[Bioc-devel] hipathia & hpAnnot failures

[Marta Hidalgo]

Hi,

Thanks to Vincent Carey and Hervé Pages, I am now able to reproduce my 
hipathia error on local:

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’

I am persuaded that this could be due to the need to update some igraph 
elements inside the RDA to the last igraph version. If this is so, I 
will need to upload some new files to AnnotationHub. Could you help me 
with this?

If anyone has any other thoughts, there will be welcomed.

Many thanks,

Marta


El 09/10/2025 a las 2:05, Marta Hidalgo escribió:
> 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
>
>
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>
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