[Debian-med-packaging] Bug#907358: ncbi-vdb: fix broken library on i386

[Steve Langasek]

Package: ncbi-vdb
Version: 2.9.1-1+dfsg-1
Severity: grave
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu cosmic ubuntu-patch

Dear Andreas,

The libncbi-vdb2 library is broken on i386, because while it has managed to
build, it has unresolvable references:

$ ldd -d -r /usr/lib/i386-linux-gnu/libncbi-vdb.so.2
	linux-gate.so.1 (0xf7f0d000)
	libmbedx509.so.0 => /usr/lib/i386-linux-gnu/libmbedx509.so.0 (0xf7a33000)
	libmbedtls.so.10 => /usr/lib/i386-linux-gnu/libmbedtls.so.10 (0xf7a03000)
	libmbedcrypto.so.1 => /usr/lib/i386-linux-gnu/libmbedcrypto.so.1 (0xf7999000)
	libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0xf797a000)
	libbz2.so.1.0 => /lib/i386-linux-gnu/libbz2.so.1.0 (0xf7968000)
	libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0xf7963000)
	libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xf7944000)
	libxml2.so.2 => /usr/lib/i386-linux-gnu/libxml2.so.2 (0xf7757000)
	libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xf7655000)
	libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xf7479000)
	/lib/ld-linux.so.2 (0xf7f0f000)
	libicuuc.so.60 => /usr/lib/i386-linux-gnu/libicuuc.so.60 (0xf72b8000)
	liblzma.so.5 => /lib/i386-linux-gnu/liblzma.so.5 (0xf728c000)
	libicudata.so.60 => /usr/lib/i386-linux-gnu/libicudata.so.60 (0xf58e2000)
	libstdc++.so.6 => /usr/lib/i386-linux-gnu/libstdc++.so.6 (0xf575b000)
	libgcc_s.so.1 => /lib/i386-linux-gnu/libgcc_s.so.1 (0xf573d000)
undefined symbol: uint64_msbit	(/usr/lib/i386-linux-gnu/libncbi-vdb.so.2)
$

This is because there is no implementation of uint64_msbit for the gcc/i386
target.

However, there doesn't appear to be anything about the gcc/x86_64
implementation which is 64-bit-specific, so attached is a patch that fixes
this bug by simply copying the x86_64 implementation to the i386 file.

This problem was discovered because it caused a build failure for sra-sdk on
i386 in Ubuntu when trying to link against the library at build time.  The
same build failure appears to exist in Debian.

It would also be perfectly reasonable to drop i386 as a supported
architecture for ncbi-vdb if you prefer; but I suggest you then make sure to
actually do this, rather than shipping a broken library package on i386.

Also, this broken library package would have been detectable at build time
if you were building with -Wl,-z,defs in LDFLAGS, as that would have
prevented ever generating a shared library with missing symbols.  That's a
good idea to do anyway, but in particular it would mean that if you didn't
want to support i386 anymore, you could just add this to build flags and not
have to worry about changing the architecture list explicitly.

Cheers,
-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
diff -Nru ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch
--- ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch	1969-12-31 16:00:00.000000000 -0800
+++ ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch	2018-08-26 14:57:18.000000000 -0700
@@ -0,0 +1,25 @@
+Description: add missing implementation of uint64_msbit for i386
+ Without this definition, we get a "successful" library build with undefined
+ symbols on i386.  We can use the same implementation of this function as on
+ x86_64.
+Author: Steve Langasek <steve.langasek at ubuntu.com>
+Last-Modified: 2018-08-26
+
+Index: ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h
+===================================================================
+--- ncbi-vdb-2.9.1-1+dfsg.orig/interfaces/cc/gcc/i386/arch-impl.h
++++ ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h
+@@ -127,6 +127,13 @@ int32_t uint32_msbit ( uint32_t self )
+     return rtn;
+ }
+ 
++static __inline__
++int32_t uint64_msbit ( uint64_t self )
++{
++    if (self==0) return -1;
++    return 63 - __builtin_clzll ( self );
++}
++
+ typedef struct int128_t int128_t;
+ struct int128_t
+ {
diff -Nru ncbi-vdb-2.9.1-1+dfsg/debian/patches/series ncbi-vdb-2.9.1-1+dfsg/debian/patches/series
--- ncbi-vdb-2.9.1-1+dfsg/debian/patches/series	2018-06-27 20:41:16.000000000 -0700
+++ ncbi-vdb-2.9.1-1+dfsg/debian/patches/series	2018-08-26 14:58:11.000000000 -0700
@@ -9,3 +9,4 @@
 add_-msse2.patch
 use_debian_packaged_libmbedx.patch
 mbedtls_ssl_init.patch
+i386-uint64_msbit.patch