Package: gsl
Version: 2.5+dfsg-4
Severity: normal
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu cosmic ubuntu-patch
Dear Dirk,
In Ubuntu, I noticed that pscan-tfbs was failing to build due to unresolved
symbols in libgsl.so. I don't know if the specific build failure is
reproducible in Debian, but I can confirm that libgsl.so.23 is also
underlinked in Debian resulting in unresolved symbols, which is not supposed
to be the case for shared libraries:
$ ldd -d -r /usr/lib/x86_64-linux-gnu/libgsl.so.23
linux-vdso.so.1 (0x00007ffd39dfc000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fde64546000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fde64389000)
/lib64/ld-linux-x86-64.so.2 (0x00007fde64b6c000)
undefined symbol: cblas_ctrmv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zswap (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zsymm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cgeru (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sgemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ctrsv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sgemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_srotg (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zgemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cdotu_sub (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dznrm2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ddot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_csymm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cher2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zdotu_sub (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sdot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sdsdot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cgerc (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_scnrm2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ctrmm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_strmm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zcopy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsyrk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cherk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zherk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zher (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ztrmv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_drotmg (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dswap (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_scopy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_scasum (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_drotg (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zdotc_sub (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_caxpy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zsyr2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssyr2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_csyr2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ztrsm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ctrsm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssymm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cdotc_sub (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zher2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_saxpy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_idamax (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_snrm2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsdot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cher (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dger (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cher2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dzasum (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsyr2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssyrk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_strmv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dgemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cgemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dasum (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsymv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_srotm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sswap (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dtrmv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_isamax (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zhemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zaxpy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dcopy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sasum (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsyr (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_strsm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_drot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ztrsv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_izamax (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssymv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_chemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zgeru (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dtrsv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_sger (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_srot (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsymm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ztrmm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zdscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zher2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssyr (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dtrmm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zgerc (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_csscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dsyr2k (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_chemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dnrm2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_drotm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_icamax (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zgemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zhemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cgemv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ssyr2 (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_strsv (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dscal (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dgemm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_srotmg (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_dtrsm (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_ccopy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_zsyrk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_cswap (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_daxpy (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
undefined symbol: cblas_csyrk (/usr/lib/x86_64-linux-gnu/libgsl.so.23)
$
Please consider applying the attached patch to the gsl package in Debian. I
have uploaded it to Ubuntu to fix the build failure of the reverse
dependency.
Corresponding changelog entries for these changes:
* debian/patches/gsl-cblas-linkage.patch: add missing linkage on
libgslcblas to libgsl.so.
* specify AUTOMAKE and ACLOCAL to dh_autoreconf, to work around upstream
hard-coding of automake-1.13.
Thanks,
--
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/
slanga...@ubuntu.com vor...@debian.org
diff -Nru gsl-2.5+dfsg/debian/patches/gsl-cblas-linkage.patch
gsl-2.5+dfsg/debian/patches/gsl-cblas-linkage.patch
--- gsl-2.5+dfsg/debian/patches/gsl-cblas-linkage.patch 1969-12-31
16:00:00.000000000 -0800
+++ gsl-2.5+dfsg/debian/patches/gsl-cblas-linkage.patch 2018-08-23
14:33:44.000000000 -0700
@@ -0,0 +1,19 @@
+Description: add missing linkage on libgslcblas to libgsl.so
+ libgsl has missing symbols because it is not linked against libgslcblas.
+ Fix it so the library is properly stand-alone.
+Author: Steve Langasek <steve.langa...@ubuntu.com>
+Last-Modified: 2018-08-23
+
+Index: gsl-2.5+dfsg/Makefile.am
+===================================================================
+--- gsl-2.5+dfsg.orig/Makefile.am
++++ gsl-2.5+dfsg/Makefile.am
+@@ -19,7 +19,7 @@
+
+ lib_LTLIBRARIES = libgsl.la
+ libgsl_la_SOURCES = version.c
+-libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS)
++libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) cblas/libgslcblas.la
+ libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION)
+ noinst_HEADERS = templates_on.h templates_off.h build.h
+
diff -Nru gsl-2.5+dfsg/debian/patches/series gsl-2.5+dfsg/debian/patches/series
--- gsl-2.5+dfsg/debian/patches/series 2018-06-25 04:24:40.000000000 -0700
+++ gsl-2.5+dfsg/debian/patches/series 2018-08-23 13:25:31.000000000 -0700
@@ -1,3 +1,4 @@
dont-disable-deprecated
## dont-disable-deprecated.full
## reset-so-number
+gsl-cblas-linkage.patch
diff -Nru gsl-2.5+dfsg/debian/rules gsl-2.5+dfsg/debian/rules
--- gsl-2.5+dfsg/debian/rules 2018-06-25 04:27:41.000000000 -0700
+++ gsl-2.5+dfsg/debian/rules 2018-08-23 14:33:27.000000000 -0700
@@ -104,7 +104,7 @@
#[ -d doc ] || mkdir doc
#cp -vax debian/Makefile.in.doc doc/Makefile.in
- dh_autoreconf
+ AUTOMAKE=automake ACLOCAL=aclocal dh_autoreconf
./configure CFLAGS="$(CFLAGS)" \
LDFLAGS="$(LDFLAGS)" \
--prefix=/usr \
@@ -131,7 +131,7 @@
#[ -d doc ] || mkdir doc
#cp -vax debian/Makefile.in.doc doc/Makefile.in
- dh_autoreconf
+ AUTOMAKE=automake ACLOCAL=aclocal dh_autoreconf
./configure CFLAGS="$(CFLAGS)" \
--prefix=/usr \
--disable-shared \
