[Debian-med-packaging] Bug#1049762: vcfanno: Fails to build binary packages again after successful build

Wed Aug 16 08:42:51 BST 2023

Source: vcfanno
Version: 0.3.5+ds-1
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ------------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package vcfanno
> dpkg-buildpackage: info: source version 0.3.5+ds-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
>  debian/rules clean
> dh clean --buildsystem=golang --with=golang
>    dh_auto_clean -O--buildsystem=golang
>    dh_autoreconf_clean -O--buildsystem=golang
>    dh_clean -O--buildsystem=golang
>  debian/rules binary
> dh binary --buildsystem=golang --with=golang
>    dh_update_autotools_config -O--buildsystem=golang
>    dh_autoreconf -O--buildsystem=golang
>    dh_auto_configure -O--buildsystem=golang
>    dh_auto_build -O--buildsystem=golang
> 	cd obj-x86_64-linux-gnu && go install -trimpath -v -p 8 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared
> encoding
> internal/goarch
> internal/unsafeheader
> runtime/internal/math
> internal/goexperiment
> internal/goos
> internal/coverage/rtcov
> internal/cpu
> internal/abi
> internal/itoa
> runtime/internal/atomic
> runtime/internal/sys
> runtime/internal/syscall
> math/bits
> unicode/utf8
> internal/race
> sync/atomic
> unicode
> unicode/utf16
> container/list
> internal/bytealg
> math
> crypto/internal/alias
> crypto/subtle
> crypto/internal/boring/sig
> vendor/golang.org/x/crypto/cryptobyte/asn1
> internal/nettrace
> vendor/golang.org/x/crypto/internal/alias
> runtime
> internal/reflectlite
> sync
> internal/testlog
> internal/godebug
> internal/singleflight
> runtime/cgo
> math/rand
> internal/intern
> errors
> sort
> io
> strconv
> internal/oserror
> internal/safefilepath
> path
> crypto/internal/nistec/fiat
> container/heap
> syscall
> vendor/golang.org/x/net/dns/dnsmessage
> bytes
> hash
> strings
> hash/crc32
> crypto/internal/randutil
> vendor/golang.org/x/text/transform
> crypto
> reflect
> crypto/rc4
> net/netip
> github.com/brentp/irelate/interfaces
> bufio
> regexp/syntax
> net/http/internal/ascii
> regexp
> internal/syscall/unix
> time
> internal/syscall/execenv
> io/fs
> github.com/BurntSushi/toml/internal
> context
> internal/poll
> embed
> internal/fmtsort
> encoding/binary
> os
> encoding/base64
> crypto/cipher
> crypto/internal/edwards25519/field
> crypto/internal/nistec
> crypto/md5
> vendor/golang.org/x/crypto/internal/poly1305
> encoding/pem
> crypto/des
> crypto/internal/boring
> vendor/golang.org/x/crypto/chacha20
> crypto/aes
> crypto/sha512
> crypto/hmac
> crypto/internal/edwards25519
> crypto/sha1
> crypto/sha256
> io/ioutil
> fmt
> path/filepath
> net
> vendor/golang.org/x/sys/cpu
> vendor/golang.org/x/crypto/hkdf
> vendor/golang.org/x/crypto/chacha20poly1305
> os/exec
> crypto/ecdh
> encoding/json
> encoding/hex
> net/url
> compress/flate
> encoding/csv
> log
> flag
> github.com/pkg/errors
> github.com/yuin/gopher-lua/ast
> github.com/brentp/vcfgo
> github.com/yuin/gopher-lua/pm
> math/big
> github.com/yuin/gopher-lua/parse
> vendor/golang.org/x/text/unicode/bidi
> compress/gzip
> github.com/klauspost/compress/flate
> github.com/biogo/hts/bgzf
> vendor/golang.org/x/text/unicode/norm
> github.com/BurntSushi/toml
> github.com/biogo/hts/bgzf/index
> vendor/golang.org/x/text/secure/bidirule
> github.com/biogo/hts/csi
> github.com/biogo/hts/internal
> github.com/yuin/gopher-lua
> vendor/golang.org/x/net/http2/hpack
> github.com/biogo/hts/tabix
> github.com/biogo/hts/sam
> mime
> vendor/golang.org/x/net/idna
> github.com/klauspost/pgzip
> mime/quotedprintable
> net/http/internal
> os/user
> crypto/elliptic
> crypto/rand
> crypto/internal/bigmod
> github.com/biogo/hts/bam
> crypto/internal/boring/bbig
> encoding/asn1
> crypto/ed25519
> crypto/rsa
> github.com/brentp/irelate/parsers
> crypto/dsa
> vendor/golang.org/x/crypto/cryptobyte
> crypto/x509/pkix
> github.com/brentp/bix
> crypto/ecdsa
> github.com/brentp/irelate
> github.com/yuin/gluare
> github.com/brentp/goluaez
> github.com/brentp/vcfanno/api
> net/textproto
> vendor/golang.org/x/net/http/httpproxy
> crypto/x509
> mime/multipart
> vendor/golang.org/x/net/http/httpguts
> crypto/tls
> net/http/httptrace
> net/http
> github.com/shenwei356/xopen
> github.com/brentp/vcfanno/shared
> github.com/brentp/vcfanno
>    dh_auto_test -O--buildsystem=golang
> 	cd obj-x86_64-linux-gnu && go test -vet=off -v -p 8 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared
> ?   	github.com/brentp/vcfanno/shared	[no test files]
> testing: warning: no tests to run
> PASS
> ok  	github.com/brentp/vcfanno	0.017s [no tests to run]
> === RUN   Test
> OK: 13 passed
> --- PASS: Test (0.06s)
> === RUN   TestHandleA
> --- PASS: TestHandleA (0.00s)
> === RUN   TestHandlAMulti
> --- PASS: TestHandlAMulti (0.00s)
> === RUN   TestByAlt
> --- PASS: TestByAlt (0.00s)
> PASS
> ok  	github.com/brentp/vcfanno/api	0.072s
>    create-stamp debian/debhelper-build-stamp
>    dh_testroot -O--buildsystem=golang
>    dh_prep -O--buildsystem=golang
>    debian/rules override_dh_auto_install
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_install -- --no-source
> 	cd obj-x86_64-linux-gnu && mkdir -p /<<BUILDDIR>>/vcfanno-0.3.5\+ds/debian/tmp/usr
> 	cd obj-x86_64-linux-gnu && cp -r bin /<<BUILDDIR>>/vcfanno-0.3.5\+ds/debian/tmp/usr
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_install -O--buildsystem=golang
>    debian/rules override_dh_installdocs
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # Regenerate bam and bam index file
> cat debian/missing-sources/ex.sam| samtools view -Sb - > example/ex.bam
> samtools index example/ex.bam example/ex.bam.bai
> # Remove corrupt gz file
> rm -rf tests/notbgz/notbgz.vcf.gz
> # Regenerate all .tbi files
> tabix example/exac.vcf.gz
> [tabix] the index file exists. Please use '-f' to overwrite.
> make[1]: *** [debian/rules:17: override_dh_installdocs] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:5: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.

The full build log is available from:
http://qa-logs.debian.net/2023/08/16/vcfanno_0.3.5+ds-1_unstable.log

If you reassign this bug to another package, please mark 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.