UPDATE: When building the component manually (unpacking, cmake and then gmake) everything is as expected, i.e.:
dsend@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 <dsendkow...@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@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@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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