Bug#907489: sambamba FTBFS
Control: forwarded -1 https://github.com/biod/sambamba/issues/362 Control: tags -1 upstream On Wed, Aug 29, 2018 at 04:14:48PM +0200, Matthias Klumpp wrote: > > This appears to be a different issue to me - this one is a bit weirder > than the BioD one. You can either apply the BioD patch and see if that > fixes the problem, It does not unfortunately. > or directly report it upstream. This does not look > Debian-specific at all, it rather looks like a generic upstream issue > that happened because we are currently in a transition to a more > recent compiler in Debian. I reported issue #362. Thanks a lot for your help Andreas. -- http://fam-tille.de
Bug#907489: sambamba FTBFS
Am Di., 28. Aug. 2018 um 20:16 Uhr schrieb Andreas Tille : > > Control: tags -1 help > > Hi Matthias, > > do you have any idea? Its most probably connected to the > libbiod bug. > [...] This appears to be a different issue to me - this one is a bit weirder than the BioD one. You can either apply the BioD patch and see if that fixes the problem, or directly report it upstream. This does not look Debian-specific at all, it rather looks like a generic upstream issue that happened because we are currently in a transition to a more recent compiler in Debian. Cheers, Matthias -- I welcome VSRE emails. See http://vsre.info/
Bug#907489: sambamba FTBFS
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@exe -I. -I.. -I/usr/include/d -enable-color -O -g
> -release -wi -of 'sambamba@exe/sambamba_sort.d.o' -c ../sambamba/sort.d
> FAILED: sambamba@exe/sambamba_sort.d.o
> ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release
> -wi -of 'sambamba@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@exe -I. -I.. -I/usr/include/d -enable-color -O -g
> -release -wi -of 'sambamba@exe/sambamba_merge.d.o' -c ../sambamba/merge.d
> FAILED: sambamba@exe/sambamba_merge.d.o
> ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release
> -wi -of 'sambamba@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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> debian-med-packag...@alioth-lists.debian.net
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--
http://fam-tille.de
Bug#907489: sambamba FTBFS
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@exe -I. -I.. -I/usr/include/d -enable-color -O -g
-release -wi -of 'sambamba@exe/sambamba_sort.d.o' -c ../sambamba/sort.d
FAILED: sambamba@exe/sambamba_sort.d.o
ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi
-of 'sambamba@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@exe -I. -I.. -I/usr/include/d -enable-color -O -g
-release -wi -of 'sambamba@exe/sambamba_merge.d.o' -c ../sambamba/merge.d
FAILED: sambamba@exe/sambamba_merge.d.o
ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi
-of 'sambamba@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
