Re: Thanks for packaging golang-github-biogo-hts-dev - help for other biology related go package needed
Hi,
On Wed, Apr 17, 2019 at 10:58:34PM +0800, Shengjing Zhu wrote:
> > 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.
> >
>
> I don't think you should recommend user any golang-*-dev package.
>
> Libraries written in Go are packaged for Debian with the only purpose
> of building other Go programs for Debian.
The task med-bio-dev is for developers of biological applications (not
for users). It recommends bioperl, biopython, biojava and bioruby. I
think it is perfectly in line to recommend golang-*-dev packages that
are dealing with biological problems. Please give me some actual
reasons why this should not make sense.
> They are specifically not
> available for users in their regular development workflow. For that,
> users should use go get. [1]
>
> > 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)
>
> You could try the dh-make-golang[2], which could create debian package
> for Go program.
>
> For the vcfanno case, run
> dh-make-golang make -type program -git_revision=v0.3.1 github.com/brentp/vcfanno
Thanks for this helpful hint. It enhanced the packaging but there are
remaining errors which to me look like missing Build-Depends which are
not packaged yet:
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 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared
src/github.com/brentp/vcfanno/api/api.go:15:2: cannot find package "github.com/brentp/bix" in any of:
/usr/lib/go-1.11/src/github.com/brentp/bix (from $GOROOT)
/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/bix (from $GOPATH)
src/github.com/brentp/vcfanno/api/api.go:16:2: cannot find package "github.com/brentp/goluaez" in any of:
/usr/lib/go-1.11/src/github.com/brentp/goluaez (from $GOROOT)
/build/vcfanno-0.3.1/obj-x86_64-linux-gnu/src/github.com/brentp/goluaez (from $GOPATH)
src/github.com/brentp/vcfanno/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)
src/github.com/brentp/vcfanno/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)
src/github.com/brentp/vcfanno/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)
src/github.com/brentp/vcfanno/api/api.go:19:2: 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)
src/github.com/brentp/vcfanno/shared/shared.go:10:2: 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 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared returned exit code 1
make: *** [debian/rules:5: build] Error 1
> Then you could find some useful tips, like what build dependencies are
> not packaged
Is there any chance that dh-make-golang failed to detect those missing
Build-Depends? Will I need to
dh-make-golang make -type library -git_revision=v0.3.1 github.com/brentp/bix
etc to get these packaged? I think for the final target the user
application vcfanno the Debian Med team is OK to maintain that
package but for about five golang libraries it might sensible to
put these into debian-go team space on alioth, right?
Kind regards and thanks a lot for your helpful hints
Andreas.
> [1] https://go-team.pages.debian.net/packaging.html#_library_or_binary_library_packages
> [2] https://packages.debian.org/sid/dh-make-golang
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