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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