Bambu stuck downloading

[Coracollar]

Hi,

I am trying to run bambu from flames for isoform identification on HPC and I keep having ssl errors:

1: In download.file(..., destfile = tmp_config, quiet = TRUE) :
URL 'https://bioconductor.org/config.yaml': status was 'Problem with the SSL CA cert (path? access rights?)'
2: In download.file(..., destfile = tmp_config, quiet = TRUE) :
URL 'https://bioconductor.org/config.yaml': status was 'Problem with the SSL CA cert (path? access rights?)'
3: In value[3L] :
Error in step isoform_identification: error in evaluating the argument 'table' in selecting a method for function '%in%': Bioconductor version cannot be validated; no internet connection? See

Apparently bambu tries to download a reference from bioconductor even though I already gave it a reference.

In order to troubleshoot this, IT at my work need to know if this download is being done by curl, git, wget or any other. Could you help me with this?

Additionally is there a way to avoid bambu to try to download from the internet?

Cheers,

Cora

[lingminhao]

Hi @Coracollar , it seems that your compute node had some restricted access or missing so standard certificate bundles that detect whether a website is safe to download data from.

The download is performed by libcurl, if you want to inform the IT.

For a quick fix, you may try out the following code to tell R to ignore security certificates, or you can change download method to wget instead of libcurl.

httr::set_config(httr::config(ssl_verifypeer = 0L)) options(rsconnect.check.certificate = FALSE)

options(download.file.method = "wget")

Feel free to let me know if the problem persists!