Lauren McIver
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 2f9ea7a |
| git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:14 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1102/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.19.0 (landing page) Lauren McIver
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the Maaslin2 package: - 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: 2024-05-19 17:36:45 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 17:39:33 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 167.5 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-mac-arm64/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 91.429 1.698 93.303
* 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-mac-arm64/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"
2024-05-19 17:38:50.900371 INFO::Writing function arguments to log file
2024-05-19 17:38:50.950348 INFO::Verifying options selected are valid
2024-05-19 17:38:50.992102 INFO::Determining format of input files
2024-05-19 17:38:50.993889 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-19 17:38:50.999882 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-19 17:38:51.001378 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-19 17:38:51.003811 INFO::Filter data based on min abundance and min prevalence
2024-05-19 17:38:51.004877 INFO::Total samples in data: 1595
2024-05-19 17:38:51.005747 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-19 17:38:51.018474 INFO::Total filtered features: 0
2024-05-19 17:38:51.020002 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-19 17:38:51.029169 INFO::Total filtered features with variance filtering: 0
2024-05-19 17:38:51.030459 INFO::Filtered feature names from variance filtering:
2024-05-19 17:38:51.031281 INFO::Running selected normalization method: TSS
2024-05-19 17:38:52.335175 INFO::Bypass z-score application to metadata
2024-05-19 17:38:52.336928 INFO::Running selected transform method: AST
2024-05-19 17:38:52.356573 INFO::Running selected analysis method: LM
2024-05-19 17:38:52.91855 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-19 17:38:53.33194 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-19 17:38:53.520716 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-19 17:38:53.692651 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-19 17:38:53.878396 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-19 17:38:54.050801 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-19 17:38:54.222106 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-19 17:38:54.399275 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-19 17:38:54.57069 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-19 17:38:54.748459 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-19 17:38:54.923106 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-19 17:38:55.097475 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-19 17:38:55.264924 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-19 17:38:55.440524 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-19 17:38:55.617634 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-19 17:38:55.804868 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-19 17:38:55.978941 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-19 17:38:56.158364 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-19 17:38:56.337961 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-19 17:38:56.53571 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-19 17:38:56.694698 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-19 17:38:56.872312 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-19 17:38:57.053715 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-19 17:38:57.227698 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-19 17:38:57.404209 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-19 17:38:57.586934 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-19 17:38:57.77156 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-19 17:38:58.240777 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-19 17:38:58.416373 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-19 17:38:58.586578 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-19 17:38:58.770664 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-19 17:38:58.942972 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-19 17:38:59.117679 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-19 17:38:59.288382 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-19 17:38:59.475565 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-19 17:38:59.633198 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-19 17:38:59.797473 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-19 17:38:59.975266 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-19 17:39:00.140226 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-19 17:39:00.295527 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-19 17:39:00.457254 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-19 17:39:00.64117 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-19 17:39:00.806643 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-19 17:39:00.979643 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-19 17:39:01.158064 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-19 17:39:01.317091 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-19 17:39:01.487742 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-19 17:39:01.665016 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-19 17:39:01.836495 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-19 17:39:01.997223 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-19 17:39:02.172523 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-19 17:39:02.336875 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-19 17:39:02.511742 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-19 17:39:02.675798 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-19 17:39:02.853783 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-19 17:39:03.021501 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-19 17:39:03.192492 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-19 17:39:03.369901 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-19 17:39:03.539702 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-19 17:39:03.709916 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-19 17:39:03.888994 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-19 17:39:04.049339 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-19 17:39:04.213034 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-19 17:39:04.396269 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-19 17:39:04.561559 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-19 17:39:04.726114 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-19 17:39:04.891837 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-19 17:39:05.069751 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-19 17:39:05.221516 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-19 17:39:05.387174 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-19 17:39:05.573343 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-19 17:39:05.751113 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-19 17:39:05.914457 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-19 17:39:06.087995 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-19 17:39:06.244802 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-19 17:39:06.407201 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-19 17:39:06.587104 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-19 17:39:06.753503 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-19 17:39:06.918682 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-19 17:39:07.388583 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-19 17:39:07.523971 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-19 17:39:07.600297 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-19 17:39:07.692944 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-19 17:39:07.768945 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-19 17:39:07.859489 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-19 17:39:08.001765 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-19 17:39:08.159889 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-19 17:39:08.322403 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-19 17:39:08.468873 INFO::Counting total values for each feature
2024-05-19 17:39:08.491475 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-19 17:39:08.605637 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-19 17:39:08.777464 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-19 17:39:08.949873 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-19 17:39:09.031678 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-19 17:39:09.075887 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-19 17:39:09.085395 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-19 17:39:09.094357 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"
2024-05-19 17:39:09.110734 INFO::Writing function arguments to log file
2024-05-19 17:39:09.11738 INFO::Verifying options selected are valid
2024-05-19 17:39:09.11841 INFO::Determining format of input files
2024-05-19 17:39:09.119524 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-19 17:39:09.125395 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-19 17:39:09.126752 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2024-05-19 17:39:09.128519 INFO::Filter data based on min abundance and min prevalence
2024-05-19 17:39:09.129515 INFO::Total samples in data: 1595
2024-05-19 17:39:09.130328 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-19 17:39:09.134946 INFO::Total filtered features: 0
2024-05-19 17:39:09.136149 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-19 17:39:09.157697 INFO::Total filtered features with variance filtering: 0
2024-05-19 17:39:09.15949 INFO::Filtered feature names from variance filtering:
2024-05-19 17:39:09.160494 INFO::Running selected normalization method: NONE
2024-05-19 17:39:09.161342 INFO::Bypass z-score application to metadata
2024-05-19 17:39:09.162156 INFO::Running selected transform method: AST
2024-05-19 17:39:09.178798 INFO::Running selected analysis method: LM
2024-05-19 17:39:09.180878 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-19 17:39:09.347462 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-19 17:39:09.51623 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-19 17:39:09.669581 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-19 17:39:09.840867 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-19 17:39:09.996974 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-19 17:39:10.163212 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-19 17:39:10.331522 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-19 17:39:10.487047 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-19 17:39:10.657018 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-19 17:39:10.818954 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-19 17:39:10.957143 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-19 17:39:11.146027 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-19 17:39:11.309114 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-19 17:39:11.456265 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-19 17:39:11.63456 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-19 17:39:11.801311 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-19 17:39:11.967419 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-19 17:39:12.130241 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-19 17:39:12.308994 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-19 17:39:12.472421 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-19 17:39:12.63817 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-19 17:39:12.798877 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-19 17:39:12.972759 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-19 17:39:13.159715 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-19 17:39:13.313471 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-19 17:39:13.484168 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-19 17:39:13.676062 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-19 17:39:13.837791 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-19 17:39:14.004809 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-19 17:39:14.177901 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-19 17:39:14.330396 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-19 17:39:14.492722 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-19 17:39:14.672588 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-19 17:39:14.837309 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-19 17:39:14.989682 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-19 17:39:15.161063 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-19 17:39:15.323432 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-19 17:39:15.485048 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-19 17:39:15.661559 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-19 17:39:15.829928 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-19 17:39:15.995473 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-19 17:39:16.170276 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-19 17:39:16.329117 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-19 17:39:16.490729 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-19 17:39:16.669016 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-19 17:39:16.831998 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-19 17:39:17.278612 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-19 17:39:17.444805 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-19 17:39:17.599573 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-19 17:39:17.761026 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-19 17:39:17.934338 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-19 17:39:18.078489 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-19 17:39:18.239957 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-19 17:39:18.382864 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-19 17:39:18.527658 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-19 17:39:18.687806 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-19 17:39:18.83925 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-19 17:39:18.995548 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-19 17:39:19.149572 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-19 17:39:19.315042 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-19 17:39:19.474425 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-19 17:39:19.623996 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-19 17:39:19.779559 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-19 17:39:19.945117 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-19 17:39:20.104415 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-19 17:39:20.259624 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-19 17:39:20.419629 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-19 17:39:20.586491 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-19 17:39:20.745587 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-19 17:39:20.896908 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-19 17:39:21.062275 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-19 17:39:21.246178 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-19 17:39:21.403842 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-19 17:39:21.460741 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-19 17:39:21.621921 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-19 17:39:21.783276 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-19 17:39:21.960222 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-19 17:39:22.117351 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-19 17:39:22.285164 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-19 17:39:22.44213 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-19 17:39:22.620653 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-19 17:39:22.781536 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-19 17:39:22.934645 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-19 17:39:23.102476 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-19 17:39:23.270478 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-19 17:39:23.419388 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-19 17:39:23.570431 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-19 17:39:23.732008 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-19 17:39:23.903643 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-19 17:39:24.10716 INFO::Counting total values for each feature
2024-05-19 17:39:24.137031 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-19 17:39:24.282384 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-19 17:39:24.42736 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-19 17:39:24.599679 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-19 17:39:24.710842 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-19 17:39:24.817895 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-19 17:39:24.827137 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-19 17:39:24.834063 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
34.574 0.757 35.351
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 91.429 | 1.698 | 93.303 | |