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Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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SSL certificate expiry #59

Closed adamp83 closed 6 years ago

adamp83 commented 6 years ago

Running any command for example GenomicDataCommons::status() gives the error

Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: certificate has expired

At the command line, running curl -v -I https://gdc-api.nci.nih.gov/status output includes:

* Server certificate:
*  subject: C=US; postalCode=60305; ST=IL; L=River Forest; street=400 Lathrop Avenue; O=Open Cloud Consortium; OU=PremiumSSL; CN=gdc-api.nci.nih.gov
*  start date: Jun 18 00:00:00 2015 GMT
*  expire date: Jun 17 23:59:59 2018 GMT
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=COMODO CA Limited; CN=COMODO RSA Organization Validation Secure Server CA
*  SSL certificate verify result: certificate has expired (10), continuing anyway.

Will the certificate be updated soon? If not, is there a workaround? Thanks

seandavi commented 6 years ago

I'll do the same, but consider reporting to the GDC folks. I'm traveling today, but I'll check for how to ignore certs in the short term. Thx for the report.

allisonheath commented 6 years ago

They have moved over to https://api.gdc.cancer.gov/status - I believe the *.nci.nih.gov URLs are depreciated.

seandavi commented 6 years ago

Upgrading to a newer version of GenomicDataCommons will fix the issue. I had missed that you were using an older version that still relied on the previous endpoint URL. Thanks for pointing out that detail.

adamp83 commented 6 years ago

Ah sorry I missed this - thought I was on the latest version but I hadn't updated R and bioconductor in a while. Thanks for the speedy support.

seandavi commented 6 years ago

@allisonheath, thanks for chipping in. I had missed that you were the one dropping the comment.