Lauren McIver
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 Multiple platform build/check report for BioC 3.20: simplified long |
|
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 | |