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 <[email protected]> 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]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- The information in this email is intended only for the p...{{dropped:12}} _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
