bioclients

• New vep_variants_all() takes any number of variants, chunks them at the 200 VEP accepts per POST and dispatches the chunks through biohttp::post_json_many(). One row per input in input order; a failed chunk becomes rows of NA carrying the envelope status in status.
• vep_variants_all() puts the input in genome order and sends a repeated variant once, before chunking, rather than once per occurrence. A duplicate now always carries the same answer at every position it was asked at, which was not guaranteed before when duplicates could land in different chunks and see different transient failures. chunk_size and the row count and order the contract promises are unchanged. It also applies a default throttle (one request per second) so an unpaced burst does not trip Ensembl's rate limiter; pass throttle = NULL to disable it.

gnomAD

• New gnomad_frequency_by_id() looks a variant up by chrom-pos-ref-alt, which names one allele where an rsID names a site, and gnomad_frequencies() does the same for many ids, alias-batched and chunked like gnomad_constraints(). gnomad_variant_id() builds the id. The flat row from gnomad_parse_variant() carries exome and genome af, ac, an and nhomalt, a derived grpmax, faf95 and filters.
• The 25-alias cost cap was re-verified against the live API for the variant query. The cost is one per alias whatever the selection set.

ClinVar

• clinvar_classification() throttles by default at the documented E-utilities rate, 3 requests a second or 10 when NCBI_API_KEY is set, and sends tool and email read from BIOHTTP_CALLER_IDENTITY and BIOHTTP_CONTACT_EMAIL when they are set.

MyGene

• mygene_genes() chunks a list longer than the 1000 identifiers MyGene takes per POST, dispatches the chunks through biohttp::post_json_many() and merges the hits back in input order.

Packaging

Everything below is for the CRAN submission. Nothing here changes how the

package behaves, and no function's arguments or output shape moved.

• Every example that calls a service now runs under \donttest{} rather than \dontrun{}, 56 of them. \dontrun{} is for an example that genuinely cannot be executed, which none of these are: they are keyless public requests, a client returns an envelope rather than raising, and biohttp's disk cache is off unless a caller turns it on. So an example run with no network prints NULL and writes nothing.
• Every help page now cites the service behind it. The 29 service files each carry the canonical publication with a DOI and the service's own documentation URL, and the other topics in the file inherit it, so all 134 exported topics have a References section. Each DOI was resolved through CrossRef and checked against the title, author and pagination written here. uniprot_features() carries two, because it calls the EBI Proteins API on a different host to the rest of the file and both are worth naming.
• The Description field cites five of those references, for Ensembl, UniProt, gnomAD, Open Targets and AlphaFold DB, in the form CRAN asks for.
• biohttp is on CRAN now, at 0.1.2. So the Remotes: line is gone and we ask for biohttp (>= 0.1.2) instead. I ran the tests against the CRAN build rather than the newer one on GitHub, to be sure nothing here needs a version CRAN cannot give you.
• cran-comments.md records the submission notes.