Error: read-modify-write operations are not allowed for shared variables.

[tillea]

Hi
the build of the Debian package of sambamba (version 0.6.7) fails since some time which is documented in the according bug report. There is the suspicion that the transition of the D compiler has uncovered this error:

[5/74] 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
[6/74] ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/sambamba_depth.d.o' -c ../sambamba/depth.d

Kind regards, Andreas.

[pjotrp]

I think was fixed in cb170d6

[pjotrp]

New release is coming soon.

[tillea]

On Wed, Aug 29, 2018 at 10:16:29PM -0700, Pjotr Prins wrote: I think was fixed in cb170d6

Thanks a lot, Andreas.

[LocutusOfBorg]

I tried the patch mentioned, with some changes (because it didn't apply on top of 0.6.7), and it failed.

Using 0.6.8-pre available for download fails too

Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
Build type: native build
Project name: Sambamba
Project version: undefined
Appending DFLAGS from environment: '-O -g -release -wi'
Appending LDFLAGS from environment: '-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now'
Native D compiler: ldc2 (llvm 1.11.0 "LDC - the LLVM D compiler (1.11.0):")
Build machine cpu family: x86_64
Build machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (0.29.1)
Native dependency undead found: YES 1.0.7
Native dependency biod found: YES 0.1.0
Native dependency liblz4 found: YES 1.8.2
Native dependency htslib found: YES 1.7-2
Program ldmd2 found: YES (/usr/bin/ldmd2)
Program mkdir found: YES (/bin/mkdir)
Build targets in project: 2
Found ninja-1.8.2 at /usr/bin/ninja
   dh_auto_build -O--buildsystem=meson
	cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v
[1/74] ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/main.d.o' -c ../main.d
FAILED: sambamba@exe/main.d.o 
ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/main.d.o' -c ../main.d
../sambamba/view.d(40): Error: module `unpack` is in file 'bio2/unpack.d' which cannot be read
import path[0] = sambamba@exe
import path[1] = .
import path[2] = ..
import path[3] = /usr/include/d
import path[4] = /usr/lib/ldc/x86_64-linux-gnu/include/d/ldc
import path[5] = /usr/lib/ldc/x86_64-linux-gnu/include/d
import path[6] = /usr/include/d
[2/74] ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
[3/74] ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/sambamba_flagstat.d.o' -c ../sambamba/flagstat.d
[4/74] ldc2 -Isambamba@exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba@exe/sambamba_depth.d.o' -c ../sambamba/depth.d
ninja: build stopped: subcommand failed.
dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:9: build] Error 1
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--------------------------------------------------------------------------------

[pjotrp]

can you show the actual error? It is not the same file Andreas had.

btw the current master was successfully built on Linux with ldc 1.11 - see the travis log. https://travis-ci.org/biod/sambamba

[LocutusOfBorg]

full build log
https://launchpadlibrarian.net/388366053/buildlog_ubuntu-cosmic-amd64.sambamba_0.6.7-2ubuntu2_BUILDING.txt.gz

[pjotrp]

Ah, OK.

   ../sambamba/view.d(40): Error: module `unpack` is in file 'bio2/unpack.d' which cannot be read

is because files got moved around in the biod submodule.

I can put out a 0.6.8 release soon which fixes all that. When do you need it?

[tillea]

On Fri, Sep 14, 2018 at 04:05:30AM -0700, Pjotr Prins wrote: I can put out a 0.6.8 release soon which fixes all that. When do you need it?

Good. I can not name a specific data but it would be nice to have it sooner. There are a lot of bugs on my table and getting rid of some of them would be helpful. Thanks for the good support of the Debian packaging Andreas.

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