[Debian-med-packaging] Bug#963439: ncbi-entrez-direct: FTBFS: obj-x86_64-linux-gnu/src/golang.org/x/sys/unix/syscall_unix.go:16:2: cannot find package "golang.org/x/sys/internal/unsafeheader" in any of:

[Lucas Nussbaum]

Source: ncbi-entrez-direct
Version: 12.0.20190816+ds-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200620 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' edirect.pl > bin/edirect
> chmod +x bin/edirect
> echo '#!/bin/sh' > bin/eaddress
> echo 'exec /usr/bin/edirect -address "$@"' >> bin/eaddress
> chmod +x bin/eaddress
> echo '#!/bin/sh' > bin/eblast
> echo 'exec /usr/bin/edirect -blast "$@"' >> bin/eblast
> chmod +x bin/eblast
> echo '#!/bin/sh' > bin/ecitmatch
> echo 'exec /usr/bin/edirect -citmatch "$@"' >> bin/ecitmatch
> chmod +x bin/ecitmatch
> echo '#!/bin/sh' > bin/econtact
> echo 'exec /usr/bin/edirect -contact "$@"' >> bin/econtact
> chmod +x bin/econtact
> echo '#!/bin/sh' > bin/efilter
> echo 'exec /usr/bin/edirect -filter "$@"' >> bin/efilter
> chmod +x bin/efilter
> echo '#!/bin/sh' > bin/elink
> echo 'exec /usr/bin/edirect -link "$@"' >> bin/elink
> chmod +x bin/elink
> echo '#!/bin/sh' > bin/enotify
> echo 'exec /usr/bin/edirect -notify "$@"' >> bin/enotify
> chmod +x bin/enotify
> echo '#!/bin/sh' > bin/epost
> echo 'exec /usr/bin/edirect -post "$@"' >> bin/epost
> chmod +x bin/epost
> echo '#!/bin/sh' > bin/eproxy
> echo 'exec /usr/bin/edirect -proxy "$@"' >> bin/eproxy
> chmod +x bin/eproxy
> echo '#!/bin/sh' > bin/esearch
> echo 'exec /usr/bin/edirect -search "$@"' >> bin/esearch
> chmod +x bin/esearch
> echo '#!/bin/sh' > bin/espell
> echo 'exec /usr/bin/edirect -spell "$@"' >> bin/espell
> chmod +x bin/espell
> echo '#!/bin/sh' > bin/esummary
> echo 'exec /usr/bin/edirect -fetch -format docsum "$@"' >> bin/esummary
> chmod +x bin/esummary
> mkdir -p bin
> sed -e 's/`has-asp`/false # &/' download-ncbi-data > bin/download-ncbi-data
> chmod +x bin/download-ncbi-data
> mkdir -p bin
> sed -e 's/`has-asp`/false # &/' download-pubmed > bin/download-pubmed
> chmod +x bin/download-pubmed
> mkdir -p bin
> sed -e 's/`has-asp`/false # &/' download-sequence > bin/download-sequence
> chmod +x bin/download-sequence
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' edirutil > bin/edirutil
> chmod +x bin/edirutil
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' ftp-cp > bin/ftp-cp
> chmod +x bin/ftp-cp
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' ftp-ls > bin/ftp-ls
> chmod +x bin/ftp-ls
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' gbf2xml > bin/gbf2xml
> chmod +x bin/gbf2xml
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' nquire > bin/nquire
> chmod +x bin/nquire
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' run-ncbi-converter > bin/run-ncbi-converter
> chmod +x bin/run-ncbi-converter
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' transmute > bin/transmute
> chmod +x bin/transmute
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fatih/
> ln -s /usr/share/gocode/src/github.com/fatih/color /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fatih/color
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/gedex/
> ln -s /usr/share/gocode/src/github.com/gedex/inflector /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/gedex/inflector
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/
> ln -s /usr/share/gocode/src/github.com/klauspost/cpuid /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/cpuid
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/
> ln -s /usr/share/gocode/src/github.com/mattn/go-colorable /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/go-colorable
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/
> ln -s /usr/share/gocode/src/github.com/mattn/go-isatty /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/go-isatty
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/pbnjay/
> ln -s /<<PKGBUILDDIR>>/debian/vendor/github.com/pbnjay/memory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/pbnjay/memory
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/rainycape/
> ln -s /usr/share/gocode/src/github.com/rainycape/unidecode /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/rainycape/unidecode
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/shirou/
> ln -s /usr/share/gocode/src/github.com/shirou/gopsutil /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/shirou/gopsutil
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/surgebase/
> ln -s /usr/share/gocode/src/github.com/surgebase/porter2 /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/surgebase/porter2
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/
> ln -s /usr/share/gocode/src/golang.org/x/sys/unix /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/unix
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/
> ln -s /usr/share/gocode/src/golang.org/x/text /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/text
> mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fiam
> ln -s ../rainycape /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fiam/gounidecode
> go build -v -gccgoflags '-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed' -o bin/j2x j2x.go 
> go build: when using gc toolchain, please pass compile flags using -gcflags, and linker flags using -ldflags
> github.com/gedex/inflector
> command-line-arguments
> go build -v -gccgoflags '-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed' -o bin/rchive rchive.go common.go
> obj-x86_64-linux-gnu/src/golang.org/x/sys/unix/syscall_unix.go:16:2: cannot find package "golang.org/x/sys/internal/unsafeheader" in any of:
> 	/usr/lib/go-1.14/src/golang.org/x/sys/internal/unsafeheader (from $GOROOT)
> 	/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/internal/unsafeheader (from $GOPATH)
> make[1]: *** [debian/rules:93: bin/rchive] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/06/20/ncbi-entrez-direct_12.0.20190816+ds-2_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.