[oi-dev] Gnu Data Language
Dariusz Sendkowski
dsendkowski at gmail.com
Tue May 30 13:32:17 UTC 2017
Hi,
I'm struggling with GDL <http://gnudatalanguage.sourceforge.net/> so that
it can be added to oi-userland. Currently it builds successfully but 4 of
178 tests fail.
The point is these tests fail due to missing symbols in gdl executable,
e.g.:
.....
symbol not found: cblas_chemm (/usr/lib/64/libgsl.so.19)
.....
Definitely it missing symbols because those symbols are located in the
/usr/lib/64/libgslcblas.so library.
Funny thing is, that CMake does attempt to link this library:
[100%] Linking CXX executable gdl
cd /projects/oi-userland/components/scientific/gdl/build/amd64/src &&
/usr/bin/cmake -E cmake_link_script CMakeFiles/gdl.dir/link.txt --verbose=1
/usr/gcc/4.9/bin/g++ -m64 -O3 -DNDEBUG -m64
CMakeFiles/gdl.dir/CFMTLexer.cpp.o CMakeFiles/gdl.dir/FMTIn.cpp.o
CMakeFiles/gdl.dir/FMTLexer.cpp.o CMakeFiles/gdl.dir/FMTOut.cpp.o
CMakeFiles/gdl.dir/FMTParser.cpp.o CMakeFiles/gdl.dir/GDLInterpreter.cpp.o
CMakeFiles/gdl.dir/GDLLexer.cpp.o CMakeFiles/gdl.dir/GDLParser.cpp.o
CMakeFiles/gdl.dir/GDLTreeParser.cpp.o CMakeFiles/gdl.dir/allix.cpp.o
CMakeFiles/gdl.dir/arrayindex.cpp.o CMakeFiles/gdl.dir/assocdata.cpp.o
CMakeFiles/gdl.dir/basegdl.cpp.o CMakeFiles/gdl.dir/basic_fun.cpp.o
CMakeFiles/gdl.dir/basic_fun_cl.cpp.o
CMakeFiles/gdl.dir/basic_fun_jmg.cpp.o CMakeFiles/gdl.dir/basic_op.cpp.o
CMakeFiles/gdl.dir/color.cpp.o CMakeFiles/gdl.dir/convert2.cpp.o
CMakeFiles/gdl.dir/convol.cpp.o CMakeFiles/gdl.dir/convol_inc0.cpp.o
CMakeFiles/gdl.dir/convol_inc1.cpp.o CMakeFiles/gdl.dir/convol_inc2.cpp.o
CMakeFiles/gdl.dir/datatypes.cpp.o CMakeFiles/gdl.dir/datatypesref.cpp.o
CMakeFiles/gdl.dir/dcommon.cpp.o CMakeFiles/gdl.dir/dcompiler.cpp.o
CMakeFiles/gdl.dir/default_io.cpp.o CMakeFiles/gdl.dir/dialog.cpp.o
CMakeFiles/gdl.dir/dinterpreter.cpp.o CMakeFiles/gdl.dir/dnode.cpp.o
CMakeFiles/gdl.dir/dpro.cpp.o CMakeFiles/gdl.dir/dstructdesc.cpp.o
CMakeFiles/gdl.dir/dstructgdl.cpp.o CMakeFiles/gdl.dir/dvar.cpp.o
CMakeFiles/gdl.dir/envt.cpp.o CMakeFiles/gdl.dir/extrat.cpp.o
CMakeFiles/gdl.dir/fftw.cpp.o CMakeFiles/gdl.dir/file.cpp.o
CMakeFiles/gdl.dir/fmtnode.cpp.o CMakeFiles/gdl.dir/gdleventhandler.cpp.o
CMakeFiles/gdl.dir/gdlexception.cpp.o CMakeFiles/gdl.dir/gdlgstream.cpp.o
CMakeFiles/gdl.dir/gdlxstream.cpp.o CMakeFiles/gdl.dir/gdljournal.cpp.o
CMakeFiles/gdl.dir/gdlpsstream.cpp.o CMakeFiles/gdl.dir/gdlpython.cpp.o
CMakeFiles/gdl.dir/gdlsvgstream.cpp.o CMakeFiles/gdl.dir/gdlwidget.cpp.o
CMakeFiles/gdl.dir/gdlwidgeteventhandler.cpp.o
CMakeFiles/gdl.dir/gdlwxstream.cpp.o CMakeFiles/gdl.dir/gdlzstream.cpp.o
CMakeFiles/gdl.dir/getfmtast.cpp.o CMakeFiles/gdl.dir/graphicsdevice.cpp.o
CMakeFiles/gdl.dir/basic_pro.cpp.o CMakeFiles/gdl.dir/basic_pro_jmg.cpp.o
CMakeFiles/gdl.dir/grib.cpp.o CMakeFiles/gdl.dir/gshhs.cpp.o
CMakeFiles/gdl.dir/gsl_fun.cpp.o CMakeFiles/gdl.dir/gsl_matrix.cpp.o
CMakeFiles/gdl.dir/hash.cpp.o CMakeFiles/gdl.dir/hdf5_fun.cpp.o
CMakeFiles/gdl.dir/hdf_fun.cpp.o CMakeFiles/gdl.dir/hdf_pro.cpp.o
CMakeFiles/gdl.dir/ifmt.cpp.o CMakeFiles/gdl.dir/image.cpp.o
CMakeFiles/gdl.dir/initct.cpp.o CMakeFiles/gdl.dir/initsysvar.cpp.o
CMakeFiles/gdl.dir/io.cpp.o CMakeFiles/gdl.dir/lapack.cpp.o
CMakeFiles/gdl.dir/least_squares.cpp.o CMakeFiles/gdl.dir/libinit.cpp.o
CMakeFiles/gdl.dir/libinit_ac.cpp.o CMakeFiles/gdl.dir/libinit_cl.cpp.o
CMakeFiles/gdl.dir/libinit_gm.cpp.o CMakeFiles/gdl.dir/libinit_jmg.cpp.o
CMakeFiles/gdl.dir/libinit_mes.cpp.o CMakeFiles/gdl.dir/libinit_ng.cpp.o
CMakeFiles/gdl.dir/libinit_jp.cpp.o CMakeFiles/gdl.dir/list.cpp.o
CMakeFiles/gdl.dir/magick_cl.cpp.o CMakeFiles/gdl.dir/math_fun.cpp.o
CMakeFiles/gdl.dir/math_fun_ac.cpp.o CMakeFiles/gdl.dir/math_fun_gm.cpp.o
CMakeFiles/gdl.dir/math_fun_jmg.cpp.o CMakeFiles/gdl.dir/math_fun_ng.cpp.o
CMakeFiles/gdl.dir/math_utl.cpp.o CMakeFiles/gdl.dir/matrix_cholesky.cpp.o
CMakeFiles/gdl.dir/matrix_invert.cpp.o CMakeFiles/gdl.dir/mpi.cpp.o
CMakeFiles/gdl.dir/ncdf_att_cl.cpp.o CMakeFiles/gdl.dir/ncdf_cl.cpp.o
CMakeFiles/gdl.dir/ncdf_dim_cl.cpp.o CMakeFiles/gdl.dir/ncdf_var_cl.cpp.o
CMakeFiles/gdl.dir/ncdf4_group.cpp.o CMakeFiles/gdl.dir/new.cpp.o
CMakeFiles/gdl.dir/newprognode.cpp.o CMakeFiles/gdl.dir/nullgdl.cpp.o
CMakeFiles/gdl.dir/objects.cpp.o CMakeFiles/gdl.dir/ofmt.cpp.o
CMakeFiles/gdl.dir/overload.cpp.o CMakeFiles/gdl.dir/plotting_axis.cpp.o
CMakeFiles/gdl.dir/plotting_contour.cpp.o
CMakeFiles/gdl.dir/plotting_convert_coord.cpp.o
CMakeFiles/gdl.dir/plotting_cursor.cpp.o
CMakeFiles/gdl.dir/plotting_device.cpp.o
CMakeFiles/gdl.dir/plotting_erase.cpp.o
CMakeFiles/gdl.dir/plotting_image.cpp.o
CMakeFiles/gdl.dir/plotting_map_proj.cpp.o
CMakeFiles/gdl.dir/plotting_misc.cpp.o
CMakeFiles/gdl.dir/plotting_oplot.cpp.o
CMakeFiles/gdl.dir/plotting_plot.cpp.o
CMakeFiles/gdl.dir/plotting_plots.cpp.o
CMakeFiles/gdl.dir/plotting_polyfill.cpp.o
CMakeFiles/gdl.dir/plotting_shade_surf.cpp.o
CMakeFiles/gdl.dir/plotting_surface.cpp.o
CMakeFiles/gdl.dir/plotting_windows.cpp.o
CMakeFiles/gdl.dir/plotting_xyouts.cpp.o CMakeFiles/gdl.dir/plotting.cpp.o
CMakeFiles/gdl.dir/print.cpp.o CMakeFiles/gdl.dir/print_tree.cpp.o
CMakeFiles/gdl.dir/prognode.cpp.o CMakeFiles/gdl.dir/prognode_lexpr.cpp.o
CMakeFiles/gdl.dir/prognodeexpr.cpp.o CMakeFiles/gdl.dir/read.cpp.o
CMakeFiles/gdl.dir/semshm.cpp.o CMakeFiles/gdl.dir/sigfpehandler.cpp.o
CMakeFiles/gdl.dir/str.cpp.o CMakeFiles/gdl.dir/terminfo.cpp.o
CMakeFiles/gdl.dir/topython.cpp.o CMakeFiles/gdl.dir/typetraits.cpp.o
CMakeFiles/gdl.dir/widget.cpp.o CMakeFiles/gdl.dir/gdl.cpp.o -o gdl
-L/usr/openwin/lib/64 antlr/libantlr.a -ldl /usr/lib/64/libncurses.so
/usr/lib/64/libform.so /usr/lib/64/libreadline.so /usr/lib/64/libhistory.so
/usr/lib/64/libz.so /usr/lib/64/libpng.so /usr/lib/64/libz.so -fopenmp
*/usr/lib/64/libgsl.so
/usr/lib/64/libgslcblas.so* /usr/lib/64/libplplotd.so
/usr/lib/64/libplplotcxxd.so /usr/lib/64/libGraphicsMagick.so
/usr/lib/64/libGraphicsMagick++.so -L/usr/lib/amd64 -pthreads -m64 -m64
-L/usr/openwin/lib/64 -lwx_baseu-2.8 -lwx_gtk2u_core-2.8 -lwx_gtk2u_adv-2.8
-lnetcdf /usr/lib/64/libhdf5.so /usr/lib/64/libhdf5_hl.so
/usr/lib/64/libhdf5.so /usr/lib/64/libz.so /usr/lib/64/libdl.so
/usr/lib/64/libm.so /usr/lib/64/libfftw3.so /usr/lib/64/libfftw3f.so
/usr/lib/64/libSM.so /usr/lib/64/libICE.so /usr/lib/64/libX11.so
/usr/lib/64/libXext.so -lsocket -lnsl /usr/lib/64/libpng.so
/usr/lib/64/libgsl.so /usr/lib/64/libgslcblas.so /usr/lib/64/libplplotd.so
/usr/lib/64/libplplotcxxd.so /usr/lib/64/libGraphicsMagick.so
/usr/lib/64/libGraphicsMagick++.so -lwx_baseu-2.8 -lwx_gtk2u_core-2.8
-lwx_gtk2u_adv-2.8 -lnetcdf /usr/lib/64/libhdf5_hl.so /usr/lib/64/libdl.so
/usr/lib/64/libm.so /usr/lib/64/libfftw3.so /usr/lib/64/libfftw3f.so
/usr/lib/64/libSM.so /usr/lib/64/libICE.so /usr/lib/64/libX11.so
/usr/lib/64/libXext.so -lsocket -lnsl -Wl,-R/usr/openwin/lib/64:/usr/lib/64:
but no *libgslcblas.so* is recorded in the gdl executable:
dsend at oi-dev:/projects/oi-userland/components/scientific/gdl$ ldd
build/prototype/i386/usr/bin/gdl
libdl.so.1 => /usr/lib/64/libdl.so.1
libreadline.so.6 => /usr/lib/64/libreadline.so.6
libz.so.1 => /usr/lib/64/libz.so.1
libpng16.so.16 => /usr/lib/64/libpng16.so.16
* libgsl.so.19 => /usr/lib/64/libgsl.so.19*
libplplotd.so.11 => /usr/lib/64/libplplotd.so.11
libplplotcxxd.so.10 => /usr/lib/64/libplplotcxxd.so.10
libGraphicsMagick++.so.12 =>
/usr/lib/64/libGraphicsMagick++.so.12
libwx_baseu-2.8.so.0 => /usr/lib/64/libwx_baseu-2.8.so.0
libwx_gtk2u_core-2.8.so.0 =>
/usr/lib/64/libwx_gtk2u_core-2.8.so.0
libwx_gtk2u_adv-2.8.so.0 =>
/usr/lib/64/libwx_gtk2u_adv-2.8.so.0
libnetcdf.so.11 => /usr/lib/64/libnetcdf.so.11
libhdf5.so.10 => /usr/lib/64/libhdf5.so.10
libm.so.2 => /usr/lib/64/libm.so.2
libfftw3.so.3 => /usr/lib/64/libfftw3.so.3
libfftw3f.so.3 => /usr/lib/64/libfftw3f.so.3
libX11.so.4 => /usr/openwin/lib/64/libX11.so.4
libsocket.so.1 => /usr/lib/64/libsocket.so.1
libnsl.so.1 => /usr/lib/64/libnsl.so.1
libstdc++.so.6 => /usr/lib/64/libstdc++.so.6
librt.so.1 => /usr/lib/64/librt.so.1
libgomp.so.1 => /usr/lib/64/libgomp.so.1
libgcc_s.so.1 => /usr/lib/64/libgcc_s.so.1
libpthread.so.1 => /usr/lib/64/libpthread.so.1
libc.so.1 => /usr/lib/64/libc.so.1
libtermcap.so.1 => /lib/64/libtermcap.so.1
libltdl.so.7 => /usr/lib/64/libltdl.so.7
libcsirocsa.so.0 => /usr/lib/64/libcsirocsa.so.0
libqsastime.so.0 => /usr/lib/64/libqsastime.so.0
libGraphicsMagick.so.3 =>
/usr/lib/amd64/libGraphicsMagick.so.3
libgtk-x11-2.0.so.0 => /usr/lib/64/libgtk-x11-2.0.so.0
libgdk-x11-2.0.so.0 => /usr/lib/64/libgdk-x11-2.0.so.0
libXinerama.so.1 => /usr/lib/64/libXinerama.so.1
libgdk_pixbuf-2.0.so.0 => /usr/lib/64/libgdk_pixbuf-2.0.so.0
libpango-1.0.so.0 => /usr/lib/64/libpango-1.0.so.0
libgobject-2.0.so.0 => /usr/lib/64/libgobject-2.0.so.0
libglib-2.0.so.0 => /usr/lib/64/libglib-2.0.so.0
libXxf86vm.so.1 => /usr/lib/64/libXxf86vm.so.1
libSM.so.6 => /usr/lib/64/libSM.so.6
libjpeg.so.62 => /usr/lib/64/libjpeg.so.62
libtiff.so.5 => /usr/lib/64/libtiff.so.5
libSDL-1.2.so.0 => /usr/lib/64/libSDL-1.2.so.0
libhdf5_hl.so.10 => /usr/lib/64/libhdf5_hl.so.10
libcurl.so.4 => /usr/lib/64/libcurl.so.4
libxcb.so.1 => /usr/lib/64/libxcb.so.1
libXext.so.0 => /usr/lib/64/libXext.so.0
libmp.so.2 => /lib/64/libmp.so.2
libmd.so.1 => /lib/64/libmd.so.1
libwebp.so.5 => /usr/lib/64/libwebp.so.5
liblcms2.so.2 => /usr/lib/64/liblcms2.so.2
libfreetype.so.6 => /usr/lib/64/libfreetype.so.6
libjasper.so.1 => /usr/lib/64/libjasper.so.1
libjpeg.so.8 => /usr/lib/libjpeg8-turbo/lib/amd64/libjpeg.so.8
libbz2.so.1 => /usr/lib/64/libbz2.so.1
libxml2.so.2 => /usr/lib/64/libxml2.so.2
libgmodule-2.0.so.0 => /usr/lib/amd64/libgmodule-2.0.so.0
libpangocairo-1.0.so.0 =>
/usr/lib/amd64/libpangocairo-1.0.so.0
libXfixes.so.1 => /usr/lib/amd64/libXfixes.so.1
libatk-1.0.so.0 => /usr/lib/amd64/libatk-1.0.so.0
libcairo.so.2 => /usr/lib/amd64/libcairo.so.2
libgio-2.0.so.0 => /usr/lib/amd64/libgio-2.0.so.0
libpangoft2-1.0.so.0 => /usr/lib/amd64/libpangoft2-1.0.so.0
libfontconfig.so.1 => /usr/lib/amd64/libfontconfig.so.1
libXrender.so.1 => /usr/lib/64/libXrender.so.1
libXrandr.so.2 => /usr/lib/64/libXrandr.so.2
libXcursor.so.1 => /usr/lib/64/libXcursor.so.1
libXcomposite.so.1 => /usr/lib/64/libXcomposite.so.1
libXdamage.so.1 => /usr/lib/64/libXdamage.so.1
libffi.so.6 => /usr/lib/amd64/libffi.so.6
libICE.so.6 => /usr/lib/64/libICE.so.6
liblzma.so.5 => /usr/lib/64/liblzma.so.5
libnghttp2.so.14 => /usr/lib/64/libnghttp2.so.14
libssh2.so.1 => /usr/lib/64/libssh2.so.1
libssl.so.1.0.0 => /lib/64/libssl.so.1.0.0
libcrypto.so.1.0.0 => /lib/64/libcrypto.so.1.0.0
libgss.so.1 => /usr/lib/64/libgss.so.1
liblber-2.4.so.2 => /usr/lib/64/liblber-2.4.so.2
libldap_r-2.4.so.2 => /usr/lib/64/libldap_r-2.4.so.2
libXau.so.6 => /usr/lib/amd64/libXau.so.6
libXdmcp.so.6 => /usr/lib/amd64/libXdmcp.so.6
libharfbuzz.so.0 => /usr/lib/64/libharfbuzz.so.0
libpixman-1.so.0 => /usr/lib/64/libpixman-1.so.0
libEGL.so.1 => /usr/lib/64/libEGL.so.1
libX11-xcb.so.1 => /usr/lib/64/libX11-xcb.so.1
libxcb-render.so.0 => /usr/lib/64/libxcb-render.so.0
libGL.so.1 => /usr/lib/64/libGL.so.1
libresolv.so.2 => /usr/lib/amd64/libresolv.so.2
libexpat.so.1 => /usr/lib/64/libexpat.so.1
libsasl.so.1 => /usr/lib/amd64/libsasl.so.1
libgraphite2.so.3 => /usr/lib/64/libgraphite2.so.3
libxcb-dri2.so.0 => /usr/lib/64/libxcb-dri2.so.0
libxcb-xfixes.so.0 => /usr/lib/64/libxcb-xfixes.so.0
libxcb-dri3.so.0 => /usr/lib/64/libxcb-dri3.so.0
libxcb-present.so.0 => /usr/lib/64/libxcb-present.so.0
libxcb-sync.so.1 => /usr/lib/64/libxcb-sync.so.1
libxshmfence.so.1 => /usr/lib/64/libxshmfence.so.1
libdrm.so.2 => /usr/lib/xorg/amd64/libdrm.so.2
libglapi.so.0 => /usr/lib/amd64/libglapi.so.0
libxcb-glx.so.0 => /usr/lib/amd64/libxcb-glx.so.0
libdevinfo.so.1 => /lib/64/libdevinfo.so.1
libnvpair.so.1 => /lib/64/libnvpair.so.1
libsec.so.1 => /lib/64/libsec.so.1
libgen.so.1 => /lib/64/libgen.so.1
libavl.so.1 => /lib/64/libavl.so.1
libidmap.so.1 => /usr/lib/64/libidmap.so.1
libuutil.so.1 => /lib/64/libuutil.so.1
libcurses.so.1 => /lib/64/libcurses.so.1
libXevie.so.1 => /usr/lib/64/libXevie.so.1
libXss.so.1 => /usr/lib/64/libXss.so.1
But that's not the end. When I copy the very same linking command executed
by CMake and execute it manually I get what I expect:
dsend at oi-dev:/projects/oi-userland/components/scientific/gdl/build/amd64/src$
ldd gdl
libdl.so.1 => /usr/lib/64/libdl.so.1
libncurses.so.5 => /usr/lib/64/libncurses.so.5
libform.so.1 => /usr/lib/64/libform.so.1
libreadline.so.6 => /usr/lib/64/libreadline.so.6
libhistory.so.6 => /usr/lib/64/libhistory.so.6
libz.so.1 => /usr/lib/64/libz.so.1
libpng16.so.16 => /usr/lib/64/libpng16.so.16
*libgsl.so.19 => /usr/lib/64/libgsl.so.19*
* libgslcblas.so.0 => /usr/lib/64/libgslcblas.so.0*
libplplotd.so.11 => /usr/lib/64/libplplotd.so.11
libplplotcxxd.so.10 => /usr/lib/64/libplplotcxxd.so.10
and boom! *libgslcblas.so *appears as expected and tests pass.
I ran out of ideas why this happens. Maybe I spent too much time on this
problem and cannot see anything right now.
Maybe I'm missing something obvious so another pair of eyes would be great
:)
Any ideas?
You can find the component package files here:
https://github.com/dsendkowski/oi-userland/tree/gdl
regards,
Darek
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