[Pkg-d-devel] Bug#875535: closed by Matthias Klumpp <mak at debian.org> (Re: Bug#875878: ldc 1.3 doesn't build any of it's reverse dependencies)

[Nobuhiro Iwamatsu]

Hi,

sambamba package has not fixed this problem with ldc 1:1.4.0-1.
Also, I confirmed that diet-ng fixed this problem.

-----
 dpkg-buildpackage -rfakeroot -us -uc
dpkg-buildpackage: info: source package sambamba
dpkg-buildpackage: info: source version 0.6.6-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build sambamba-0.6.6
dpkg-buildpackage: info: host architecture amd64
 fakeroot debian/rules clean
dh clean --buildsystem=meson
   dh_auto_clean -O--buildsystem=meson
   dh_autoreconf_clean -O--buildsystem=meson
   dh_clean -O--buildsystem=meson
 dpkg-source -b sambamba-0.6.6
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building sambamba using existing ./sambamba_0.6.6.orig.tar.gz
dpkg-source: info: building sambamba in sambamba_0.6.6-1.debian.tar.xz
dpkg-source: info: building sambamba in sambamba_0.6.6-1.dsc
 debian/rules build
dh build --buildsystem=meson
   dh_update_autotools_config -O--buildsystem=meson
   dh_autoreconf -O--buildsystem=meson
   dh_auto_configure -O--buildsystem=meson
        meson .. --wrap-mode=nodownload --buildtype=plain
--prefix=/usr --sysconfdir=/etc --localstatedir=/var
--libdir=lib/x86_64-linux-gnu --libexecdir=lib/x86_64-linux-gnu
Warning: You are using 'ANSI_X3.4-1968' which is not a a
Unicode-compatible locale.
You might see errors if you use UTF-8 strings as filenames, as
strings, or as file contents.
Please switch to a UTF-8 locale for your platform.
The Meson build system
Version: 0.42.1
Source dir: /home/iwa/t3/sambamba-0.6.6
Build dir: /home/iwa/t3/sambamba-0.6.6/obj-x86_64-linux-gnu
Build type: native build
Project name: Sambamba
Native D compiler: ldc2 (llvm 1.4.0)
Appending DFLAGS from environment: '-O2 -g -release'
Appending LDFLAGS from environment: '-Wl,-z,relro'
Build machine cpu family: x86_64
Build machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (0.29)
Native dependency undead found: YES 1.0.7
Native dependency biod found: YES 0.1.0
Native dependency liblz4 found: YES 1.8.0
Native dependency htslib found: YES 1.5-1
Program ldmd2 found: YES (/usr/bin/ldmd2)
Program mkdir found: YES (/bin/mkdir)
Build targets in project: 2
   dh_auto_build -O--buildsystem=meson
        ninja -j8 -v
[1/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/main.d.o' -c ../main.d
../sambamba/utils/common/readstorage.d(22): Deprecation: module
std.c.stdlib is deprecated - Import core.stdc.stdlib or
core.sys.posix.stdlib instead
../sambamba/utils/common/readstorage.d(23): Deprecation: module
std.c.string is deprecated - Import core.stdc.string instead
../sambamba/utils/common/readstorage.d(23): Deprecation: module
std.c.string is deprecated - Import core.stdc.string instead
../sambamba/sort.d(45): Deprecation: module std.c.stdlib is deprecated
- Import core.stdc.stdlib or core.sys.posix.stdlib instead
../sambamba/sort.d(46): Deprecation: module std.c.string is deprecated
- Import core.stdc.string instead
../sambamba/markdup.d(37): Deprecation: module std.c.stdlib is
deprecated - Import core.stdc.stdlib or core.sys.posix.stdlib instead
../sambamba/depth.d(1154): Deprecation: Implicit string concatenation
is deprecated, use "mapping_quality > 0 and " ~ "not duplicate and "
instead
../sambamba/depth.d(1155): Deprecation: Implicit string concatenation
is deprecated, use "not duplicate and " ~ "not failed_quality_control"
instead
[2/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_index.d.o' -c ../sambamba/index.d
[3/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
[4/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_depth.d.o' -c ../sambamba/depth.d
FAILED: sambamba at exe/sambamba_depth.d.o
ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
-enable-color -O2 -g -release  -of 'sambamba at exe/sambamba_depth.d.o'
-c ../sambamba/depth.d
../sambamba/depth.d(1154): Deprecation: Implicit string concatenation
is deprecated, use "mapping_quality > 0 and " ~ "not duplicate and "
instead
../sambamba/depth.d(1155): Deprecation: Implicit string concatenation
is deprecated, use "not duplicate and " ~ "not failed_quality_control"
instead
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7fec38558cda]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7fec38556fc6]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0e3)[0x7fec385570e3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7fec376d10c0]
ldc2(+0x2d6242)[0x59e7bce242]
ldc2(+0x35b517)[0x59e7c53517]
ldc2(+0x35babb)[0x59e7c53abb]
ldc2(+0x31e1d0)[0x59e7c161d0]
ldc2(+0x3183d1)[0x59e7c103d1]
ldc2(+0x3237c6)[0x59e7c1b7c6]
ldc2(+0x319831)[0x59e7c11831]
ldc2(+0x307835)[0x59e7bff835]
ldc2(+0x306614)[0x59e7bfe614]
ldc2(+0x304834)[0x59e7bfc834]
ldc2(+0x2cf041)[0x59e7bc7041]
ldc2(+0x2c59d0)[0x59e7bbd9d0]
ldc2(+0x2c580b)[0x59e7bbd80b]
ldc2(+0x2c62e4)[0x59e7bbe2e4]
ldc2(+0x2e1ed5)[0x59e7bd9ed5]
ldc2(+0x378112)[0x59e7c70112]
ldc2(+0x351612)[0x59e7c49612]
ldc2(+0x251d3f)[0x59e7b49d3f]
ldc2(+0x353cbf)[0x59e7c4bcbf]
ldc2(+0x39ce5f)[0x59e7c94e5f]
ldc2(+0x39ce24)[0x59e7c94e24]
ldc2(+0x39cd43)[0x59e7c94d43]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7fec36aa92e1]
ldc2(+0x121c1a)[0x59e7a19c1a]
Segmentation fault
[5/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_markdup.d.o' -c ../sambamba/markdup.d
FAILED: sambamba at exe/sambamba_markdup.d.o
ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
-enable-color -O2 -g -release  -of 'sambamba at exe/sambamba_markdup.d.o'
-c ../sambamba/markdup.d
../sambamba/markdup.d(37): Deprecation: module std.c.stdlib is
deprecated - Import core.stdc.stdlib or core.sys.posix.stdlib instead
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7efdad38acda]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7efdad388fc6]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0e3)[0x7efdad3890e3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7efdac5030c0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7efdac5030c0]
ldc2(+0x2d6242)[0x6901b0242]
ldc2(+0x35b517)[0x690235517]
ldc2(+0x35babb)[0x690235abb]
ldc2(+0x31e1d0)[0x6901f81d0]
ldc2(+0x3183d1)[0x6901f23d1]
ldc2(+0x3237c6)[0x6901fd7c6]
ldc2(+0x319831)[0x6901f3831]
ldc2(+0x307835)[0x6901e1835]
ldc2(+0x306614)[0x6901e0614]
ldc2(+0x304834)[0x6901de834]
ldc2(+0x2cf041)[0x6901a9041]
ldc2(+0x2c59d0)[0x69019f9d0]
ldc2(+0x2c580b)[0x69019f80b]
ldc2(+0x2c62e4)[0x6901a02e4]
ldc2(+0x2e1ed5)[0x6901bbed5]
ldc2(+0x378112)[0x690252112]
ldc2(+0x351612)[0x69022b612]
ldc2(+0x251d3f)[0x69012bd3f]
ldc2(+0x353cbf)[0x69022dcbf]
ldc2(+0x39ce5f)[0x690276e5f]
ldc2(+0x39ce24)[0x690276e24]
ldc2(+0x39cd43)[0x690276d43]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7efdab8db2e1]
ldc2(+0x121c1a)[0x68fffbc1a]
Segmentation fault
[6/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_pileup.d.o' -c ../sambamba/pileup.d
FAILED: sambamba at exe/sambamba_pileup.d.o
ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
-enable-color -O2 -g -release  -of 'sambamba at exe/sambamba_pileup.d.o'
-c ../sambamba/pileup.d
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7fbf74b43cda]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7fbf74b41fc6]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0e3)[0x7fbf74b420e3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7fbf73cbc0c0]
ldc2(+0x2d6242)[0xa88698242]
ldc2(+0x35b517)[0xa8871d517]
ldc2(+0x35babb)[0xa8871dabb]
ldc2(+0x31e1d0)[0xa886e01d0]
ldc2(+0x3183d1)[0xa886da3d1]
ldc2(+0x3237c6)[0xa886e57c6]
ldc2(+0x319831)[0xa886db831]
ldc2(+0x307835)[0xa886c9835]
ldc2(+0x306614)[0xa886c8614]
ldc2(+0x304834)[0xa886c6834]
ldc2(+0x2cf041)[0xa88691041]
ldc2(+0x2c59d0)[0xa886879d0]
ldc2(+0x2c580b)[0xa8868780b]
ldc2(+0x2c62e4)[0xa886882e4]
ldc2(+0x2e1ed5)[0xa886a3ed5]
ldc2(+0x378112)[0xa8873a112]
ldc2(+0x351612)[0xa88713612]
ldc2(+0x251d3f)[0xa88613d3f]
ldc2(+0x353cbf)[0xa88715cbf]
ldc2(+0x39ce5f)[0xa8875ee5f]
ldc2(+0x39ce24)[0xa8875ee24]
ldc2(+0x39cd43)[0xa8875ed43]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7fbf730942e1]
ldc2(+0x121c1a)[0xa884e3c1a]
Segmentation fault
[7/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_slice.d.o' -c ../sambamba/slice.d
[8/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_flagstat.d.o' -c ../sambamba/flagstat.d
[9/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_utils_common_bed.d.o' -c
../sambamba/utils/common/bed.d
[10/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_sort.d.o' -c ../sambamba/sort.d
../sambamba/sort.d(45): Deprecation: module std.c.stdlib is deprecated
- Import core.stdc.stdlib or core.sys.posix.stdlib instead
../sambamba/sort.d(46): Deprecation: module std.c.string is deprecated
- Import core.stdc.string instead
/usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1848):
Deprecation: read-modify-write operations are not allowed for shared
variables. Use core.atomic.atomicOp!"+="(s, e) instead.
/usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1874):
Deprecation: read-modify-write operations are not allowed for shared
variables. Use core.atomic.atomicOp!"*="(e, f) instead.
[11/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O2 -g -release  -of
'sambamba at exe/sambamba_merge.d.o' -c ../sambamba/merge.d
../sambamba/utils/common/readstorage.d(22): Deprecation: module
std.c.stdlib is deprecated - Import core.stdc.stdlib or
core.sys.posix.stdlib instead
../sambamba/utils/common/readstorage.d(23): Deprecation: module
std.c.string is deprecated - Import core.stdc.string instead
/usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1848):
Deprecation: read-modify-write operations are not allowed for shared
variables. Use core.atomic.atomicOp!"+="(s, e) instead.
/usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1874):
Deprecation: read-modify-write operations are not allowed for shared
variables. Use core.atomic.atomicOp!"*="(e, f) instead.
ninja: build stopped: subcommand failed.
dh_auto_build: ninja -j8 -v returned exit code 1
debian/rules:16: recipe for target 'build' failed
make: *** [build] Error 1
dpkg-buildpackage: error: debian/rules build gave error exit status 2

-----

Could you confirm this on your envirnment?

Best regards,
  Nobuhiro

2017-09-20 5:18 GMT+09:00 Debian Bug Tracking System <owner at bugs.debian.org>:
> This is an automatic notification regarding your Bug report
> which was filed against the src:ldc package:
>
> #875535: ldc 1.3 doesn't build any of it's reverse dependencies
>
> It has been closed by Matthias Klumpp <mak at debian.org>.
>
> Their explanation is attached below along with your original report.
> If this explanation is unsatisfactory and you have not received a
> better one in a separate message then please contact Matthias Klumpp <mak at debian.org> by
> replying to this email.
>
>
> --
> 875878: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=875878
> Debian Bug Tracking System
> Contact owner at bugs.debian.org with problems
>
>
> ---------- 転送メッセージ ----------
> From: Matthias Klumpp <mak at debian.org>
> To: 875878-close at bugs.debian.org
> Cc:
> Bcc:
> Date: Tue, 19 Sep 2017 22:14:44 +0200
> Subject: Re: Bug#875878: ldc 1.3 doesn't build any of it's reverse dependencies
> Source: ldc
> Source-Version: 1:1.4.0-1
>
> It appears like this magically fixed itself when building LDC 1.4.0
> against LLVM 5. Apparently, this was an LLVM issue, or some weird bug
> in how LLVM was used by LDC.
>
> Cheers,
>     Matthias
>



-- 
Nobuhiro Iwamatsu
   iwamatsu at {nigauri.org / debian.org}
   GPG ID: 40AD1FA6