Bug#907266: RM: sra-sdk [i386] -- ROM; Does not build fir i386 any more - please remove old version of arch i386
> > I am not sure, but is there something specific to x86_64 in this > > implementation or does it fit also for i386? > > I admit I have no idea. However, usually upstream of this type of > software is concentrating on amd64 exclusively since this is what is > practically used for gene sequencing. > > > But even if this implementation is copied then later a file atomic64.h > > is missing, that exists for x86_64 but not i386. > > Am I understand correctly that this might be a good reason to make > ncbi-vdb amd64 only? Latest build log[1] on i386 ends in ... gcc -c -DNDEBUG -m32 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux32 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<>/sra-sdk-2.9.2+dfsg/interfaces/override -I/<>/sra-sdk-2.9.2+dfsg/tools/fasterq-dump/linux -I/<>/sra-sdk-2.9.2+dfsg/tools/fasterq-dump/unix -I/<>/sra-sdk-2.9.2+dfsg/tools/fasterq-dump -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/i386 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<>/sra-sdk-2.9.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o progress_thread.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 /<>/sra-sdk-2.9.2+dfsg/tools/fasterq-dump/progress_thread.c -D__mod_name__=tools/fasterq-dump -D__file_name__=progress_thread -D__file_ext__=c /<>/sra-sdk-2.9.2+dfsg/tools/fasterq-dump/progress_thread.c:43:10: fatal error: atomic64.h: No such file or directory #include ^~~~ So I'll stop i386 support here and will upload with Architecture: amd64. Please remove the remaining i386 builds of this package. Thanks for your work as ftpmaster Andreas. [1] https://buildd.debian.org/status/fetch.php?pkg=sra-sdk=i386=2.9.2%2Bdfsg-1=1536567486=0 -- http://fam-tille.de
Bug#907266: RM: sra-sdk [i386] -- ROM; Does not build fir i386 any more - please remove old version of arch i386
Hello Andreas, >> But even if this implementation is copied then later a file atomic64.h >> is missing, that exists for x86_64 but not i386. > > Am I understand correctly that this might be a good reason to make > ncbi-vdb amd64 only? Probably it was too late yesterday, because today I cannot get this atomic64.h failure again (instead error: unknown type name ‘HttpProxy’). Nevertheless, dropping 32 bit platforms might be reasonable because upstream is not caring about them anymore, like mentioned in 2016 in the issue "Please remove explicit -m32/-m64 switch" reported by you to upstream: ... We do have workaround code in all known places, but we no longer test our code under 32-bits and ... In the meantime bug [2] got opened in Debian against ncbi-vdb that is exactly this issue about uint64_msbit found by Ubuntu with the same proposed change. Kind regards, Bernhard [1] https://github.com/ncbi/ncbi-vdb/commit/ec24d0c332cdb738a2f4516ad8bf53dd55743457 [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=907358
Bug#907266: RM: sra-sdk [i386] -- ROM; Does not build fir i386 any more - please remove old version of arch i386
Hi Bernhard, On Sun, Aug 26, 2018 at 10:41:13PM +0200, Bernhard Übelacker wrote: > Hello, > just tried to find out why the i386 build is failing. Thanks a lot for the investigation. > I think the fault lies in libncbi-vdb-dev, as it does not > supply an implementation for i386 for function uint64_msbit, > like it does for x86_64. > (And it should probably use something like "-Wl,--no-undefined".) > > The implementation for amd64 is inside this file: > ./ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/x86_64/arch-impl.h > > And should probably be also here: > ./ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h > > I am not sure, but is there something specific to x86_64 in this > implementation or does it fit also for i386? I admit I have no idea. However, usually upstream of this type of software is concentrating on amd64 exclusively since this is what is practically used for gene sequencing. > But even if this implementation is copied then later a file atomic64.h > is missing, that exists for x86_64 but not i386. Am I understand correctly that this might be a good reason to make ncbi-vdb amd64 only? Kind regards Andreas. -- http://fam-tille.de
Bug#907266: RM: sra-sdk [i386] -- ROM; Does not build fir i386 any more - please remove old version of arch i386
Hello, just tried to find out why the i386 build is failing. I think the fault lies in libncbi-vdb-dev, as it does not supply an implementation for i386 for function uint64_msbit, like it does for x86_64. (And it should probably use something like "-Wl,--no-undefined".) The implementation for amd64 is inside this file: ./ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/x86_64/arch-impl.h And should probably be also here: ./ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h I am not sure, but is there something specific to x86_64 in this implementation or does it fit also for i386? But even if this implementation is copied then later a file atomic64.h is missing, that exists for x86_64 but not i386. Kind regards, Bernhard
Bug#907266: RM: sra-sdk [i386] -- ROM; Does not build fir i386 any more - please remove old version of arch i386
Package: ftp.debian.org Severity: normal Please remove sra-sdk for architecture i386 to enable migration of a bug free amd64 version in sid. Kind regards Andreas.
