[Debian-med-packaging] Bug#907489: sambamba FTBFS

[Andreas Tille]

Control: tags -1 help

Hi Matthias,

do you have any idea?  Its most probably connected to the
libbiod bug.

Kind regards

     Andreas.

On Tue, Aug 28, 2018 at 08:32:32PM +0300, Adrian Bunk wrote:
> Source: sambamba
> Version: 0.6.7-2
> Severity: serious
> Tags: ftbfs
> 
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/sambamba.html
> 
> ...
> [5/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_sort.d.o' -c ../sambamba/sort.d
> FAILED: sambamba at exe/sambamba_sort.d.o 
> ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_sort.d.o' -c ../sambamba/sort.d
> /usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1845): Error: 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(1871): Error: read-modify-write operations are not allowed for `shared` variables. Use `core.atomic.atomicOp!"*="(e, f)` instead.
> ../sambamba/sort.d(427): Error: template instance `std.numeric.normalize!(shared(float)[])` error instantiating
> ../sambamba/sort.d(265):        instantiated from here: `mergeSortedChunks!(compareReadNames)`
> ../sambamba/sort.d(445): Error: forward reference to inferred return type of function call `function (ulong j)
> {
> return (lazy float progress)
> {
> atomicStore(merging_progress[j], progress);
> synchronized(bar) {
> bar.update(dotProduct(merging_progress, weights));
> }
> }
> ;
> }
> (i)`
> ../sambamba/sort.d(267): Error: template instance `sambamba.sort.Sorter.mergeSortedChunks!(mixedCompareReadNames)` error instantiating
> ../sambamba/sort.d(269): Error: template instance `sambamba.sort.Sorter.mergeSortedChunks!(compareCoordinatesAndStrand)` error instantiating
> [6/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_merge.d.o' -c ../sambamba/merge.d
> FAILED: sambamba at exe/sambamba_merge.d.o 
> ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_merge.d.o' -c ../sambamba/merge.d
> /usr/lib/ldc/x86_64-linux-gnu/include/d/std/numeric.d(1845): Error: 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(1871): Error: read-modify-write operations are not allowed for `shared` variables. Use `core.atomic.atomicOp!"*="(e, f)` instead.
> ../sambamba/merge.d(407): Error: template instance `std.numeric.normalize!(shared(float)[])` error instantiating
> 
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