Hi all, Libundead was removed as dependency for biod, but it may be there are some other issues now because the D ecosystem keeps moving.
My main interest is sambamba and we are working on a fix for one of the main outstanding bugs building against the latest D compilers. I suggest to drop the packages until we have fixed them. Not many takers anyway (right now). Andreas, I think we'll meet in Paris in November. May be a good time to hack. Pj. On Wed, Sep 18, 2019 at 08:39:52PM +0200, Andreas Tille wrote: > Hi, > > [Pjotr as upstream in CC] > > On Wed, Sep 18, 2019 at 04:54:16PM +0200, Matthias Klumpp wrote: > > Am Fr., 13. Sept. 2019 um 22:51 Uhr schrieb Andreas Tille > > <andr...@an3as.eu>: > > > > > > On Fri, Sep 13, 2019 at 03:37:32PM +0200, Matthias Klumpp wrote: > > > > Am Fr., 13. Sept. 2019 um 15:21 Uhr schrieb Andreas Tille > > > > <andr...@an3as.eu>: > > > > > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of > > > > > '_d_execBssBegAddr' > > > > > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here > > > > > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of > > > > > '_d_execBssEndAddr' > > > > > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here > > > > > collect2: error: ld returned 1 exit status > > > > > [...] > > > > > > > > It's very likely that undeaD needs to be updated first in order to > > > > compile this again. > > > > Has upgrading that been attempted yet? > > > > > > I just upgraded libundead and re-added it to libbiod (I assumed libundead > > > would not have been needed for libbiod any more and thus it was removed) > > > Now the error is: > > > > When I try to compile libbiod now, I get this error: > > ``` > > ../bio/bam/baseinfo.d-mixin-165(165): Error: Options at > > ../bio/bam/baseinfo.d(579) conflicts with Options at > > ../bio/bam/baseinfo.d(482) > > ../bio/bam/baseinfo.d(175): called from here: getRangeMethods() > > ../bio/bam/baseinfo.d(278): Error: template instance > > `bio.bam.baseinfo.PerBaseInfo!(BamRead, "FZ", "MD", cast(Option)0, > > cast(Option)1, cast(Option)2, cast(Option)3)` error instantiating > > ../test/unittests.d(382): instantiated from here: > > basesWith!(BamRead, MixinArg!(string, "flowOrder"), MixinArg!(string, > > "keySequence")) > > [100/177] ldc2 -I=biod_test@exe -I=. -I=.. -I/usr/include/d > > -enable-color -O -g -release -wi -unittest > > -of='biod_test@exe/bio_bam_cigar.d.o' -c ../bio/bam/cigar.d > > [101/177] ldc2 -I=biod_test@exe -I=. -I=.. -I/usr/include/d > > -enable-color -O -g -release -wi -unittest > > -of='biod_test@exe/bio_bam_tagvalue.d.o' -c ../bio/bam/tagvalue.d > > [102/177] ldc2 -I=biod_test@exe -I=. -I=.. -I/usr/include/d > > -enable-color -O -g -release -wi -unittest > > -of='biod_test@exe/bio_bam_bai_indexing.d.o' -c > > ../bio/bam/bai/indexing.d > > [103/177] ldc2 -I=biod_test@exe -I=. -I=.. -I/usr/include/d > > -enable-color -O -g -release -wi -unittest > > -of='biod_test@exe/bio_bam_iontorrent_flowcall.d.o' -c > > ../bio/bam/iontorrent/flowcall.d > > [104/177] ldc2 -I=biod_test@exe -I=. -I=.. -I/usr/include/d > > -enable-color -O -g -release -wi -unittest > > -of='biod_test@exe/bio_bam_thirdparty_msgpack.d.o' -c > > ../bio/bam/thirdparty/msgpack.d > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -header, use '-preview=intpromote' switch or > > -cast(int)(header) > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -header, use '-preview=intpromote' switch or > > -cast(int)(header) > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -cast(byte)-header, use '-preview=intpromote' switch or > > -cast(int)(cast(byte)-header) > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -header, use '-preview=intpromote' switch or > > -cast(int)(header) > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -cast(short)-header, use '-preview=intpromote' switch or > > -cast(int)(cast(short)-header) > > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion > > not done for -header, use '-preview=intpromote' switch or > > -cast(int)(header) > > ninja: build stopped: subcommand failed. > > dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j6 -v > > returned exit code 1 > > ``` > > This is definitely an error in BioD itself, caused by a deprecation > > that turned into an error in recent LDC versions. > > So, libbiod will need to be upgraded for sure to fix this. > > @Pjotr: Can you comment on this? > > > In order to support all architectures and generate a pkg-config file I > > would have to reintroduce the Meson build definition (which upstream > > apparently has removed) or apply some hacks around the existing > > Makefile to make that work in a Debian context, which is quite a bit > > more work. > > As I told you before: I have no idea about meson. It would be great if > we could get it working but if we restrict the package to those > architectures where it builds out of the box and save some manpower I > bet the world will keep on turning round. > > > Btw, if libundead has no users anymore, removing it completely may be > > a good idea - we don't need to maintain something that's dead and has > > no users. > > I was about to file a removal request to ftpmaster before you said in > your last mail that the former build issue might have been caused due > to the lack of libundead. I would really love to get rid of unneeded > packages. > > Kind regards > > Andreas. > > -- > http://fam-tille.de