Sorry, my previous mail went to the wrong bug report. ----- Weitergeleitete Nachricht von Andreas Tille <[email protected]> -----
Date: Thu, 9 Dec 2021 09:33:04 +0100 From: Andreas Tille <[email protected]> To: Pjotr Prins <[email protected]> Cc: [email protected] Subject: Re: [biod/BioD] Fails to build with ldc 1.28.0 (Issue #55) Hi Pjotr, in issue #55 [1] you wrote: Thanks @tillea. I wonder if anyone is using BioD. Sambamba imported a subset of BioD, but no longer does that. unfortunately and thus I reassigned the FTBFS bug #908670 [2] to ftpmaster to ask for removal. Unfortunately the meson.build file of sambamba explicitly asks for biod and even if I patch biod out from meson[3] the build fails: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_depth.d.o.deps -of=sambamba.p/sambamba_depth.d.o -c ../sambamba/depth.d FAILED: sambamba.p/sambamba_depth.d.o ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_depth.d.o.deps -of=sambamba.p/sambamba_depth.d.o -c ../sambamba/depth.d ../sambamba/depth.d(22): Error: module `reader` is in file 'bio/std/hts/bam/reader.d' which cannot be read import path[0] = sambamba.p import path[1] = . import path[2] = .. import path[3] = /usr/lib/ldc/x86_64-linux-gnu/include/d import path[4] = /usr/include/d [2/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_main.d.o.deps -of=sambamba.p/sambamba_main.d.o -c ../sambamba/main.d FAILED: sambamba.p/sambamba_main.d.o ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_main.d.o.deps -of=sambamba.p/sambamba_main.d.o -c ../sambamba/main.d ../utils/version_.d(6): Error: module `header` is in file 'bio/std/hts/sam/header.d' which cannot be read import path[0] = sambamba.p import path[1] = . import path[2] = .. import path[3] = /usr/lib/ldc/x86_64-linux-gnu/include/d import path[4] = /usr/include/d [3/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_flagstat.d.o.deps -of=sambamba.p/sambamba_flagstat.d.o -c ../sambamba/flagstat.d FAILED: sambamba.p/sambamba_flagstat.d.o ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_flagstat.d.o.deps -of=sambamba.p/sambamba_flagstat.d.o -c ../sambamba/flagstat.d ../sambamba/flagstat.d(23): Error: module `reader` is in file 'bio/std/hts/bam/reader.d' which cannot be read import path[0] = sambamba.p import path[1] = . import path[2] = .. import path[3] = /usr/lib/ldc/x86_64-linux-gnu/include/d import path[4] = /usr/include/d [4/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d FAILED: sambamba.p/sambamba_fixbins.d.o ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d ../sambamba/fixbins.d(25): Error: module `reader` is in file 'bio/std/hts/bam/reader.d' which cannot be read import path[0] = sambamba.p import path[1] = . import path[2] = .. import path[3] = /usr/lib/ldc/x86_64-linux-gnu/include/d import path[4] = /usr/include/d ninja: build stopped: subcommand failed. dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1 Pjotr, can you please have a look? Kind regards Andreas. [1] https://github.com/biod/BioD/issues/55 [2] https://bugs.debian.org/908670 [3] https://salsa.debian.org/med-team/sambamba/-/blob/master/debian/patches/no_biod_needed.patch -- http://fam-tille.de ----- Ende weitergeleitete Nachricht ----- -- http://fam-tille.de
