Bug#878837: sambamba: FTBFS with ldc 1.4.0

2017-10-18 Thread Matthias Klumpp 
2017-10-18 9:52 GMT+02:00 Andreas Tille :
> Hi Matthias,
>
> as usual I do not have the slightest idea what to do.  Could I again ask
> for your kind help?  Feel free to commit right to Git if you have any
> patch.

As usual, this is a LLVM/LDC bug, I will file the bugs in Debian's
bugtracker soon and tag this one accordingly.
Thanks for pinging me, I almost forgot to do that.

Cheers,
Matthias


> On Tue, Oct 17, 2017 at 12:42:28PM +0900, Nobuhiro Iwamatsu wrote:
>> Package: sambamba
>> Version: 0.6.6-1
>> Severity: serious
>> Tags: buster sid
>> Justification: FTBFS on amd64
>>
>> Hi,
>>
>> Dear Maintainer,
>>
>> sambamba FTBFS with ldc 1.4.0 on sid.
>>
>> https://buildd.debian.org/status/fetch.php?pkg=sambamba=amd64=0.6.6-1%2Bb1=1507088043=0
>>
>> -
>> [1/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
>> -I/usr/include/htslib -enable-color -O3 -g -release  -of
>> 'sambamba@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/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@exe -I. -I.. -I/usr/include/d/
>> -I/usr/include/htslib -enable-color -O3 -g -release  -of
>> 'sambamba@exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
>> [3/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
>> -I/usr/include/htslib -enable-color -O3 -g -release  -of
>> 'sambamba@exe/sambamba_depth.d.o' -c ../sambamba/depth.d
>> FAILED: sambamba@exe/sambamba_depth.d.o
>> ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
>> -enable-color -O3 -g -release  -of 'sambamba@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
>> ldc2: /build/ldc-1.4.0/ir/irvar.cpp:44: IrGlobal*
>> getIrGlobal(VarDeclaration*, bool): Assertion `decl->ir->irGlobal !=
>> NULL' failed.
>> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7f4948132cea]
>> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7f4948130fd6]
>> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0f3)[0x7f49481310f3]
>> /lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7f49472ab0c0]
>> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcf)[0x7f494647bfff]
>> /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f494647d42a]
>> /lib/x86_64-linux-gnu/libc.so.6(+0x2be67)[0x7f4946474e67]
>> /lib/x86_64-linux-gnu/libc.so.6(+0x2bf12)[0x7f4946474f12]
>> -
>>
>> Perhaps this is not a problem with this package, but I think it is a
>> problem of Dlang.
>> Please forward if necessary.
>>  https://github.com/ldc-developers/ldc/issues/2357
>>
>> Best regards,
>>   Nobuhiro
>>
>>
>> --
>> Nobuhiro Iwamatsu
>>iwamatsu at {nigauri.org / debian.org}
>>GPG ID: 40AD1FA6
>>
>> ___
>> Debian-med-packaging mailing list
>> debian-med-packag...@lists.alioth.debian.org
>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>
>
> --
> http://fam-tille.de



-- 
Debian Developer | Freedesktop-Developer
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Bug#878837: sambamba: FTBFS with ldc 1.4.0

2017-10-18 Thread Andreas Tille 
Hi Matthias,

as usual I do not have the slightest idea what to do.  Could I again ask
for your kind help?  Feel free to commit right to Git if you have any
patch.

Thanks a lot

 Andreas.

On Tue, Oct 17, 2017 at 12:42:28PM +0900, Nobuhiro Iwamatsu wrote:
> Package: sambamba
> Version: 0.6.6-1
> Severity: serious
> Tags: buster sid
> Justification: FTBFS on amd64
> 
> Hi,
> 
> Dear Maintainer,
> 
> sambamba FTBFS with ldc 1.4.0 on sid.
> 
> https://buildd.debian.org/status/fetch.php?pkg=sambamba=amd64=0.6.6-1%2Bb1=1507088043=0
> 
> -
> [1/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release  -of
> 'sambamba@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/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@exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release  -of
> 'sambamba@exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
> [3/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release  -of
> 'sambamba@exe/sambamba_depth.d.o' -c ../sambamba/depth.d
> FAILED: sambamba@exe/sambamba_depth.d.o
> ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
> -enable-color -O3 -g -release  -of 'sambamba@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
> ldc2: /build/ldc-1.4.0/ir/irvar.cpp:44: IrGlobal*
> getIrGlobal(VarDeclaration*, bool): Assertion `decl->ir->irGlobal !=
> NULL' failed.
> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7f4948132cea]
> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7f4948130fd6]
> /usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0f3)[0x7f49481310f3]
> /lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7f49472ab0c0]
> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcf)[0x7f494647bfff]
> /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f494647d42a]
> /lib/x86_64-linux-gnu/libc.so.6(+0x2be67)[0x7f4946474e67]
> /lib/x86_64-linux-gnu/libc.so.6(+0x2bf12)[0x7f4946474f12]
> -
> 
> Perhaps this is not a problem with this package, but I think it is a
> problem of Dlang.
> Please forward if necessary.
>  https://github.com/ldc-developers/ldc/issues/2357
> 
> Best regards,
>   Nobuhiro
> 
> 
> -- 
> Nobuhiro Iwamatsu
>iwamatsu at {nigauri.org / debian.org}
>GPG ID: 40AD1FA6
> 
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de

Bug#878837: sambamba: FTBFS with ldc 1.4.0

2017-10-16 Thread Nobuhiro Iwamatsu 
Package: sambamba
Version: 0.6.6-1
Severity: serious
Tags: buster sid
Justification: FTBFS on amd64

Hi,

Dear Maintainer,

sambamba FTBFS with ldc 1.4.0 on sid.

https://buildd.debian.org/status/fetch.php?pkg=sambamba=amd64=0.6.6-1%2Bb1=1507088043=0

-
[1/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O3 -g -release  -of
'sambamba@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/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@exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O3 -g -release  -of
'sambamba@exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
[3/74] ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/
-I/usr/include/htslib -enable-color -O3 -g -release  -of
'sambamba@exe/sambamba_depth.d.o' -c ../sambamba/depth.d
FAILED: sambamba@exe/sambamba_depth.d.o
ldc2  -Isambamba@exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
-enable-color -O3 -g -release  -of 'sambamba@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
ldc2: /build/ldc-1.4.0/ir/irvar.cpp:44: IrGlobal*
getIrGlobal(VarDeclaration*, bool): Assertion `decl->ir->irGlobal !=
NULL' failed.
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys15PrintStackTraceERNS_11raw_ostreamE+0x1a)[0x7f4948132cea]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(_ZN4llvm3sys17RunSignalHandlersEv+0x56)[0x7f4948130fd6]
/usr/lib/x86_64-linux-gnu/libLLVM-5.0.so.1(+0x86e0f3)[0x7f49481310f3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7f49472ab0c0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcf)[0x7f494647bfff]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f494647d42a]
/lib/x86_64-linux-gnu/libc.so.6(+0x2be67)[0x7f4946474e67]
/lib/x86_64-linux-gnu/libc.so.6(+0x2bf12)[0x7f4946474f12]
-

Perhaps this is not a problem with this package, but I think it is a
problem of Dlang.
Please forward if necessary.
 https://github.com/ldc-developers/ldc/issues/2357

Best regards,
  Nobuhiro


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