===============================
R CMD BUILD
===============================
* checking for file OMA/DESCRIPTION ... OK
* preparing OMA:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building stub.Rmd using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata,
e.g. by using --metadata pagetitle="..." on the command line.
Falling back to 'stub.knit'
--- finished re-building stub.Rmd
quarto render ../inst/
[1m[34m
[ 1/32] index.qmd[39m[22m
[31m
processing file: index.qmd
[39m1/3
2/3 [intro]
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[31moutput file: index.knit.md
[39mError adding css vars block SCSSParsingError: SCSS Parsing Error: Expecting punctuation: "}" (13299:53)
at cssVarsBlock (file:///opt/quarto/bin/quarto.js:87668:11)
at file:///opt/quarto/bin/quarto.js:88117:31
at file:///opt/quarto/bin/quarto.js:87850:29
at eventLoopTick (ext:core/01_core.js:178:7)
at async handleVarsBlock (file:///opt/quarto/bin/quarto.js:88130:23)
at async file:///opt/quarto/bin/quarto.js:88157:17
at async SassCache.setFromHash (file:///opt/quarto/bin/quarto.js:80672:7)
at async compileSass (file:///opt/quarto/bin/quarto.js:87960:19)
at async resolveSassBundles (file:///opt/quarto/bin/quarto.js:109337:17)
at async resolveExtras (file:///opt/quarto/bin/quarto.js:114166:14) {
name: "SCSSParsingError"
}
The resulting CSS file will not have SCSS color variables exported as CSS.
This is likely a Quarto bug.
Please consider reporting it at https://github.com/quarto-dev/quarto-cli,
along with the _quarto_internal_scss_error.scss file that can be found in the current working directory.
[1m[34m
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[31moutput file: intro.knit.md
[39m[1m[34m
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processing file: miaverse.qmd
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[31moutput file: miaverse.knit.md
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processing file: containers.qmd
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[31moutput file: containers.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
[39m[31mWarning: stack imbalance in 'vapply', 10 then 12
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processing file: import.qmd
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Data sets in package 'mia':
GlobalPatterns Global patterns of 16S rRNA diversity at a
depth of millions of sequences per sample.
HintikkaXOData Multiomics dataset from 40 rat samples
Tengeler2020 Gut microbiota profiles of 27 individuals
with ADHD and healthy controls
Tito2024QMP Fecal microbiota samples from 589 patients
across different colorectal cancer stages
dmn_se Twins' microbiome data from 278 individuals
enterotype Human gut microbiome dataset from 22 subjects
based on shotgun DNA sequencing
esophagus Human esophageal community from 3 individuals
ibdmdb IBDMDB 2-omic demo dataset (MGX + MTX)
peerj13075 Skin microbial profiles 58 genetically
unrelated individuals
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[31moutput file: import.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
[39m[31mWarning: stack imbalance in 'vapply', 10 then 12
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processing file: convert.qmd
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[31moutput file: convert.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
[39m[31mWarning: stack imbalance in 'vapply', 10 then 12
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processing file: taxonomy.qmd
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[31moutput file: taxonomy.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
[39m[31mWarning: stack imbalance in 'vapply', 10 then 12
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processing file: wrangling.qmd
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[31moutput file: wrangling.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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processing file: preprocess.qmd
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[31moutput file: preprocess.knit.md
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processing file: quality_control.qmd
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[31moutput file: quality_control.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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processing file: subsetting.qmd
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[31moutput file: subsetting.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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[31moutput file: agglomeration.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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[31moutput file: transformation.knit.md
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[31moutput file: composition.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
[39m[31mRegistered S3 method overwritten by 'seriation':
method from
reorder.hclust vegan
[39m[31mWarning: stack imbalance in 'vapply', 10 then 12
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processing file: alpha_diversity.qmd
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[31moutput file: alpha_diversity.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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processing file: community_similarity.qmd
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[31moutput file: community_similarity.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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[31mError in `UseMethod()`:
! no applicable method for 'as.dendrogram' applied to an object of class "NULL"
Backtrace:
1. stats::as.dendrogram(hclust_data)
[39m[31m
Quitting from clustering.qmd:124-155 [hclust2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'as.dendrogram' applied to an object of class "NULL"
---
Backtrace:
1. stats::as.dendrogram(hclust_data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39m[33mWARN: Error encountered when rendering files[39m
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted