[oi-dev] Gnu Data Language
Dariusz Sendkowski
dsendkowski at gmail.com
Tue May 30 17:14:46 UTC 2017
UPDATE:
When building the component manually (unpacking, cmake and then gmake)
everything is as expected, i.e.:
dsend at oi-dev:/projects/oi-userland/components/scientific/gdl/build$ ldd
src/gdl | grep gsl
libgsl.so.19 => /usr/lib/64/libgsl.so.19
libgslcblas.so.0 => /usr/lib/64/libgslcblas.so.0
When building from the component package Makefile (gmake build)
libgslcblas.so.0 record in gdl is missing.
Am I missing something in the Makefile?
2017-05-30 15:32 GMT+02:00 Dariusz Sendkowski <dsendkowski at gmail.com>:
> 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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