[Debian-med-packaging] Bug#1013608: ncbi-entrez-direct: FTBFS: cannot find package "github.com/shirou/gopsutil/mem"

[Lucas Nussbaum]

Source: ncbi-entrez-direct
Version: 14.6.20210224+dfsg-5
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220624 ftbfs-bookworm

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 "$@"' >> bin/econtact
> chmod +x bin/econtact
> echo '#!/bin/sh' > bin/enotify
> echo 'exec /usr/bin/edirect -notify "$@"' >> bin/enotify
> chmod +x bin/enotify
> echo '#!/bin/sh' > bin/eproxy
> echo 'exec /usr/bin/edirect -proxy "$@"' >> bin/eproxy
> chmod +x bin/eproxy
> echo '#!/bin/sh' > bin/espell
> echo 'exec /usr/bin/edirect -spell "$@"' >> bin/espell
> chmod +x bin/espell
> echo '#!/bin/sh' > bin/ftp-cp
> echo 'exec /usr/bin/edirect -ftpcp "$@"' >> bin/ftp-cp
> chmod +x bin/ftp-cp
> echo '#!/bin/sh' > bin/ftp-ls
> echo 'exec /usr/bin/edirect -ftpls "$@"' >> bin/ftp-ls
> chmod +x bin/ftp-ls
> sed -e 's,xml2json,/usr/lib/ncbi-entrez-direct/&,; s/python/&3/; /to precompiled/q' \
>     transmute > bin/transmute.sh
> echo 'exec /usr/lib/ncbi-entrez-direct/transmute "$@"' >> bin/transmute.sh
> chmod +x bin/transmute.sh
> sed -e 's,xml2json,/usr/lib/ncbi-entrez-direct/&,; s/python/&3/; /to precompiled/q' \
>     xtract > bin/xtract.sh
> echo 'exec /usr/lib/ncbi-entrez-direct/xtract "$@"' >> bin/xtract.sh
> chmod +x bin/xtract.sh
> mkdir -p bin
> sed -e '1s,^#!/bin/sh,#!/bin/bash,' index-extras > bin/index-extras
> chmod +x bin/index-extras
> 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,' run-ncbi-converter > bin/run-ncbi-converter
> chmod +x bin/run-ncbi-converter
> mkdir -p bin
> sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' xml2json > bin/xml2json
> chmod +x bin/xml2json
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' efetch > bin/efetch
> chmod +x bin/efetch
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' efilter > bin/efilter
> chmod +x bin/efilter
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' einfo > bin/einfo
> chmod +x bin/einfo
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' elink > bin/elink
> chmod +x bin/elink
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' epost > bin/epost
> chmod +x bin/epost
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' esearch > bin/esearch
> chmod +x bin/esearch
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s,"$pth"/ec,/usr/lib/ncbi-entrez-direct/ec,g' esummary > bin/esummary
> chmod +x bin/esummary
> mkdir -p bin
> sed -e 's/edirect\.pl/edirect/g; s/ --no-check-certificate / /' nquire > bin/nquire
> chmod +x bin/nquire
> 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
> make[1]: Circular /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/cpuid <- /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/cpuid dependency dropped.
> 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/
> ln -s /usr/share/gocode/src/golang.org/x/sys /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys
> 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/klauspost
> ln -s /usr/share/gocode/src/github.com/klauspost/cpuid/v2 \
>     /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/cpuid
> 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 -ffile-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/github.com/pbnjay/memory/memory.go:3:9: cannot find package "github.com/shirou/gopsutil/mem" in any of:
> 	/usr/lib/go-1.18/src/github.com/shirou/gopsutil/mem (from $GOROOT)
> 	/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/shirou/gopsutil/mem (from $GOPATH)
> make[1]: *** [debian/rules:144: bin/rchive] Error 1


The full build log is available from:
http://qa-logs.debian.net/2022/06/24/ncbi-entrez-direct_14.6.20210224+dfsg-5_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220624;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220624&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

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!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.