[Debian-med-packaging] Bug#862039: r-bioc-gviz: accesses the internet during build
edd at debian.org
Tue May 9 14:00:09 UTC 2017
On 9 May 2017 at 14:57, Andreas Tille wrote:
| 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 184.108.40.206, A 220.127.116.11, A 18.104.22.168, A 22.214.171.124, A 126.96.36.199, A 188.8.131.52, A 184.108.40.206, A 220.127.116.11 (298)
| > 00:00:03.306580 IP 5f02d4499efa.44448 > 18.104.22.168.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 22.214.171.124.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 > 126.96.36.199.https: Flags [.], ack 1, win 229, options [nop,nop,TS val 493652169 ecr 1448496045], length 0
| > 00:00:03.450001 IP 5f02d4499efa.44448 > 188.8.131.52.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 184.108.40.206.https > 5f02d4499efa.44448: Flags [.], ack 518, win 118, options [nop,nop,TS val 1448496060 ecr 493652195], length 0
| > 00:00:03.495857 IP 220.127.116.11.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
| Thus I'm forwarding the bug to Debian Science list for further advise.
I am fairly certain that this must be coming from the BioConductor side of
things. R does call 'home' when you 'R CMD check --as-cran', but we of
course do not do that during builds. We just call 'R CMD INSTALL ...'
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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