Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:17 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1094/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.14.1 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / 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. |
Package: Maaslin2 |
Version: 1.14.1 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Maaslin2_1.14.1.tar.gz |
StartedAt: 2023-10-16 03:35:51 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 03:38:37 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 166.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Maaslin2_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck' * using R version 4.3.1 (2023-06-16 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Maaslin2/DESCRIPTION' ... OK * this is package 'Maaslin2' version '1.14.1' * 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 * 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 89.02 6.23 95.61 * checking for unstated dependencies in 'tests' ... OK * checking tests ... 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 NOTE See 'F:/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck/00check.log' for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'Maaslin2' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** 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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 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" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2023-10-16 03:38:01.201302 INFO::Writing function arguments to log file 2023-10-16 03:38:01.236752 INFO::Verifying options selected are valid 2023-10-16 03:38:01.270279 INFO::Determining format of input files 2023-10-16 03:38:01.272585 INFO::Input format is data samples as rows and metadata samples as rows 2023-10-16 03:38:01.279382 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2023-10-16 03:38:01.281495 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2023-10-16 03:38:01.284643 INFO::Filter data based on min abundance and min prevalence 2023-10-16 03:38:01.286357 INFO::Total samples in data: 1595 2023-10-16 03:38:01.288039 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2023-10-16 03:38:01.293451 INFO::Total filtered features: 0 2023-10-16 03:38:01.295439 INFO::Filtered feature names from abundance and prevalence filtering: 2023-10-16 03:38:01.304192 INFO::Total filtered features with variance filtering: 0 2023-10-16 03:38:01.314047 INFO::Filtered feature names from variance filtering: 2023-10-16 03:38:01.315798 INFO::Running selected normalization method: TSS 2023-10-16 03:38:02.442672 INFO::Bypass z-score application to metadata 2023-10-16 03:38:02.445411 INFO::Running selected transform method: AST 2023-10-16 03:38:02.466621 INFO::Running selected analysis method: LM 2023-10-16 03:38:03.048968 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2023-10-16 03:38:03.511674 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2023-10-16 03:38:03.714026 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2023-10-16 03:38:03.884079 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2023-10-16 03:38:04.051791 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2023-10-16 03:38:04.199901 INFO::Fitting model to feature number 6, Bacteroides.caccae 2023-10-16 03:38:04.336551 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2023-10-16 03:38:04.466165 INFO::Fitting model to feature number 8, Bacteroides.dorei 2023-10-16 03:38:04.648751 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2023-10-16 03:38:04.852877 WARNING::Fitting problem for feature 9 a warning was issued 2023-10-16 03:38:05.003675 INFO::Fitting model to feature number 10, Bacteroides.faecis 2023-10-16 03:38:05.163567 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2023-10-16 03:38:05.337593 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2023-10-16 03:38:05.557272 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2023-10-16 03:38:05.735352 WARNING::Fitting problem for feature 13 a warning was issued 2023-10-16 03:38:05.883029 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2023-10-16 03:38:06.023398 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2023-10-16 03:38:06.162068 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2023-10-16 03:38:06.296282 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2023-10-16 03:38:06.439406 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2023-10-16 03:38:06.570677 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2023-10-16 03:38:06.693647 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2023-10-16 03:38:06.824523 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2023-10-16 03:38:07.027671 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2023-10-16 03:38:07.201667 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2023-10-16 03:38:07.349773 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2023-10-16 03:38:07.483693 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2023-10-16 03:38:07.634122 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2023-10-16 03:38:07.78028 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2023-10-16 03:38:07.916062 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2023-10-16 03:38:08.048318 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2023-10-16 03:38:08.227742 INFO::Fitting model to feature number 30, Paraprevotella.clara 2023-10-16 03:38:08.390091 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2023-10-16 03:38:08.559866 INFO::Fitting model to feature number 32, Prevotella.copri 2023-10-16 03:38:08.697878 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2023-10-16 03:38:08.827581 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2023-10-16 03:38:08.949921 INFO::Fitting model to feature number 35, Alistipes.putredinis 2023-10-16 03:38:09.099773 INFO::Fitting model to feature number 36, Alistipes.shahii 2023-10-16 03:38:09.229401 INFO::Fitting model to feature number 37, Alistipes.unclassified 2023-10-16 03:38:09.366074 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2023-10-16 03:38:09.493376 INFO::Fitting model to feature number 39, Clostridium.bolteae 2023-10-16 03:38:09.622833 INFO::Fitting model to feature number 40, Clostridium.citroniae 2023-10-16 03:38:09.760818 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2023-10-16 03:38:09.890071 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2023-10-16 03:38:10.024267 INFO::Fitting model to feature number 43, Clostridium.leptum 2023-10-16 03:38:10.185051 INFO::Fitting model to feature number 44, Clostridium.nexile 2023-10-16 03:38:10.337823 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2023-10-16 03:38:10.464044 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2023-10-16 03:38:10.599628 INFO::Fitting model to feature number 47, Eubacterium.eligens 2023-10-16 03:38:10.730726 INFO::Fitting model to feature number 48, Eubacterium.hallii 2023-10-16 03:38:10.862839 INFO::Fitting model to feature number 49, Eubacterium.rectale 2023-10-16 03:38:10.986431 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2023-10-16 03:38:11.131539 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2023-10-16 03:38:11.2612 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2023-10-16 03:38:11.405494 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2023-10-16 03:38:11.546287 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2023-10-16 03:38:11.68516 INFO::Fitting model to feature number 55, Ruminococcus.torques 2023-10-16 03:38:11.832674 INFO::Fitting model to feature number 56, Coprococcus.comes 2023-10-16 03:38:11.998792 INFO::Fitting model to feature number 57, Dorea.longicatena 2023-10-16 03:38:12.151379 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2023-10-16 03:38:12.294566 WARNING::Fitting problem for feature 58 a warning was issued 2023-10-16 03:38:12.455906 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2023-10-16 03:38:12.599308 INFO::Fitting model to feature number 60, Roseburia.hominis 2023-10-16 03:38:12.73442 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2023-10-16 03:38:12.860447 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2023-10-16 03:38:13.209598 INFO::Fitting model to feature number 63, Roseburia.unclassified 2023-10-16 03:38:13.344096 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2023-10-16 03:38:13.480891 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2023-10-16 03:38:13.608074 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2023-10-16 03:38:13.730442 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2023-10-16 03:38:13.847632 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2023-10-16 03:38:13.978739 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2023-10-16 03:38:14.129646 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2023-10-16 03:38:14.259327 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2023-10-16 03:38:14.387018 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2023-10-16 03:38:14.52141 INFO::Fitting model to feature number 73, Dialister.invisus 2023-10-16 03:38:14.644108 INFO::Fitting model to feature number 74, Veillonella.atypica 2023-10-16 03:38:14.772517 INFO::Fitting model to feature number 75, Veillonella.dispar 2023-10-16 03:38:14.896756 INFO::Fitting model to feature number 76, Veillonella.parvula 2023-10-16 03:38:15.023935 INFO::Fitting model to feature number 77, Veillonella.unclassified 2023-10-16 03:38:15.172046 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2023-10-16 03:38:15.302214 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2023-10-16 03:38:15.442211 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2023-10-16 03:38:15.563878 INFO::Fitting model to feature number 81, Bilophila.unclassified 2023-10-16 03:38:15.692674 INFO::Fitting model to feature number 82, Escherichia.coli 2023-10-16 03:38:15.823431 INFO::Fitting model to feature number 83, Escherichia.unclassified 2023-10-16 03:38:15.943388 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2023-10-16 03:38:16.089955 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2023-10-16 03:38:16.229347 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2023-10-16 03:38:16.349522 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2023-10-16 03:38:16.517638 INFO::Counting total values for each feature 2023-10-16 03:38:16.551903 INFO::Writing filtered data to file output/features/filtered_data.tsv 2023-10-16 03:38:16.814658 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2023-10-16 03:38:17.129054 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2023-10-16 03:38:17.46081 INFO::Writing residuals to file output/fits/residuals.rds 2023-10-16 03:38:17.502941 INFO::Writing fitted values to file output/fits/fitted.rds 2023-10-16 03:38:17.52612 INFO::Writing extracted random effects to file output/fits/ranef.rds 2023-10-16 03:38:17.532549 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2023-10-16 03:38:17.554493 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" 2023-10-16 03:38:17.592119 INFO::Writing function arguments to log file 2023-10-16 03:38:17.615825 INFO::Verifying options selected are valid 2023-10-16 03:38:17.618785 INFO::Determining format of input files 2023-10-16 03:38:17.621842 INFO::Input format is data samples as rows and metadata samples as rows 2023-10-16 03:38:17.632024 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2023-10-16 03:38:17.635124 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2023-10-16 03:38:17.639111 INFO::Filter data based on min abundance and min prevalence 2023-10-16 03:38:17.641926 INFO::Total samples in data: 1595 2023-10-16 03:38:17.644681 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2023-10-16 03:38:17.651559 INFO::Total filtered features: 0 2023-10-16 03:38:17.654648 INFO::Filtered feature names from abundance and prevalence filtering: 2023-10-16 03:38:17.666502 INFO::Total filtered features with variance filtering: 0 2023-10-16 03:38:17.669757 INFO::Filtered feature names from variance filtering: 2023-10-16 03:38:17.672637 INFO::Running selected normalization method: NONE 2023-10-16 03:38:17.675353 INFO::Bypass z-score application to metadata 2023-10-16 03:38:17.678188 INFO::Running selected transform method: AST 2023-10-16 03:38:17.711602 INFO::Running selected analysis method: LM 2023-10-16 03:38:17.715778 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2023-10-16 03:38:17.866504 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2023-10-16 03:38:18.012181 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2023-10-16 03:38:18.167828 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2023-10-16 03:38:18.30935 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2023-10-16 03:38:18.439231 INFO::Fitting model to feature number 6, Bacteroides.caccae 2023-10-16 03:38:18.573913 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2023-10-16 03:38:18.697891 INFO::Fitting model to feature number 8, Bacteroides.dorei 2023-10-16 03:38:18.828444 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2023-10-16 03:38:18.950904 INFO::Fitting model to feature number 10, Bacteroides.faecis 2023-10-16 03:38:19.100093 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2023-10-16 03:38:19.260138 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2023-10-16 03:38:19.385028 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2023-10-16 03:38:19.48992 WARNING::Fitting problem for feature 13 a warning was issued 2023-10-16 03:38:19.63307 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2023-10-16 03:38:19.75668 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2023-10-16 03:38:19.892972 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2023-10-16 03:38:20.027104 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2023-10-16 03:38:20.194927 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2023-10-16 03:38:20.355011 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2023-10-16 03:38:20.472739 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2023-10-16 03:38:20.660007 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2023-10-16 03:38:20.831906 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2023-10-16 03:38:20.993137 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2023-10-16 03:38:21.136125 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2023-10-16 03:38:21.259371 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2023-10-16 03:38:21.39615 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2023-10-16 03:38:21.519813 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2023-10-16 03:38:21.664356 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2023-10-16 03:38:21.783964 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2023-10-16 03:38:21.934005 INFO::Fitting model to feature number 30, Paraprevotella.clara 2023-10-16 03:38:22.094829 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2023-10-16 03:38:22.221981 INFO::Fitting model to feature number 32, Prevotella.copri 2023-10-16 03:38:22.353644 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2023-10-16 03:38:22.484973 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2023-10-16 03:38:22.606696 INFO::Fitting model to feature number 35, Alistipes.putredinis 2023-10-16 03:38:22.744901 INFO::Fitting model to feature number 36, Alistipes.shahii 2023-10-16 03:38:22.869923 INFO::Fitting model to feature number 37, Alistipes.unclassified 2023-10-16 03:38:22.990726 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2023-10-16 03:38:23.131429 INFO::Fitting model to feature number 39, Clostridium.bolteae 2023-10-16 03:38:23.246509 INFO::Fitting model to feature number 40, Clostridium.citroniae 2023-10-16 03:38:23.376527 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2023-10-16 03:38:23.513818 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2023-10-16 03:38:23.633994 INFO::Fitting model to feature number 43, Clostridium.leptum 2023-10-16 03:38:23.758871 INFO::Fitting model to feature number 44, Clostridium.nexile 2023-10-16 03:38:23.892953 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2023-10-16 03:38:24.014356 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2023-10-16 03:38:24.154143 INFO::Fitting model to feature number 47, Eubacterium.eligens 2023-10-16 03:38:24.270307 INFO::Fitting model to feature number 48, Eubacterium.hallii 2023-10-16 03:38:24.393963 INFO::Fitting model to feature number 49, Eubacterium.rectale 2023-10-16 03:38:24.523398 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2023-10-16 03:38:24.637642 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2023-10-16 03:38:24.773885 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2023-10-16 03:38:24.888356 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2023-10-16 03:38:25.020209 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2023-10-16 03:38:25.142442 INFO::Fitting model to feature number 55, Ruminococcus.torques 2023-10-16 03:38:25.287302 INFO::Fitting model to feature number 56, Coprococcus.comes 2023-10-16 03:38:25.413247 INFO::Fitting model to feature number 57, Dorea.longicatena 2023-10-16 03:38:25.541821 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2023-10-16 03:38:25.661843 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2023-10-16 03:38:25.788837 INFO::Fitting model to feature number 60, Roseburia.hominis 2023-10-16 03:38:25.91627 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2023-10-16 03:38:26.037024 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2023-10-16 03:38:26.198258 INFO::Fitting model to feature number 63, Roseburia.unclassified 2023-10-16 03:38:26.319281 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2023-10-16 03:38:26.439915 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2023-10-16 03:38:26.573243 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2023-10-16 03:38:26.689728 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2023-10-16 03:38:26.796063 WARNING::Fitting problem for feature 67 a warning was issued 2023-10-16 03:38:26.939418 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2023-10-16 03:38:27.062465 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2023-10-16 03:38:27.202267 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2023-10-16 03:38:27.332173 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2023-10-16 03:38:27.464978 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2023-10-16 03:38:27.511501 WARNING::Fitting problem for feature 72 a warning was issued 2023-10-16 03:38:27.636681 INFO::Fitting model to feature number 73, Dialister.invisus 2023-10-16 03:38:27.770589 INFO::Fitting model to feature number 74, Veillonella.atypica 2023-10-16 03:38:27.893524 INFO::Fitting model to feature number 75, Veillonella.dispar 2023-10-16 03:38:28.02926 INFO::Fitting model to feature number 76, Veillonella.parvula 2023-10-16 03:38:28.200901 INFO::Fitting model to feature number 77, Veillonella.unclassified 2023-10-16 03:38:28.376725 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2023-10-16 03:38:28.542245 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2023-10-16 03:38:28.692634 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2023-10-16 03:38:28.838956 INFO::Fitting model to feature number 81, Bilophila.unclassified 2023-10-16 03:38:28.973389 INFO::Fitting model to feature number 82, Escherichia.coli 2023-10-16 03:38:29.107699 INFO::Fitting model to feature number 83, Escherichia.unclassified 2023-10-16 03:38:29.251181 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2023-10-16 03:38:29.369762 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2023-10-16 03:38:29.501509 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2023-10-16 03:38:29.624797 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2023-10-16 03:38:29.783447 INFO::Counting total values for each feature 2023-10-16 03:38:29.806166 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2023-10-16 03:38:30.104931 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2023-10-16 03:38:30.375191 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2023-10-16 03:38:30.666728 INFO::Writing residuals to file output2/fits/residuals.rds 2023-10-16 03:38:30.723733 INFO::Writing fitted values to file output2/fits/fitted.rds 2023-10-16 03:38:30.778739 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2023-10-16 03:38:30.787271 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2023-10-16 03:38:30.805326 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 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 29.98 0.90 30.89
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 89.02 | 6.23 | 95.61 | |