[Bioc-devel] hipathia & hpAnnot failures

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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