[Bioc-devel] hipathia & hpAnnot failures

[Marta Hidalgo]

Hi,

I am trying to upload new files to AnnotationHub but last time was some 
years ago and I don't remember the procedure.

I am using aws, and I keep the code I used before:

aws --profile AnnotationContributor s3 cp [folder] 
s3://annotation-contributor/hpAnnot/[version] --recursive --acl public-read

However, I changed my laptop and now I get error "The config profile 
(AnnotationContributor) could not be found". Can anyone help me with that?

Thank you,

Marta


El 12/10/2025 a las 1:07, Marta Hidalgo escribió:
> 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
>>
>>
>>     [[alternative HTML version deleted]]
>>
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