--- Begin Message ---
Package: src:nim-hts
Version: 0.3.19+ds-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
# Regenerate repacked files
cat tests/sa.sam | samtools view -Sb - > tests/sa.bam
samtools index tests/sa.bam tests/sa.bam.bai
cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam
samtools index tests/HG02002.bam tests/HG02002.bam.bai
tabix tests/test.vcf.gz
bcftools index tests/test.bcf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/nim-hts-dev.debhelper.log
debian/nim-hts-examples.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
nim c --nimcache:/<<PKGBUILDDIR>>/tests/nimcache tests/all.nim
Hint: used config file '/etc/nim/nim.cfg' [Conf]
Hint: used config file '/etc/nim/config.nims' [Conf]
Hint: used config file '/<<PKGBUILDDIR>>/tests/nim.cfg' [Conf]
.............................................................................................................
/<<PKGBUILDDIR>>/src/hts/bam/flag.nim(1, 18) Hint: duplicate import of 'hts_concat';
previous import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(1, 17) [DuplicateModuleImport]
.
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(1, 18) Hint: duplicate import of 'hts_concat';
previous import here: /<<PKGBUILDDIR>>/src/hts/bam/flag.nim(1, 18) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(2, 8) Hint: duplicate import of 'strutils'; previous
import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(4, 8) [DuplicateModuleImport]
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(57, 34) Warning: target type is larger
than source type [CastSizes]
/<<PKGBUILDDIR>>/src/hts/bam.nim(248, 34) template/generic instantiation of
`bam_get_cigar` from here
/<<PKGBUILDDIR>>/src/hts/bam/cigar.nim(52, 46) Warning: target type is larger
than source type [CastSizes]
/<<PKGBUILDDIR>>/src/hts/bam.nim(262, 52) Warning: implicit conversion to
'cstring' from a non-const location: region; this will become a compile time error in the
future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/bam.nim(373, 28) Warning: implicit conversion to
'cstring' from a non-const location: mode; this will become a compile time error in the
future [CStringConv]
..
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(3, 1) Hint: duplicate import of 'strformat';
previous import here: /<<PKGBUILDDIR>>/src/hts/bam.nim(3, 8) [DuplicateModuleImport]
....
/<<PKGBUILDDIR>>/src/hts/vcf.nim(118, 18) Warning: conversion to enum with
holes is unsafe: Status(ret) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(119, 16) Warning: conversion to enum with
holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(181, 16) Warning: conversion to enum with
holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(190, 16) Warning: conversion to enum with
holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(288, 18) Warning: conversion to enum with
holes is unsafe: Status(int(bcf_update_format(f.v.vcf.header.hdr, f.v.c, cstring(key), nil,
0,
cint(htype)))) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(297, 20) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(309, 22) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(320, 22) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(352, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(359, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(366, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(376, 20) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(391, 20) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(405, 20) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(432, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(436, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(441, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(461, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(467, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(527, 23) Warning: conversion to enum with
holes is unsafe: BCF_TYPE(fmt.type) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(542, 23) Warning: conversion to enum with
holes is unsafe: BCF_TYPE(fld.type) [HoleEnumConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(601, 27) Warning: implicit conversion to
'cstring' from a non-const location: v.fname; this will become a compile time error in the
future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(603, 31) Warning: implicit conversion to
'cstring' from a non-const location: v.fname; this will become a compile time error in the
future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(645, 30) Warning: implicit conversion to
'cstring' from a non-const location: v.fname; this will become a compile time error in the
future [CStringConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(664, 36) Warning: implicit conversion to
'cstring' from a non-const location: `[]`(region) do:
0 .. pred(cidx, 1); this will become a compile time error in the future
[CStringConv]
/<<PKGBUILDDIR>>/src/hts/vcf.nim(700, 32) Warning: implicit conversion to
'cstring' from a non-const location: v.fname; this will become a compile time error in the
future [CStringConv]
.
/<<PKGBUILDDIR>>/src/hts/fai.nim(38, 24) Warning: See corresponding Defect;
IndexError is deprecated [Deprecated]
...
/<<PKGBUILDDIR>>/src/hts/csi.nim(17, 51) Warning: implicit conversion to 'cstring' from a
non-const location: base_path & ".csi"; this will become a compile time error in the future
[CStringConv]
...
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(10, 18) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(53, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(13, 19) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(71, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(13, 19) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(17, 19) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(63, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(17, 19) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(4, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(17, 19) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
/<<PKGBUILDDIR>>/tests/auxtest.nim(3, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(25, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/auxtest.nim(40, 18) template/generic instantiation of
`tag` from here
/<<PKGBUILDDIR>>/src/hts/bam/auxtags.nim(58, 7) Warning: unreachable code after
'return' statement or '{.noReturn.}' proc [UnreachableCode]
.
/<<PKGBUILDDIR>>/tests/vcftest.nim(23, 7) template/generic instantiation of
`suite` from here
/<<PKGBUILDDIR>>/tests/vcftest.nim(46, 8) template/generic instantiation of
`test` from here
/<<PKGBUILDDIR>>/tests/vcftest.nim(63, 13) template/generic instantiation of
`check` from here
/<<PKGBUILDDIR>>/src/hts/vcf.nim(448, 16) Warning: conversion to enum with
holes is unsafe: Status(int(ret)) [HoleEnumConv]
/<<PKGBUILDDIR>>/tests/vcftest.nim(404, 7) Hint: 'current_line' is declared but
not used [XDeclaredButNotUsed]
/<<PKGBUILDDIR>>/tests/vcftest.nim(406, 7) Hint: 'currentBlock' is declared but
not used [XDeclaredButNotUsed]
/<<PKGBUILDDIR>>/tests/vcftest.nim(411, 7) Hint: 'block_pos_i' is declared but
not used [XDeclaredButNotUsed]
.....
CC: ../../../../usr/lib/nim/lib/std/private/digitsutils.nim
CC: ../../../../usr/lib/nim/lib/system/assertions.nim
CC: ../../../../usr/lib/nim/lib/system/formatfloat.nim
CC: ../../../../usr/lib/nim/lib/system/dollars.nim
CC: ../../../../usr/lib/nim/lib/system/io.nim
CC: ../../../../usr/lib/nim/lib/system.nim
CC: ../../../../usr/lib/nim/lib/std/exitprocs.nim
CC: ../../../../usr/lib/nim/lib/pure/parseutils.nim
CC: ../../../../usr/lib/nim/lib/pure/math.nim
CC: ../../../../usr/lib/nim/lib/pure/algorithm.nim
CC: ../../../../usr/lib/nim/lib/pure/unicode.nim
CC: ../../../../usr/lib/nim/lib/pure/strutils.nim
CC: ../../../../usr/lib/nim/lib/pure/streams.nim
CC: ../../../../usr/lib/nim/lib/pure/times.nim
CC: ../../../../usr/lib/nim/lib/pure/hashes.nim
CC: ../../../../usr/lib/nim/lib/pure/collections/sets.nim
CC: ../../../../usr/lib/nim/lib/pure/os.nim
CC: ../../../../usr/lib/nim/lib/pure/strformat.nim
CC: ../../../../usr/lib/nim/lib/pure/terminal.nim
CC: ../../../../usr/lib/nim/lib/pure/unittest.nim
CC: ../src/hts/private/hts_concat.nim
CC: ../src/hts/bam/flag.nim
CC: flagtest.nim
CC: ../src/hts/bam.nim
CC: cigartest.nim
CC: htstest.nim
CC: ../src/hts/vcf.nim
CC: ../src/hts/fai.nim
CC: ../src/hts/bgzf.nim
CC: ../src/hts/csi.nim
CC: ../src/hts/bgzf/bgzi.nim
CC: ../src/hts/stats.nim
CC: ../src/hts.nim
CC: bgzftest.nim
CC: faitest.nim
CC: auxtest.nim
CC: vcftest.nim
/<<PKGBUILDDIR>>/tests/nimcache/@mvcftest.nim.c: In function
‘write_linked_blocks__vcftest_4811’:
/<<PKGBUILDDIR>>/tests/nimcache/@mvcftest.nim.c:6188:51: error: assignment to
‘int (**)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, NI64 *, NI64
*)’ {aka ‘int (**)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, long
int *, long int *)’} from incompatible pointer type ‘tyProc__Z5AehsnnjAUfWA9bh4O4nAA’ {aka
‘int (*)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, long int *,
long int *)’} [-Wincompatible-pointer-types]
6188 | read_func = Dl_1644167502_;
| ^
/<<PKGBUILDDIR>>/tests/nimcache/@mvcftest.nim.c:6370:41: error: assignment to
‘int (**)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, NI64 *, NI64
*)’ {aka ‘int (**)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, long
int *, long int *)’} from incompatible pointer type ‘tyProc__Z5AehsnnjAUfWA9bh4O4nAA’ {aka
‘int (*)(tyObject_BGZF__f1gxKVGOf9aYba9agDE6I9aAw *, void *, void *, int *, long int *,
long int *)’} [-Wincompatible-pointer-types]
6370 | read_fn = Dl_1644168003_;
| ^
CC: bamtest.nim
Error: execution of an external compiler program 'gcc -c -w -fmax-errors=3 -I/usr/lib/nim/lib
-I/<<PKGBUILDDIR>>/tests -o /<<PKGBUILDDIR>>/tests/nimcache/@mvcftest.nim.c.o
/<<PKGBUILDDIR>>/tests/nimcache/@mvcftest.nim.c' failed with exit code: 1
make[1]: *** [debian/rules:20: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202409/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
pgpsi02YVdHfJ.pgp
