Lauren McIver
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1cacd4c |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 2024-11-19 23:33:45 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 23:39:26 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 340.3 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 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 61.764 1.064 63.061
* 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-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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"
2024-11-19 23:38:59.707888 INFO::Writing function arguments to log file
2024-11-19 23:38:59.741083 INFO::Verifying options selected are valid
2024-11-19 23:38:59.769768 INFO::Determining format of input files
2024-11-19 23:38:59.771102 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-19 23:38:59.776211 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-19 23:38:59.777459 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-19 23:38:59.779805 INFO::Filter data based on min abundance and min prevalence
2024-11-19 23:38:59.780731 INFO::Total samples in data: 1595
2024-11-19 23:38:59.781625 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-19 23:38:59.791102 INFO::Total filtered features: 0
2024-11-19 23:38:59.792088 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-19 23:38:59.799589 INFO::Total filtered features with variance filtering: 0
2024-11-19 23:38:59.800553 INFO::Filtered feature names from variance filtering:
2024-11-19 23:38:59.801422 INFO::Running selected normalization method: TSS
2024-11-19 23:39:00.658811 INFO::Bypass z-score application to metadata
2024-11-19 23:39:00.66015 INFO::Running selected transform method: AST
2024-11-19 23:39:00.674478 INFO::Running selected analysis method: LM
2024-11-19 23:39:01.058966 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-19 23:39:01.323289 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-19 23:39:01.632884 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-19 23:39:01.752814 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-19 23:39:01.859472 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-19 23:39:01.962818 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-19 23:39:02.068428 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-19 23:39:02.167609 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-19 23:39:02.275691 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-19 23:39:02.380853 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-19 23:39:02.501952 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-19 23:39:02.606609 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-19 23:39:02.704282 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-19 23:39:02.796613 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-19 23:39:02.907802 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-19 23:39:03.015746 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-19 23:39:03.147835 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-19 23:39:03.247545 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-19 23:39:03.351405 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-19 23:39:03.466429 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-19 23:39:03.562035 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-19 23:39:03.657712 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-19 23:39:03.763493 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-19 23:39:03.869128 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-19 23:39:03.969315 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-19 23:39:04.07146 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-19 23:39:04.176757 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-19 23:39:04.271698 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-19 23:39:04.374305 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-19 23:39:04.474898 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-19 23:39:04.573875 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-19 23:39:04.665678 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-19 23:39:04.771245 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-19 23:39:04.869641 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-19 23:39:04.969253 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-19 23:39:05.067425 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-19 23:39:05.159959 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-19 23:39:05.255968 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-19 23:39:05.35687 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-19 23:39:05.445105 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-19 23:39:05.536756 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-19 23:39:05.642805 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-19 23:39:05.738202 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-19 23:39:05.833736 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-19 23:39:05.930079 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-19 23:39:06.02755 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-19 23:39:06.12123 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-19 23:39:06.218737 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-19 23:39:06.323953 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-19 23:39:06.416616 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-19 23:39:06.506656 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-19 23:39:06.602616 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-19 23:39:06.693023 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-19 23:39:06.789751 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-19 23:39:06.898244 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-19 23:39:06.988249 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-19 23:39:07.080803 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-19 23:39:07.187062 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-19 23:39:07.27394 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-19 23:39:07.36619 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-19 23:39:07.461627 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-19 23:39:07.554199 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-19 23:39:07.833242 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-19 23:39:07.927965 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-19 23:39:08.024404 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-19 23:39:08.124934 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-19 23:39:08.232021 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-19 23:39:08.334236 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-19 23:39:08.433387 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-19 23:39:08.541548 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-19 23:39:08.646562 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-19 23:39:08.749197 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-19 23:39:08.852349 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-19 23:39:08.94758 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-19 23:39:09.046013 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-19 23:39:09.154282 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-19 23:39:09.2542 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-19 23:39:09.357183 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-19 23:39:09.468253 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-19 23:39:09.569355 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-19 23:39:09.674101 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-19 23:39:09.780594 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-19 23:39:09.885312 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-19 23:39:09.988996 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-19 23:39:10.085129 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-19 23:39:10.18344 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-19 23:39:10.459873 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-19 23:39:10.562483 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-19 23:39:10.693341 INFO::Counting total values for each feature
2024-11-19 23:39:10.719913 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-19 23:39:10.80602 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-19 23:39:10.908078 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-19 23:39:11.018627 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-19 23:39:11.055121 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-19 23:39:11.074345 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-19 23:39:11.078984 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-19 23:39:11.084069 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"
2024-11-19 23:39:11.09547 INFO::Writing function arguments to log file
2024-11-19 23:39:11.101956 INFO::Verifying options selected are valid
2024-11-19 23:39:11.102936 INFO::Determining format of input files
2024-11-19 23:39:11.103954 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-19 23:39:11.116589 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-19 23:39:11.117718 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-11-19 23:39:11.119092 INFO::Filter data based on min abundance and min prevalence
2024-11-19 23:39:11.119899 INFO::Total samples in data: 1595
2024-11-19 23:39:11.120664 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-19 23:39:11.123749 INFO::Total filtered features: 0
2024-11-19 23:39:11.124586 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-19 23:39:11.130311 INFO::Total filtered features with variance filtering: 0
2024-11-19 23:39:11.131271 INFO::Filtered feature names from variance filtering:
2024-11-19 23:39:11.132094 INFO::Running selected normalization method: NONE
2024-11-19 23:39:11.132864 INFO::Bypass z-score application to metadata
2024-11-19 23:39:11.133607 INFO::Running selected transform method: AST
2024-11-19 23:39:11.143429 INFO::Running selected analysis method: LM
2024-11-19 23:39:11.144843 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-19 23:39:11.235112 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-19 23:39:11.326816 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-19 23:39:11.443232 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-19 23:39:11.537271 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-19 23:39:11.635255 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-19 23:39:11.737498 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-19 23:39:11.843323 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-19 23:39:11.940894 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-19 23:39:12.039362 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-19 23:39:12.141513 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-19 23:39:12.25059 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-19 23:39:12.346704 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-19 23:39:12.429104 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-19 23:39:12.539205 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-19 23:39:12.63664 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-19 23:39:12.746803 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-19 23:39:12.839414 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-19 23:39:12.938535 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-19 23:39:13.037966 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-19 23:39:13.138425 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-19 23:39:13.239918 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-19 23:39:13.339124 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-19 23:39:13.438569 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-19 23:39:13.542404 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-19 23:39:13.639426 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-19 23:39:13.73589 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-19 23:39:13.827768 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-19 23:39:13.938962 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-19 23:39:14.027175 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-19 23:39:14.113671 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-19 23:39:14.205977 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-19 23:39:14.306272 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-19 23:39:14.399542 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-19 23:39:14.487631 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-19 23:39:14.585844 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-19 23:39:14.691253 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-19 23:39:14.789014 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-19 23:39:14.886684 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-19 23:39:14.986523 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-19 23:39:15.084875 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-19 23:39:15.173059 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-19 23:39:15.268046 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-19 23:39:15.362787 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-19 23:39:15.462688 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-19 23:39:15.553792 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-19 23:39:15.642593 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-19 23:39:15.741389 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-19 23:39:15.82597 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-19 23:39:15.915821 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-19 23:39:16.005645 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-19 23:39:16.094597 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-19 23:39:16.187082 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-19 23:39:16.271842 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-19 23:39:16.364503 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-19 23:39:16.450655 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-19 23:39:16.537029 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-19 23:39:16.635316 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-19 23:39:16.72151 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-19 23:39:16.813171 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-19 23:39:16.910693 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-19 23:39:17.013281 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-19 23:39:17.10675 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-19 23:39:17.200473 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-19 23:39:17.299016 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-19 23:39:17.38744 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-19 23:39:17.482516 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-19 23:39:17.57701 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-19 23:39:17.655257 WARNING::Fitting problem for feature 67 a warning was issued
2024-11-19 23:39:17.758841 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-19 23:39:17.854866 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-19 23:39:17.950404 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-19 23:39:18.05306 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-19 23:39:18.144668 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-19 23:39:18.176882 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-19 23:39:18.270933 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-19 23:39:18.382815 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-19 23:39:18.475393 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-19 23:39:18.566078 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-19 23:39:18.662352 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-19 23:39:18.767116 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-19 23:39:18.860037 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-19 23:39:18.957663 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-19 23:39:19.050102 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-19 23:39:19.152033 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-19 23:39:19.240762 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-19 23:39:19.32977 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-19 23:39:19.419535 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-19 23:39:19.519907 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-19 23:39:19.612805 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-19 23:39:19.72578 INFO::Counting total values for each feature
2024-11-19 23:39:19.742634 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-19 23:39:19.825407 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-19 23:39:19.908797 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-19 23:39:20.011709 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-19 23:39:20.094879 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-19 23:39:20.145584 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-19 23:39:20.150625 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-19 23:39:20.164431 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
20.860 0.497 21.427
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 61.764 | 1.064 | 63.061 | |