Bug#862039: r-bioc-gviz: accesses the internet during build
Hi Andreas, > you have set severity important. Should I file an unblock request > anyway? No; it is not release critical, in both the technical and practical senses of that term IMHO. :) Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
Bug#862039: r-bioc-gviz: accesses the internet during build
Hi Chris, On Tue, May 09, 2017 at 04:03:43PM +0100, Chris Lamb wrote: > > Just in case it helps, in other packages I've seen that exporting an > HTTP_PROXY environment variable to some deliberately broken or empty > value has prevented these calls… > > … but YMMV, untested, etc. :) Not tested with tcpdump but the solution sounds convincing. BTW, you have set severity important. Should I file an unblock request anyway? Kind regards Andreas. -- http://fam-tille.de
Bug#862039: r-bioc-gviz: accesses the internet during build
Andreas Tille wrote: > the gviz package received a bug report about trying to access a remote > location at package build time which is forbidden by Debian policy. […] > Do you have any hints how this access could be prevented? Just in case it helps, in other packages I've seen that exporting an HTTP_PROXY environment variable to some deliberately broken or empty value has prevented these calls… … but YMMV, untested, etc. :) Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
Bug#862039: r-bioc-gviz: accesses the internet during build
Hi, the gviz package received a bug report about trying to access a remote location at package build time which is forbidden by Debian policy. I wonder if there is an easy way to prevent this. Due to so called Build-Depends it is granted that biocinstaller code is installed on the building machine so there should be no reason to access http://bioconductor.org/BiocInstaller.dcf at least for my possibly naive understanding. Do you have any hints how this access could be prevented? Kind regards Andreas. On Tue, May 09, 2017 at 09:00:09AM -0500, Dirk Eddelbuettel wrote: > > 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. > | > > | >00:00:00.00 IP 5f02d4499efa.36140 > dns.z9.domain: 4778+ A? > bioconductor.org. (34) > | >00:00:00.51 IP 5f02d4499efa.36140 > dns.z9.domain: 45901+ ? > 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.8 > 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.8: 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.8 > 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.8 > 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.8: 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.8: 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. > > 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 ...' > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > -- http://fam-tille.de
Bug#862039: r-bioc-gviz: accesses the internet during build
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. | > | >00:00:00.00 IP 5f02d4499efa.36140 > dns.z9.domain: 4778+ A? bioconductor.org. (34) | >00:00:00.51 IP 5f02d4499efa.36140 > dns.z9.domain: 45901+ ? 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.8 > 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.8: 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.8 > 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.8 > 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.8: 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.8: 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. 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 ...' Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#862039: r-bioc-gviz: accesses the internet during build
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. > >00:00:00.00 IP 5f02d4499efa.36140 > dns.z9.domain: 4778+ A? > bioconductor.org. (34) >00:00:00.51 IP 5f02d4499efa.36140 > dns.z9.domain: 45901+ ? > 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.8 > 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.8: 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.8 > 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.8 > 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.8: 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.8: 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
Bug#862039: r-bioc-gviz: accesses the internet during build
Source: r-bioc-gviz Version: 1.18.1-1 Severity: important Justification: Policy 4.9 User: la...@debian.org Usertags: network-access Dear Maintainer, Whilst r-bioc-gviz builds successfully on unstable/amd64, according to Debian Policy 4.9 packages may not attempt network access during a build. 00:00:00.00 IP 5f02d4499efa.36140 > dns.z9.domain: 4778+ A? bioconductor.org. (34) 00:00:00.51 IP 5f02d4499efa.36140 > dns.z9.domain: 45901+ ? 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.8 > 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.8: 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.8 > 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.8 > 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.8: 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.8: 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. Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `- r-bioc-gviz.1.18.1-1.unstable.amd64.log.txt.gz Description: Binary data
