[Debian-med-packaging] Bug#1114433: vcfanno: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

Fri Sep 5 19:28:12 BST 2025

Package: src:vcfanno
Version: 0.3.5+ds-2
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:vcfanno, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=golang --with=golang
   debian/rules execute_before_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
find . -type f -name *.tbi | xargs rm -rf
find . -type f -name ex.bam* | xargs rm -rf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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 2 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared
encoding
internal/goarch
internal/unsafeheader
internal/abi
internal/cpu
internal/bytealg
internal/byteorder
internal/chacha8rand
internal/coverage/rtcov
internal/godebugs
internal/goexperiment
internal/goos
internal/profilerecord
internal/runtime/atomic
internal/asan
internal/msan
internal/race
internal/runtime/math
internal/runtime/exithook
internal/runtime/sys
internal/runtime/syscall
internal/runtime/maps
internal/stringslite
cmp
internal/itoa
math/bits
math
runtime
unicode/utf8
sync/atomic
internal/sync
unicode
unicode/utf16
log/internal
github.com/dsnet/compress/bzip2/internal/sais
github.com/dsnet/compress/internal
crypto/internal/fips140/alias
crypto/internal/fips140deps/byteorder
crypto/internal/fips140deps/cpu
crypto/internal/fips140/subtle
crypto/internal/boring/sig
github.com/klauspost/compress
github.com/klauspost/compress/internal/cpuinfo
github.com/klauspost/compress/internal/le
github.com/ulikunitz/xz/internal/hash
container/list
vendor/golang.org/x/crypto/cryptobyte/asn1
vendor/golang.org/x/crypto/internal/alias
internal/nettrace
internal/reflectlite
iter
sync
errors
slices
strconv
io
internal/oserror
path
internal/bisect
reflect
internal/godebug
syscall
time
io/fs
internal/fmtsort
internal/syscall/unix
internal/filepathlite
internal/poll
internal/syscall/execenv
internal/testlog
strings
os
bytes
bufio
encoding/binary
encoding/base64
fmt
github.com/BurntSushi/toml/internal
sort
hash
hash/crc32
container/heap
flag
github.com/brentp/irelate/interfaces
encoding/json
compress/flate
compress/gzip
github.com/biogo/hts/bgzf
github.com/biogo/hts/bgzf/index
github.com/biogo/hts/csi
github.com/BurntSushi/toml
github.com/biogo/hts/internal
github.com/biogo/hts/tabix
encoding/hex
maps
net/url
github.com/biogo/hts/sam
encoding/csv
log
regexp/syntax
github.com/biogo/hts/bam
github.com/pkg/errors
context
github.com/yuin/gopher-lua/ast
regexp
github.com/yuin/gopher-lua/parse
github.com/brentp/vcfgo
github.com/yuin/gopher-lua/pm
io/ioutil
math/rand
github.com/brentp/irelate/parsers
path/filepath
os/exec
github.com/brentp/bix
github.com/yuin/gopher-lua
github.com/brentp/irelate
github.com/dsnet/compress/internal/errors
github.com/dsnet/compress
github.com/dsnet/compress/internal/prefix
github.com/dsnet/compress/bzip2
crypto
crypto/internal/fips140deps/godebug
crypto/internal/fips140
crypto/internal/impl
crypto/internal/fips140/sha256
crypto/internal/fips140/sha3
crypto/internal/fips140/sha512
crypto/internal/fips140/hmac
crypto/internal/fips140/check
crypto/internal/fips140/aes
crypto/internal/sysrand
crypto/internal/entropy
math/rand/v2
crypto/internal/randutil
crypto/internal/fips140/drbg
crypto/internal/fips140/aes/gcm
crypto/internal/fips140only
crypto/subtle
crypto/cipher
github.com/yuin/gluare
crypto/internal/boring
github.com/brentp/goluaez
math/big
github.com/brentp/vcfanno/api
github.com/cespare/xxhash
github.com/klauspost/compress/fse
github.com/klauspost/compress/huff0
crypto/rand
github.com/klauspost/compress/internal/snapref
runtime/debug
github.com/klauspost/compress/flate
github.com/klauspost/compress/zstd
github.com/klauspost/pgzip
crypto/sha256
github.com/ulikunitz/xz/internal/xlog
github.com/ulikunitz/xz/lzma
hash/crc64
crypto/aes
crypto/des
github.com/ulikunitz/xz
crypto/internal/fips140/nistec/fiat
crypto/internal/fips140/edwards25519/field
crypto/internal/boring/bbig
crypto/internal/fips140/bigmod
crypto/sha3
crypto/internal/fips140hash
crypto/sha512
encoding/asn1
crypto/internal/fips140/nistec
vendor/golang.org/x/crypto/cryptobyte
crypto/internal/fips140/edwards25519
crypto/internal/fips140/ed25519
crypto/ed25519
crypto/hmac
crypto/internal/fips140/ecdh
crypto/elliptic
crypto/ecdh
crypto/internal/fips140/ecdsa
crypto/internal/fips140/hkdf
crypto/internal/fips140/mlkem
crypto/internal/fips140/tls12
crypto/ecdsa
crypto/internal/fips140/tls13
vendor/golang.org/x/crypto/chacha20
vendor/golang.org/x/crypto/internal/poly1305
vendor/golang.org/x/sys/cpu
vendor/golang.org/x/crypto/chacha20poly1305
crypto/internal/hpke
crypto/md5
crypto/rc4
crypto/internal/fips140/rsa
crypto/sha1
crypto/tls/internal/fips140tls
crypto/dsa
crypto/x509/pkix
encoding/pem
crypto/rsa
vendor/golang.org/x/net/dns/dnsmessage
internal/singleflight
weak
unique
runtime/cgo
net/netip
vendor/golang.org/x/text/transform
vendor/golang.org/x/text/unicode/bidi
vendor/golang.org/x/text/secure/bidirule
vendor/golang.org/x/text/unicode/norm
net
vendor/golang.org/x/net/idna
vendor/golang.org/x/net/http2/hpack
mime
mime/quotedprintable
net/http/internal
net/http/internal/ascii
os/user
net/textproto
crypto/x509
vendor/golang.org/x/net/http/httpguts
vendor/golang.org/x/net/http/httpproxy
mime/multipart
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 2 github.com/brentp/vcfanno github.com/brentp/vcfanno/api github.com/brentp/vcfanno/shared
testing: warning: no tests to run
PASS
ok  	github.com/brentp/vcfanno	0.003s [no tests to run]
=== RUN   Test
OK: 13 passed
--- PASS: Test (0.01s)
=== 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	0.008s
?   	github.com/brentp/vcfanno/shared	[no test files]
   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 example/fitcons.bed.gz
tabix tests/astar/astar.anno.vcf.gz
tabix tests/by_alt_float/annotation.tsv.gz
[E::get_intv] Failed to parse TBX_GENERIC: was wrong -p [type] used?
The offending line was: "2	41647	A	G	0.591814	8.493"
tbx_index_build3 failed: tests/by_alt_float/annotation.tsv.gz
make[1]: *** [debian/rules:24: 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
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