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Re: Thanks for packaging golang-github-biogo-hts-dev - help for other biology related go package needed

On 4/17/19 1:28 PM, Andreas Tille wrote:
> 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)

though I never packaged for Go in Debian, I did some Go in dev.

Your dependencies are not found by compiler, it seems to look for them
in /usr/lib/go-1.11/src

In Debian package, I see that file are installed under

did you install/require the -dev packages? such as
https://packages.debian.org/fr/sid/golang-github-burntsushi-toml-dev for
the first import error.

else may be a go packaging issue to specify to Go where to look at for


>         /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
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu

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