[Debian-med-packaging] Bug#862039: r-bioc-gviz: accesses the internet during build

[Andreas Tille]

Hi Chris,

On Sun, May 07, 2017 at 06:06:10PM +0100, Chris Lamb wrote:
> 
> Whilst r-bioc-gviz builds successfully on unstable/amd64, according to
> Debian Policy 4.9 packages may not attempt network access during
> a build.
> 
>    00:00:00.000000 IP 5f02d4499efa.36140 > dns.z9.domain: 4778+ A? bioconductor.org. (34)
>    00:00:00.000051 IP 5f02d4499efa.36140 > dns.z9.domain: 45901+ AAAA? bioconductor.org. (34)
>    00:00:01.725656 IP dns.z9.domain > 5f02d4499efa.36140: 45901 0/1/0 (121)
>    00:00:03.219280 IP dns.z9.domain > 5f02d4499efa.36140: 4778 8/4/0 A 52.222.253.6, A 52.222.253.158, A 52.222.253.218, A 52.222.253.224, A 52.222.253.45, A 52.222.253.252, A 52.222.253.94, A 52.222.253.219 (298)
>    00:00:03.306580 IP 5f02d4499efa.44448 > 52.222.253.6.https: Flags [S], seq 4243355363, win 29200, options [mss 1460,sackOK,TS val 493652159 ecr 0,nop,wscale 7], length 0
>    00:00:03.347988 IP 52.222.253.6.https > 5f02d4499efa.44448: Flags [S.], seq 1407308632, ack 4243355364, win 28960, options [mss 1412,sackOK,TS val 1448496045 ecr 493652159,nop,wscale 8], length 0
>    00:00:03.348046 IP 5f02d4499efa.44448 > 52.222.253.6.https: Flags [.], ack 1, win 229, options [nop,nop,TS val 493652169 ecr 1448496045], length 0
>    00:00:03.450001 IP 5f02d4499efa.44448 > 52.222.253.6.https: Flags [P.], seq 1:518, ack 1, win 229, options [nop,nop,TS val 493652195 ecr 1448496045], length 517
>    00:00:03.491891 IP 52.222.253.6.https > 5f02d4499efa.44448: Flags [.], ack 518, win 118, options [nop,nop,TS val 1448496060 ecr 493652195], length 0
>    00:00:03.495857 IP 52.222.253.6.https > 5f02d4499efa.44448: Flags [.], seq 1:1401, ack 518, win 118, options [nop,nop,TS val 1448496060 ecr 493652195], length 1400
> 
>   [..]
> 
> The full build log (including tcpdump output) is attached.

I can confirm that the build log contains

  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't connect to server'

when using pbuilder or sbuild.  I guess the problem remained hidden
since so far nobody did a tcpdump while building the package and since
the build runs fine after checking that the resource is not available
nobody noticed so far.

I admit I'm a bit clueless how to fix the issue since the build process
of R packages is a bit "encapsulated" and I'm afraid about simply
seeking the said URL and patching it out.  I'm not sure about the
potential side effects for the resulting deb at package installation
time.

Thus I'm forwarding the bug to Debian Science list for further advise.

Kind regards

      Andreas.

-- 
http://fam-tille.de