Fix ensemblVEP.Rmd: guard API-dependent chunks against Ensembl REST failures

[Copilot]

The bioccheck / check (devel) CI job was failing because ensemblVEP.Rmd makes a live POST to https://rest.ensembl.org/vep/homo_sapiens/region during the package build. A transient HTTP 500 from Ensembl caused httr::stop_for_status() to throw, crashing vignette compilation.

Changes to vignettes/ensemblVEP.Rmd

• setup chunk: initialise vep_avail <- FALSE so the flag is always defined before any chunk references it.
• lksnv chunk: wrap vep_by_region() in tryCatch; on any error, emit a message and return NULL. Set vep_avail <- !is.null(res) and compute jans only on success.
• All API-dependent chunks (doj1, doj2, doj3, lktaaaa, lkmakeg, lkmc): add eval=vep_avail so they are skipped when the API is unavailable.

res = tryCatch(
    vep_by_region(r22[1:100], snv_only=FALSE, chk_max=FALSE),
    error = function(e) {
        message("Ensembl VEP REST API not available: ", conditionMessage(e))
        NULL
    }
)
vep_avail = !is.null(res)
if (vep_avail) jans = toJSON(content(res))

When the API is reachable the vignette renders in full; when it is not, the dependent chunks are skipped and the build succeeds.

The magick warnings in VariantAnnotation.Rmd are non-blocking and are expected to be addressed upstream in the bioconductor_docker image.