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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (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 1094/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.14.1  (landing page)
Lauren McIver
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_17
git_last_commit: cec4c89
git_last_commit_date: 2023-06-08 11:22:17 -0400 (Thu, 08 Jun 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for Maaslin2 on palomino3


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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

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)

Tests output

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 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin289.02 6.2395.61