Skip to content

[Bioc-devel] hipathia & hpAnnot failures

5 messages · Marta Hidalgo, Vincent Carey, Shepherd, Lori

Marta Hidalgo
# 
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:
"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
Vincent Carey
# 
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 <marta.hidalgo at outlook.es> wrote:

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      Marta Hidalgo
    

    

      
      #
    

  


  

      
Hi,

Thanks to Vincent Carey and Herv? 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 escribi?:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
14 days later

    

      
      

        


  

        

      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 escribi?:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
      #
    

  


  

      
I can assist with this request.  I apologize I did not see the other posting about uploading files.

The procedure for uploading files has changed.  Two questions before we proceed.


  1.
 How large is the total number of files needed to upload?  We would need this information to create a temporary upload space
  2.
We are encouraging data to be hosted outside Bioconductor space but still be listed in the AnnotationHub/ExperimentHub to handle download and caching.  Would it be appropriate to move these files to a location like zenodo or dryad?
  3.
 Why are graph objects considered and being included in AnnotationHub?

????

Cheers


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263