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 --------------------------------------------------------------------------------
