[Bioc-devel] hipathia & hpAnnot failures
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
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Marta Hidalgo <marta.hidalgo at outlook.es>
Sent: Sunday, October 26, 2025 5:30 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] hipathia & hpAnnot failures
Sent: Sunday, October 26, 2025 5:30 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] hipathia & hpAnnot failures
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?: > 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?: >> Dear all, >> >> Annotation package hpAnnot is failing in BioC 3.22 >> <https://secure-web.cisco.com/1RTIpz7iNeBjs12XnaJq2ysfURNAtSktXIkmNmUCvYFjFixY606nR0nG7Cd6DWRghJaOJe1QpSGHwzS9D9a3y6LpV5CbO87nu5Uo1i8e69VIMVHO4vNSlG_vkutsCcZvsND3YmIv7Qv0SmfkEhTKEuOj_w1D-jeYVQhUrhA4wMrH4rK0FvBODQeFgJ6LsCaguzFFdLOivibz0S3p7GMfzSq0hWamiOjaTEgMSurDkDTjtbZKPe7CemjRAsuz4cN1zPe11iRAsaATU8TyLQba9A8MH2-f-Q4nrNmf8DV2eHPWIbDDpaeI-8FULydDmedl8/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.22%2Fdata-annotation-LATEST%2FhpAnnot%2Fnebbiolo2-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://secure-web.cisco.com/1fEZvK32RHVqAP14NEc-yXk7sZpEeHOR2j3vsArkG0i5AKNQUiQnm8ffXSwUTeKgFafwGsvHtNtNN8x2d4WK2vvCc6z_zMe85dM3KlDyGQnmpGLDcOYls_GtrklkiAUU-GcolrPUhVgPnFmtNFkZQpz9rL8QloIAJHt2PWi26-P9AL0es1zePDm7c4aTJgWJ1354M-dXWcsPSMLclHFre9Pqkulx32Q6vaiPeJB_AgOd_orYXQCOJhmBIarwlRxCeiNXtU3k5TV7Kre3HRW5KyFCBUz7VLcpXlagsZcJTvESpw2u57Y_GhgHzQ-u4oN3b/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.22%2Fbioc-LATEST%2Fhipathia%2Fnebbiolo2-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]] >> >> _______________________________________________ >> Bioc-devel at r-project.org mailing list >> https://secure-web.cisco.com/1TWiM2RUiTHvaCPMO7_eFwcztcIryMdjwJ4DxMr7-1YkOItrCan2hO8ROwI2j9Onv0nKe5Y6nCLjNygXtw6JZAYGd3NVBV9oATxncQWS_DI9MyFppPF_IlAjOlBjeiLaKQwqxuBZ_zCFDuoRQQKkQ0vSbtYn9p2VftxSUnpvNTwpKn3edA-2T_rRyFsWdNxDUyRs8GrTKDJTZaaNb8WbrqpoyV0ylA3LRXtHV6WqUK0EA7sAl7lkzBZReXbi2dVsCujJ6A9VH3hroQLibvUGyhJ6VucbLPBjedjQ_W1Sb8J75CBwzVfoqkIYAx5R0KAiJ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://secure-web.cisco.com/1TWiM2RUiTHvaCPMO7_eFwcztcIryMdjwJ4DxMr7-1YkOItrCan2hO8ROwI2j9Onv0nKe5Y6nCLjNygXtw6JZAYGd3NVBV9oATxncQWS_DI9MyFppPF_IlAjOlBjeiLaKQwqxuBZ_zCFDuoRQQKkQ0vSbtYn9p2VftxSUnpvNTwpKn3edA-2T_rRyFsWdNxDUyRs8GrTKDJTZaaNb8WbrqpoyV0ylA3LRXtHV6WqUK0EA7sAl7lkzBZReXbi2dVsCujJ6A9VH3hroQLibvUGyhJ6VucbLPBjedjQ_W1Sb8J75CBwzVfoqkIYAx5R0KAiJ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1TWiM2RUiTHvaCPMO7_eFwcztcIryMdjwJ4DxMr7-1YkOItrCan2hO8ROwI2j9Onv0nKe5Y6nCLjNygXtw6JZAYGd3NVBV9oATxncQWS_DI9MyFppPF_IlAjOlBjeiLaKQwqxuBZ_zCFDuoRQQKkQ0vSbtYn9p2VftxSUnpvNTwpKn3edA-2T_rRyFsWdNxDUyRs8GrTKDJTZaaNb8WbrqpoyV0ylA3LRXtHV6WqUK0EA7sAl7lkzBZReXbi2dVsCujJ6A9VH3hroQLibvUGyhJ6VucbLPBjedjQ_W1Sb8J75CBwzVfoqkIYAx5R0KAiJ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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