Re: [Bioc-devel] Errors on package post 3.18 deadline

2023-10-20 Thread Hervé Pagès
Hi Burak, On 10/20/23 21:12, Burak Ogan Mancarci wrote: > Hi, > > I am a developer working on the bioconductor package gemma.R > . > This is a API package that interacts with our servers and we had an > unfortunate case of

[Bioc-devel] Errors on package post 3.18 deadline

2023-10-20 Thread Burak Ogan Mancarci
Hi, I am a developer working on the bioconductor package gemma.R . This is a API package that interacts with our servers and we had an unfortunate case of updating our databases when the tests were running. I was wondering h

Re: [Bioc-devel] Failed to obtain 'hguid' cookie

2023-10-20 Thread Martin, Tiphaine via Bioc-devel
thank Herve for answering and pointing the discussion! Thanks, Tiphaine Tiphaine Martin Assistant Professor Department of Oncological Sciences The Tisch Cancer Institute at Mount Sinai Icahn School of Medicine at Mount Sinai Hess Cen

Re: [Bioc-devel] Failed to obtain 'hguid' cookie

2023-10-20 Thread Hervé Pagès
Hi Tiphaine, This is a known issue with the rtracklayer package. The issue itself is caused by a change that was made earlier this week on the UCSC servers. The rtracklayer issue is being discussed here https://github.com/lawremi/rtracklayer/issues/95. I'm waiting for my PR to be merged, hopef

[Bioc-devel] Failed to obtain 'hguid' cookie

2023-10-20 Thread Martin, Tiphaine via Bioc-devel
Hi, I have my package that failed to build its vignette because of failing to obtain 'hguid' cookie. Could you please tell me how I can solve this? thanks, Tiphaine Tiphaine Martin Assistant Professor Department of Oncological Sc

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

2023-10-20 Thread Chau, Reina
Hi Martin, Agreed that FMA [1] could be the cause. Anyhow, I had disabled that specific unit-test. That is the quickest fix right now to meet the Bioconductor 3.18 release date. I will try to revisit the C code that you mentioned and see if I can fix the problem. Thanks so much for your help!

Re: [Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine

2023-10-20 Thread Martin Grigorov
Hi Reina, I tried to debug it but without success! I think the problem is at https://code.bioconductor.org/browse/CaDrA/blob/devel/src/score_fun.c#L613 because it fails only with method = "ks_score" It does a lot of calculations with doubles and I am almost sure FMA [1] is to blame. You could try