[pkg-go] Thanks for packaging golang-github-biogo-hts-dev - help for other biology related go package needed

[Andreas Tille]

Hi Shengjing,

by chance I realised that you have packaged biogo[1].  This is quite
interesting for the Debian Med team and we have added the package to the
"Biology development" task of our team[2] (since I now realised that the
package exists in Debian).

The goal of the Debian Med team is to provide simple and straightforward
access to the package pool of Debian for users in life sciences and to
advertise on a single entry point - the tasks pages and the according
metapackage (in this case med-bio-dev) - all relevant packages.  Despite
I'm observing the package pool quite closely this package escaped my
attention until I now had a need for it and was explicitly seeking for
it.

In case there are more packages packaged by the golang team that would
fit into any science (there are more Blends[3] than Debian Med and I'd
volunteer to maintain the tasks files for other sciences) please let me
know.

The actual problem I had was the packaging of vcfanno.  You can find
my really poor attempt in Salsa[4].  I had never before touched a
package written in go and I'd be happy to get some helping hand how
to fix:


...
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/vcfanno-0.3.1'
cp -a *.go obj-x86_64-linux-gnu
dh_auto_build
go: warning: "/..." matched no packages
        cd obj-x86_64-linux-gnu && go install -gcflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -asmflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -v -p 4
vcfanno.go:17:2: cannot find package "github.com/BurntSushi/toml" in any of:
        /usr/lib/go-1.11/src/github.com/BurntSushi/toml (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/BurntSushi/toml (from $GOPATH)
vcfanno.go:19:2: cannot find package "github.com/brentp/irelate" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/irelate (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/irelate (from $GOPATH)
vcfanno.go:20:2: cannot find package "github.com/brentp/irelate/interfaces" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/irelate/interfaces (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/irelate/interfaces (from $GOPATH)
vcfanno.go:21:2: cannot find package "github.com/brentp/irelate/parsers" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/irelate/parsers (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/irelate/parsers (from $GOPATH)
vcfanno.go:22:2: cannot find package "github.com/brentp/vcfanno/api" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/vcfanno/api (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/vcfanno/api (from $GOPATH)
vcfanno.go:23:2: cannot find package "github.com/brentp/vcfanno/shared" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/vcfanno/shared (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/vcfanno/shared (from $GOPATH)
vcfanno.go:24:2: cannot find package "github.com/brentp/vcfgo" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/vcfgo (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/vcfgo (from $GOPATH)
vcfanno.go:25:2: cannot find package "github.com/brentp/xopen" in any of:
        /usr/lib/go-1.11/src/github.com/brentp/xopen (from $GOROOT)
        /build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/xopen (from $GOPATH)
dh_auto_build: cd obj-x86_64-linux-gnu && go install -gcflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -asmflags=all=\"-trimpath=/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src\" -v -p 4 returned exit code 1
...

which I get when trying to build in a pbuilder chroot.

Kind regards

       Andreas.

PS: I'm not subscribed to debian-go list - please CC me.


[1] https://salsa.debian.org/go-team/packages/golang-github-biogo-hts
[2] https://blends.debian.org/med/tasks/bio-dev#golang-github-biogo-hts-dev
[3] https://www.debian.org/blends/
[4] https://salsa.debian.org/med-team/vcfanno

-- 
http://fam-tille.de