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### Running command:
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### /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data HMP16SData
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* checking for file ‘HMP16SData/DESCRIPTION’ ... OK
* preparing ‘HMP16SData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HMP16SData.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
snapshotDate(): 2022-02-15
Attaching package: 'phyloseq'
The following object is masked from 'package:SummarizedExperiment':
distance
The following object is masked from 'package:Biobase':
sampleNames
The following object is masked from 'package:GenomicRanges':
distance
The following object is masked from 'package:IRanges':
distance
Attaching package: 'magrittr'
The following object is masked from 'package:GenomicRanges':
subtract
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:matrixStats':
count
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Registered S3 method overwritten by 'dendextend':
method from
rev.hclust vegan
---------------------
Welcome to dendextend version 1.15.2
Type citation('dendextend') for how to cite the package.
Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/
Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
You may ask questions at stackoverflow, use the r and dendextend tags:
https://stackoverflow.com/questions/tagged/dendextend
To suppress this message use: suppressPackageStartupMessages(library(dendextend))
---------------------
Attaching package: 'dendextend'
The following object is masked from 'package:stats':
cutree
========================================
circlize version 0.4.14
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
in R. Bioinformatics 2014.
This message can be suppressed by:
suppressPackageStartupMessages(library(circlize))
========================================
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: 'dbplyr'
The following objects are masked from 'package:dplyr':
ident, sql
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
Attaching package: 'gridExtra'
The following object is masked from 'package:dplyr':
combine
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
snapshotDate(): 2022-02-15
Quitting from lines 115-117 (HMP16SData.Rmd)
Error: processing vignette 'HMP16SData.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘HMP16SData.Rmd’
SUMMARY: processing the following file failed:
‘HMP16SData.Rmd’
Error: Vignette re-building failed.
Execution halted