v2.0 fails to build from source on Debian Unstable

[mr-c]

Severity: serious -- without a fix, khmer will be removed from Debian, which is about to have a major release

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=851830

[betatim]

Not super familiar with debian: The failure is just for arm and sparc or also other archs?

Do you have a pointer to the set of commands the build machine runs so I can try and reproduce it locally (modulo it being limited to sparc/arm)?

So far I found:

• git clone https://anonscm.debian.org/git/debian-med/khmer.git
• cd khmer
• dpkg-buildpackage

but that is missing some build dependencies.

[mr-c]

Hey @betatim

sudo apt-get build-dep khmer
apt-get source khmer
cd khmer-*
dpkg-buildpackage -r fakeroot

[mr-c]

The only failures are on arm64/sparc64 -- but only arm64 has to be fixed (or excluded) to keep the package in:

https://buildd.debian.org/status/package.php?p=khmer

[betatim]

Using the debian:unstable docker image, after installing the build tools and apt-get update I still get apt-get source khmer telling me that I need to put URIs in my source.lost. It contains one though:

$ cat /etc/apt/sources.list
deb http://deb.debian.org/debian unstable main

Ideas?

[betatim]

Pragmatic question for the management: are there known khmer users/uses of arm64?

[mr-c]

@betatim

sudo su -c 'echo "deb-src http://deb.debian.org/debian unstable main" >> /etc/apt/sources.list'
sudo apt-get update

I am okay with disabling this build, though it used to work: https://buildd.debian.org/status/logs.php?pkg=khmer&arch=arm64

[ctb]

Not particularly, but I'm still trying to understand why it doesn't build :).

[mr-c]

It builds, but some tests fail. Cpython has some rough edges. Pe 20 ian. 2017 14:57, "C. Titus Brown" <notifications@github.com> a scris:

…

Not particularly, but I'm still trying to understand why it doesn't build :). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1576 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABROCFjG6XJDvQwtJu1ngDmCi3rmuwDyks5rUL1EgaJpZM4LpET8> .

[luizirber]

@mr-c would you recommend using qemu for debugging this? https://wiki.debian.org/Arm64Qemu

[mr-c]

It seems the obvious thing to try. Alas I'm not a full Debian Developer yet, so I can't login to a test node. Pe 20 ian. 2017 20:42, "Luiz Irber" <notifications@github.com> a scris:

…

@mr-c <https://github.com/mr-c> would you recommend using qemu for debugging this? https://wiki.debian.org/Arm64Qemu — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1576 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABROCHveJOqXd7LB-usq0aA26lQoE5smks5rUQ4KgaJpZM4LpET8> .

[tillea]

Any news for this issue?

[mr-c]

@tillea The last two releases built fine on arm64. Perhaps the build dependencies fixed the bug.