65263 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2024-06-10 23:45:15.719156 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2024-06-10 23:45:15.798194 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2024-06-10 23:45:15.891264 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2024-06-10 23:45:16.006609 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2024-06-10 23:45:16.18382 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2024-06-10 23:45:16.338021 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2024-06-10 23:45:16.488412 INFO::Fitting model to feature number 30, Paraprevotella.clara 2024-06-10 23:45:16.64803 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2024-06-10 23:45:16.82219 INFO::Fitting model to feature number 32, Prevotella.copri 2024-06-10 23:45:16.987673 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2024-06-10 23:45:17.142526 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2024-06-10 23:45:17.303001 INFO::Fitting model to feature number 35, Alistipes.putredinis 2024-06-10 23:45:17.508431 INFO::Fitting model to feature number 36, Alistipes.shahii 2024-06-10 23:45:17.671439 INFO::Fitting model to feature number 37, Alistipes.unclassified 2024-06-10 23:45:17.83714 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2024-06-10 23:45:18.013869 INFO::Fitting model to feature number 39, Clostridium.bolteae 2024-06-10 23:45:18.179808 INFO::Fitting model to feature number 40, Clostridium.citroniae 2024-06-10 23:45:18.335058 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2024-06-10 23:45:18.494584 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2024-06-10 23:45:18.653988 INFO::Fitting model to feature number 43, Clostridium.leptum 2024-06-10 23:45:18.832942 INFO::Fitting model to feature number 44, Clostridium.nexile 2024-06-10 23:45:19.001152 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2024-06-10 23:45:19.160097 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2024-06-10 23:45:19.326384 INFO::Fitting model to feature number 47, Eubacterium.eligens 2024-06-10 23:45:19.49339 INFO::Fitting model to feature number 48, Eubacterium.hallii 2024-06-10 23:45:19.652543 INFO::Fitting model to feature number 49, Eubacterium.rectale 2024-06-10 23:45:19.808156 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2024-06-10 23:45:19.95387 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2024-06-10 23:45:20.130001 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2024-06-10 23:45:20.27439 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2024-06-10 23:45:20.421628 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2024-06-10 23:45:20.578838 INFO::Fitting model to feature number 55, Ruminococcus.torques 2024-06-10 23:45:20.754364 INFO::Fitting model to feature number 56, Coprococcus.comes 2024-06-10 23:45:20.921505 INFO::Fitting model to feature number 57, Dorea.longicatena 2024-06-10 23:45:21.088738 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2024-06-10 23:45:21.251018 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2024-06-10 23:45:21.424312 INFO::Fitting model to feature number 60, Roseburia.hominis 2024-06-10 23:45:21.589158 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2024-06-10 23:45:21.743096 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2024-06-10 23:45:21.897078 INFO::Fitting model to feature number 63, Roseburia.unclassified 2024-06-10 23:45:22.056854 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2024-06-10 23:45:22.223472 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2024-06-10 23:45:22.381164 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2024-06-10 23:45:22.537261 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2024-06-10 23:45:22.994569 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2024-06-10 23:45:23.147055 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2024-06-10 23:45:23.307938 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2024-06-10 23:45:23.474876 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2024-06-10 23:45:23.647555 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2024-06-10 23:45:23.706301 WARNING::Fitting problem for feature 72 a warning was issued 2024-06-10 23:45:23.875501 INFO::Fitting model to feature number 73, Dialister.invisus 2024-06-10 23:45:24.042406 INFO::Fitting model to feature number 74, Veillonella.atypica 2024-06-10 23:45:24.208864 INFO::Fitting model to feature number 75, Veillonella.dispar 2024-06-10 23:45:24.381377 INFO::Fitting model to feature number 76, Veillonella.parvula 2024-06-10 23:45:24.541617 INFO::Fitting model to feature number 77, Veillonella.unclassified 2024-06-10 23:45:24.695086 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2024-06-10 23:45:24.85048 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2024-06-10 23:45:25.025615 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2024-06-10 23:45:25.185752 INFO::Fitting model to feature number 81, Bilophila.unclassified 2024-06-10 23:45:25.362204 INFO::Fitting model to feature number 82, Escherichia.coli 2024-06-10 23:45:25.522191 INFO::Fitting model to feature number 83, Escherichia.unclassified 2024-06-10 23:45:25.684825 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2024-06-10 23:45:25.839019 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2024-06-10 23:45:26.002928 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2024-06-10 23:45:26.180925 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2024-06-10 23:45:26.383836 INFO::Counting total values for each feature 2024-06-10 23:45:26.410973 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2024-06-10 23:45:26.556753 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2024-06-10 23:45:26.701731 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2024-06-10 23:45:26.874818 INFO::Writing residuals to file output2/fits/residuals.rds 2024-06-10 23:45:26.985916 INFO::Writing fitted values to file output2/fits/fitted.rds 2024-06-10 23:45:27.092773 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2024-06-10 23:45:27.10265 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2024-06-10 23:45:27.110624 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 35.061 0.831 35.917
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 90.040 | 1.647 | 91.948 | |