[Debian-med-packaging] Bug#878837: sambamba: FTBFS with ldc 1.4.0

[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&arch=amd64&ver=0.6.6-1%2Bb1&stamp=1507088043&raw=0
> 
> -----
> [1/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -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/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 -O3 -g -release  -of
> 'sambamba at exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
> [3/74] ldc2  -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -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 -O3 -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
> 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
> 
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