Message-ID: <CAANT7+W=DbBsbLV0KD1a78r9ww-p73js91UseOZ72ObDrs3=2A@mail.gmail.com>
Date: 2025-10-09T01:27:16Z
From: Vincent Carey
Subject: [Bioc-devel] hipathia & hpAnnot failures
In-Reply-To: <DB9P194MB14347E03AA6884779BFC7A988EEEA@DB9P194MB1434.EURP194.PROD.OUTLOOK.COM>
The problem with "AH69111" in devel branch AnnotationHub can be mitigated by
installing the very latest BiocGenerics 0.55.3 from source. Thanks to
Herve Pages
for identifying the problem and providing a solution.
On Wed, Oct 8, 2025 at 8:05?PM Marta Hidalgo <marta.hidalgo at outlook.es> wrote:
>
> Dear all,
>
> Annotation package hpAnnot is failing in BioC 3.22
> <https://bioconductor.org/checkResults/3.22/data-annotation-LATEST/hpAnnot/nebbiolo2-checksrc.html>
> with error
>
> Error: processing vignette 'hpAnnot-vignette.Rmd' failed with diagnostics:
> there is no package called 'AnnotationHub'
> --- failed re-building ?hpAnnot-vignette.Rmd?
>
> I added the AnnotationHub dependency to the DESCRIPTION file, in case
> this may solve the problem, but it has been running for years as it was.
>
> Also, package hipathia is failing in BioC 3.22
> <https://bioconductor.org/checkResults/3.22/bioc-LATEST/hipathia/nebbiolo2-buildsrc.html>,
> may be due to the failure in hpAnnot, with error
>
> Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics:
> failed to load resource
> name: AH69111
> title: meta_graph_info_hsa_v2.rda
> reason: At vendor/cigraph/src/graph/iterators.c:828 : Cannot create iterator, invalid vertex ID. Invalid vertex ID
> --- failed re-building ?hipathia-vignette.Rmd?
>
> Hipathia imports file meta_graph_info_hsa_v2.rda from hpAnnot via
> AnnotationHub. But when I try to reproduce the error and get file
> AH69111 from AnnotationHub, I get another error:
>
> > library(AnnotationHub) > ah <- AnnotationHub() > hp <- query(ah,
> "hpAnnot") > hp[["AH69111"]]
>
> Error: failed to load resource name: AH69111 title:
> meta_graph_info_hsa_v2.rda reason: C stack usage 15925760 is too close
> to the limit
>
> With previous versions resource AH69111 is perfectly available, I don't
> understand what can be going on. Maybe I missed some AnnotationHub
> features update?
>
> Any help will be appreciated.
>
> Best wishes,
>
> Marta
>
>
> [[alternative HTML version deleted]]
>
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