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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data LRBaseDbi
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* checking for file ‘LRBaseDbi/DESCRIPTION’ ... OK
* preparing ‘LRBaseDbi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘LRBaseDbi.Rnw’ using Sweave
LRBase.XXX.eg.db-type packages are deprecated since Bioconductor 3.14. Use AnnotationHub instead. For details, check the vignette of LRBaseDbi
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead
Error while performing HEAD request.
Proceeding without cache information.
Warning: download failed
web resource path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/AnnotationHub/file15e056edd12d9’
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [annotationhub.bioconductor.org]:
Connection timed out after 10003 milliseconds
Warning: bfcdownload() failed
rid: BFC1
file: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
reason: download failed
Warning: Could not check database for updates.
Database source currently unreachable.
This should only be a temporary interruption.
Using previously cached version.
Error: processing vignette 'LRBaseDbi.Rnw' failed with diagnostics:
chunk 2
Error in value[[3L]](cond) : failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10003 milliseconds
Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘LRBaseDbi.Rnw’
SUMMARY: processing the following file failed:
‘LRBaseDbi.Rnw’
Error: Vignette re-building failed.
Execution halted