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 /usr/share/gocode/src/ 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 sources.... Olivier > > /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 F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
