updated bioc version / avoid bioc in CI+CRAN

[aronatkins]

What is the long-term answer to this type of test fragility?

[aronatkins]

@hadley - any insight into why pak cannot install / find Biobase?

[hadley]

Can we use https://bioconductor.org/packages/release ?

[hadley]

@gaborcsardi any idea why pak isn't finding Biobase here? It's suspicious that it only happens on older R versions.

[gaborcsardi]

Seems like the main Bioconductor site is broken:

❯ curl -vL https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES
*   Trying 108.157.109.107:443...
* Connected to bioconductor.org (108.157.109.107) port 443 (#0)
* ALPN: offers h2
* ALPN: offers http/1.1
*  CAfile: /etc/ssl/cert.pem
*  CApath: none
* [CONN-0-0][CF-SSL] (304) (OUT), TLS handshake, Client hello (1):
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Server hello (2):
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Unknown (8):
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Certificate (11):
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, CERT verify (15):
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Finished (20):
* [CONN-0-0][CF-SSL] (304) (OUT), TLS handshake, Finished (20):
* SSL connection using TLSv1.3 / AEAD-AES128-GCM-SHA256
* ALPN: server did not agree on a protocol. Uses default.
* Server certificate:
*  subject: CN=*.bioconductor.org
*  start date: Aug 25 07:16:46 2022 GMT
*  expire date: Sep 26 07:16:46 2023 GMT
*  subjectAltName: host "bioconductor.org" matched cert's "bioconductor.org"
*  issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
*  SSL certificate verify ok.
> GET /packages/3.16/bioc/src/contrib/PACKAGES HTTP/1.1
> Host: bioconductor.org
> User-Agent: curl/7.87.0
> Accept: */*
>
* Mark bundle as not supporting multiuse
< HTTP/1.1 302 Moved Temporarily
< Content-Type: text/html; charset=iso-8859-1
< Content-Length: 384
< Connection: keep-alive
< Date: Sat, 12 Aug 2023 14:22:49 GMT
< Server: Apache/2.4.18 (Ubuntu)
< Location: https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES
< Cache-Control: max-age=600
< Expires: Sat, 12 Aug 2023 14:32:49 GMT
< X-Cache: Miss from cloudfront
< Via: 1.1 ce94d6e65a03f67ef06d53000e8a30b6.cloudfront.net (CloudFront)
< X-Amz-Cf-Pop: MAD56-P2
< X-Amz-Cf-Id: 3Ebr63Rf15lujn2Si8t2oWICqwE0FZrFoT3zFUs1ypApCA1s89AW2w==
<
* Ignoring the response-body
* Connection #0 to host bioconductor.org left intact
* Issue another request to this URL: 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
*   Trying 192.69.103.247:443...
* connect to 192.69.103.247 port 443 failed: Connection refused
*   Trying 192.69.103.246:443...
* connect to 192.69.103.246 port 443 failed: Connection refused
*   Trying 192.69.103.248:443...
* connect to 192.69.103.248 port 443 failed: Connection refused
* Failed to connect to mghp.osn.xsede.org port 443 after 2402 ms: Couldn't connect to server
* Closing connection 1
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 2402 ms: Couldn't connect to server

[aronatkins]

Community discussion about bioc mirror outage: https://support.bioconductor.org/p/9153734/

[aronatkins]

Updated bioc tests to skip in CI and CRAN and asked pak to ignore the bioc packages when installing test dependencies.