<div dir="ltr"><div><div><br>UPDATE:<br><br></div>When building the component manually (unpacking, cmake and then gmake) everything is as expected, i.e.:<br><br><span style="font-family:monospace,monospace">dsend@oi-dev:/projects/oi-userland/components/scientific/gdl/build$ ldd src/gdl | grep gsl<br> libgsl.so.19 => /usr/lib/64/libgsl.so.19<br> libgslcblas.so.0 => /usr/lib/64/libgslcblas.so.0</span><br><br></div>When building from the component package Makefile (<span style="font-family:monospace,monospace">gmake build</span>) <span style="font-family:monospace,monospace">libgslcblas.so.0</span><span style="font-family:arial,helvetica,sans-serif"> record in <span style="font-family:monospace,monospace">gdl</span> is missing.</span><span style="font-family:monospace,monospace"><br></span><div><br></div><div>Am I missing something in the Makefile?<br></div><div><br><div><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-05-30 15:32 GMT+02:00 Dariusz Sendkowski <span dir="ltr"><<a href="mailto:dsendkowski@gmail.com" target="_blank">dsendkowski@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi,<br><br><br></div>I'm struggling with <a href="http://gnudatalanguage.sourceforge.net/" target="_blank">GDL</a> so that it can be added to oi-userland. Currently it builds successfully but 4 of 178 tests fail.<br></div>The point is these tests fail due to missing symbols in <span style="font-family:monospace,monospace">gdl</span> executable, e.g.:<br><br><br>.....<br><span style="font-family:monospace,monospace">symbol not found: cblas_chemm (/usr/lib/64/libgsl.so.19)</span><br>.....<br><div><br></div><div>Definitely it missing symbols because those symbols are located in the <span style="font-family:monospace,monospace">/usr/lib/64/libgslcblas.so</span> library.<br></div><div>Funny thing is, that <span style="font-family:monospace,monospace">CMake</span> does attempt to link this library:<br><br><br><br><span style="font-family:monospace,monospace">[100%] Linking CXX executable gdl<br>cd /projects/oi-userland/<wbr>components/scientific/gdl/<wbr>build/amd64/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gdl.dir/link.txt --verbose=1<br>/usr/gcc/4.9/bin/g++ -m64 -O3 -DNDEBUG -m64 CMakeFiles/gdl.dir/CFMTLexer.<wbr>cpp.o CMakeFiles/gdl.dir/FMTIn.cpp.o CMakeFiles/gdl.dir/FMTLexer.<wbr>cpp.o CMakeFiles/gdl.dir/FMTOut.cpp.<wbr>o CMakeFiles/gdl.dir/FMTParser.<wbr>cpp.o CMakeFiles/gdl.dir/<wbr>GDLInterpreter.cpp.o CMakeFiles/gdl.dir/GDLLexer.<wbr>cpp.o CMakeFiles/gdl.dir/GDLParser.<wbr>cpp.o CMakeFiles/gdl.dir/<wbr>GDLTreeParser.cpp.o CMakeFiles/gdl.dir/allix.cpp.o CMakeFiles/gdl.dir/arrayindex.<wbr>cpp.o CMakeFiles/gdl.dir/assocdata.<wbr>cpp.o CMakeFiles/gdl.dir/basegdl.<wbr>cpp.o CMakeFiles/gdl.dir/basic_fun.<wbr>cpp.o CMakeFiles/gdl.dir/basic_fun_<wbr>cl.cpp.o CMakeFiles/gdl.dir/basic_fun_<wbr>jmg.cpp.o CMakeFiles/gdl.dir/basic_op.<wbr>cpp.o CMakeFiles/gdl.dir/color.cpp.o CMakeFiles/gdl.dir/convert2.<wbr>cpp.o CMakeFiles/gdl.dir/convol.cpp.<wbr>o CMakeFiles/gdl.dir/convol_<wbr>inc0.cpp.o CMakeFiles/gdl.dir/convol_<wbr>inc1.cpp.o CMakeFiles/gdl.dir/convol_<wbr>inc2.cpp.o CMakeFiles/gdl.dir/datatypes.<wbr>cpp.o CMakeFiles/gdl.dir/<wbr>datatypesref.cpp.o CMakeFiles/gdl.dir/dcommon.<wbr>cpp.o 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CMakeFiles/gdl.dir/gdlzstream.<wbr>cpp.o CMakeFiles/gdl.dir/getfmtast.<wbr>cpp.o CMakeFiles/gdl.dir/<wbr>graphicsdevice.cpp.o CMakeFiles/gdl.dir/basic_pro.<wbr>cpp.o CMakeFiles/gdl.dir/basic_pro_<wbr>jmg.cpp.o CMakeFiles/gdl.dir/grib.cpp.o CMakeFiles/gdl.dir/gshhs.cpp.o CMakeFiles/gdl.dir/gsl_fun.<wbr>cpp.o CMakeFiles/gdl.dir/gsl_matrix.<wbr>cpp.o CMakeFiles/gdl.dir/hash.cpp.o CMakeFiles/gdl.dir/hdf5_fun.<wbr>cpp.o CMakeFiles/gdl.dir/hdf_fun.<wbr>cpp.o CMakeFiles/gdl.dir/hdf_pro.<wbr>cpp.o CMakeFiles/gdl.dir/ifmt.cpp.o CMakeFiles/gdl.dir/image.cpp.o CMakeFiles/gdl.dir/initct.cpp.<wbr>o CMakeFiles/gdl.dir/initsysvar.<wbr>cpp.o CMakeFiles/gdl.dir/io.cpp.o CMakeFiles/gdl.dir/lapack.cpp.<wbr>o CMakeFiles/gdl.dir/least_<wbr>squares.cpp.o CMakeFiles/gdl.dir/libinit.<wbr>cpp.o CMakeFiles/gdl.dir/libinit_ac.<wbr>cpp.o CMakeFiles/gdl.dir/libinit_cl.<wbr>cpp.o CMakeFiles/gdl.dir/libinit_gm.<wbr>cpp.o CMakeFiles/gdl.dir/libinit_<wbr>jmg.cpp.o CMakeFiles/gdl.dir/libinit_<wbr>mes.cpp.o CMakeFiles/gdl.dir/libinit_ng.<wbr>cpp.o CMakeFiles/gdl.dir/libinit_jp.<wbr>cpp.o CMakeFiles/gdl.dir/list.cpp.o CMakeFiles/gdl.dir/magick_cl.<wbr>cpp.o CMakeFiles/gdl.dir/math_fun.<wbr>cpp.o CMakeFiles/gdl.dir/math_fun_<wbr>ac.cpp.o CMakeFiles/gdl.dir/math_fun_<wbr>gm.cpp.o CMakeFiles/gdl.dir/math_fun_<wbr>jmg.cpp.o CMakeFiles/gdl.dir/math_fun_<wbr>ng.cpp.o CMakeFiles/gdl.dir/math_utl.<wbr>cpp.o CMakeFiles/gdl.dir/matrix_<wbr>cholesky.cpp.o CMakeFiles/gdl.dir/matrix_<wbr>invert.cpp.o CMakeFiles/gdl.dir/mpi.cpp.o CMakeFiles/gdl.dir/ncdf_att_<wbr>cl.cpp.o CMakeFiles/gdl.dir/ncdf_cl.<wbr>cpp.o CMakeFiles/gdl.dir/ncdf_dim_<wbr>cl.cpp.o CMakeFiles/gdl.dir/ncdf_var_<wbr>cl.cpp.o CMakeFiles/gdl.dir/ncdf4_<wbr>group.cpp.o CMakeFiles/gdl.dir/new.cpp.o CMakeFiles/gdl.dir/<wbr>newprognode.cpp.o CMakeFiles/gdl.dir/nullgdl.<wbr>cpp.o CMakeFiles/gdl.dir/objects.<wbr>cpp.o CMakeFiles/gdl.dir/ofmt.cpp.o CMakeFiles/gdl.dir/overload.<wbr>cpp.o CMakeFiles/gdl.dir/plotting_<wbr>axis.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>contour.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>convert_coord.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>cursor.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>device.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>erase.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>image.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>map_proj.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>misc.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>oplot.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>plot.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>plots.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>polyfill.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>shade_surf.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>surface.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>windows.cpp.o CMakeFiles/gdl.dir/plotting_<wbr>xyouts.cpp.o CMakeFiles/gdl.dir/plotting.<wbr>cpp.o CMakeFiles/gdl.dir/print.cpp.o CMakeFiles/gdl.dir/print_tree.<wbr>cpp.o CMakeFiles/gdl.dir/prognode.<wbr>cpp.o CMakeFiles/gdl.dir/prognode_<wbr>lexpr.cpp.o CMakeFiles/gdl.dir/<wbr>prognodeexpr.cpp.o CMakeFiles/gdl.dir/read.cpp.o CMakeFiles/gdl.dir/semshm.cpp.<wbr>o CMakeFiles/gdl.dir/<wbr>sigfpehandler.cpp.o CMakeFiles/gdl.dir/str.cpp.o CMakeFiles/gdl.dir/terminfo.<wbr>cpp.o CMakeFiles/gdl.dir/topython.<wbr>cpp.o CMakeFiles/gdl.dir/typetraits.<wbr>cpp.o CMakeFiles/gdl.dir/widget.cpp.<wbr>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 <font size="4"><b>/usr/lib/64/libgsl.so /usr/lib/64/libgslcblas.so</b></font> /usr/lib/64/libplplotd.so /usr/lib/64/libplplotcxxd.so /usr/lib/64/libGraphicsMagick.<wbr>so /usr/lib/64/libGraphicsMagick+<wbr>+.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.<wbr>so /usr/lib/64/libGraphicsMagick+<wbr>+.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:/<wbr>usr/lib/64:</span><br><br></div><div>but no <span style="font-family:monospace,monospace"><b>libgslcblas.so</b><span class="m_-6539132618753477155gmail-"> </span></span>is recorded in the <span style="font-family:monospace,monospace">gdl</span> executable:<br><br><span style="font-family:monospace,monospace">dsend@oi-dev:/projects/oi-<wbr>userland/components/<wbr>scientific/gdl$ ldd build/prototype/i386/usr/bin/<wbr>gdl <br> libdl.so.1 => /usr/lib/64/libdl.so.1<br> libreadline.so.6 => /usr/lib/64/libreadline.so.6<br> libz.so.1 => /usr/lib/64/libz.so.1<br> libpng16.so.16 => /usr/lib/64/libpng16.so.16<br> <b> libgsl.so.19 => /usr/lib/64/libgsl.so.19</b><br> libplplotd.so.11 => /usr/lib/64/libplplotd.so.11<br> libplplotcxxd.so.10 => /usr/lib/64/libplplotcxxd.so.<wbr>10<br> libGraphicsMagick++.so.12 => /usr/lib/64/libGraphicsMagick+<wbr>+.so.12<br> libwx_baseu-2.8.so.0 => /usr/lib/64/libwx_baseu-2.8.<wbr>so.0<br> libwx_gtk2u_core-2.8.so.0 => /usr/lib/64/libwx_gtk2u_core-<wbr>2.8.so.0<br> libwx_gtk2u_adv-2.8.so.0 => /usr/lib/64/libwx_gtk2u_adv-2.<wbr>8.so.0<br> libnetcdf.so.11 => /usr/lib/64/libnetcdf.so.11<br> libhdf5.so.10 => /usr/lib/64/libhdf5.so.10<br> libm.so.2 => /usr/lib/64/libm.so.2<br> libfftw3.so.3 => /usr/lib/64/libfftw3.so.3<br> libfftw3f.so.3 => /usr/lib/64/libfftw3f.so.3<br> libX11.so.4 => /usr/openwin/lib/64/libX11.so.<wbr>4<br> libsocket.so.1 => /usr/lib/64/libsocket.so.1<br> libnsl.so.1 => /usr/lib/64/libnsl.so.1<br> libstdc++.so.6 => /usr/lib/64/libstdc++.so.6<br> librt.so.1 => /usr/lib/64/librt.so.1<br> libgomp.so.1 => /usr/lib/64/libgomp.so.1<br> libgcc_s.so.1 => /usr/lib/64/libgcc_s.so.1<br> libpthread.so.1 => /usr/lib/64/libpthread.so.1<br> libc.so.1 => /usr/lib/64/libc.so.1<br> libtermcap.so.1 => /lib/64/libtermcap.so.1<br> libltdl.so.7 => /usr/lib/64/libltdl.so.7<br> libcsirocsa.so.0 => /usr/lib/64/libcsirocsa.so.0<br> libqsastime.so.0 => /usr/lib/64/libqsastime.so.0<br> libGraphicsMagick.so.3 => /usr/lib/amd64/<wbr>libGraphicsMagick.so.3<br> libgtk-x11-2.0.so.0 => /usr/lib/64/<a href="http://libgtk-x11-2.0.so">libgtk-x11-2.0.so</a>.<wbr>0<br> libgdk-x11-2.0.so.0 => /usr/lib/64/<a href="http://libgdk-x11-2.0.so">libgdk-x11-2.0.so</a>.<wbr>0<br> libXinerama.so.1 => /usr/lib/64/libXinerama.so.1<br> libgdk_pixbuf-2.0.so.0 => /usr/lib/64/libgdk_pixbuf-2.0.<wbr>so.0<br> libpango-1.0.so.0 => /usr/lib/64/libpango-1.0.so.0<br> libgobject-2.0.so.0 => /usr/lib/64/<a href="http://libgobject-2.0.so">libgobject-2.0.so</a>.<wbr>0<br> libglib-2.0.so.0 => /usr/lib/64/libglib-2.0.so.0<br> libXxf86vm.so.1 => /usr/lib/64/libXxf86vm.so.1<br> libSM.so.6 => /usr/lib/64/libSM.so.6<br> libjpeg.so.62 => /usr/lib/64/libjpeg.so.62<br> libtiff.so.5 => /usr/lib/64/libtiff.so.5<br> libSDL-1.2.so.0 => /usr/lib/64/libSDL-1.2.so.0<br> libhdf5_hl.so.10 => /usr/lib/64/libhdf5_hl.so.10<br> libcurl.so.4 => /usr/lib/64/libcurl.so.4<br> libxcb.so.1 => /usr/lib/64/libxcb.so.1<br> libXext.so.0 => /usr/lib/64/libXext.so.0<br> libmp.so.2 => /lib/64/libmp.so.2<br> libmd.so.1 => /lib/64/libmd.so.1<br> libwebp.so.5 => /usr/lib/64/libwebp.so.5<br> liblcms2.so.2 => /usr/lib/64/liblcms2.so.2<br> libfreetype.so.6 => /usr/lib/64/libfreetype.so.6<br> libjasper.so.1 => /usr/lib/64/libjasper.so.1<br> libjpeg.so.8 => /usr/lib/libjpeg8-turbo/lib/<wbr>amd64/libjpeg.so.8<br> libbz2.so.1 => /usr/lib/64/libbz2.so.1<br> libxml2.so.2 => /usr/lib/64/libxml2.so.2<br> libgmodule-2.0.so.0 => /usr/lib/amd64/libgmodule-2.0.<wbr>so.0<br> libpangocairo-1.0.so.0 => /usr/lib/amd64/libpangocairo-<wbr>1.0.so.0<br> libXfixes.so.1 => /usr/lib/amd64/libXfixes.so.1<br> libatk-1.0.so.0 => /usr/lib/amd64/libatk-1.0.so.0<br> libcairo.so.2 => /usr/lib/amd64/libcairo.so.2<br> libgio-2.0.so.0 => /usr/lib/amd64/libgio-2.0.so.0<br> libpangoft2-1.0.so.0 => /usr/lib/amd64/libpangoft2-1.<wbr>0.so.0<br> libfontconfig.so.1 => /usr/lib/amd64/libfontconfig.<wbr>so.1<br> libXrender.so.1 => /usr/lib/64/libXrender.so.1<br> libXrandr.so.2 => /usr/lib/64/libXrandr.so.2<br> libXcursor.so.1 => /usr/lib/64/libXcursor.so.1<br> libXcomposite.so.1 => /usr/lib/64/libXcomposite.so.1<br> libXdamage.so.1 => /usr/lib/64/libXdamage.so.1<br> libffi.so.6 => /usr/lib/amd64/libffi.so.6<br> libICE.so.6 => /usr/lib/64/libICE.so.6<br> liblzma.so.5 => /usr/lib/64/liblzma.so.5<br> libnghttp2.so.14 => /usr/lib/64/libnghttp2.so.14<br> libssh2.so.1 => /usr/lib/64/libssh2.so.1<br> libssl.so.1.0.0 => /lib/64/libssl.so.1.0.0<br> libcrypto.so.1.0.0 => /lib/64/libcrypto.so.1.0.0<br> libgss.so.1 => /usr/lib/64/libgss.so.1<br> liblber-2.4.so.2 => /usr/lib/64/liblber-2.4.so.2<br> libldap_r-2.4.so.2 => /usr/lib/64/libldap_r-2.4.so.2<br> libXau.so.6 => /usr/lib/amd64/libXau.so.6<br> libXdmcp.so.6 => /usr/lib/amd64/libXdmcp.so.6<br> libharfbuzz.so.0 => /usr/lib/64/libharfbuzz.so.0<br> libpixman-1.so.0 => /usr/lib/64/libpixman-1.so.0<br> libEGL.so.1 => /usr/lib/64/libEGL.so.1<br> libX11-xcb.so.1 => /usr/lib/64/libX11-xcb.so.1<br> libxcb-render.so.0 => /usr/lib/64/libxcb-render.so.0<br> libGL.so.1 => /usr/lib/64/libGL.so.1<br> libresolv.so.2 => /usr/lib/amd64/libresolv.so.2<br> libexpat.so.1 => /usr/lib/64/libexpat.so.1<br> libsasl.so.1 => /usr/lib/amd64/libsasl.so.1<br> libgraphite2.so.3 => /usr/lib/64/libgraphite2.so.3<br> libxcb-dri2.so.0 => /usr/lib/64/libxcb-dri2.so.0<br> libxcb-xfixes.so.0 => /usr/lib/64/libxcb-xfixes.so.0<br> libxcb-dri3.so.0 => /usr/lib/64/libxcb-dri3.so.0<br> libxcb-present.so.0 => /usr/lib/64/libxcb-present.so.<wbr>0<br> libxcb-sync.so.1 => /usr/lib/64/libxcb-sync.so.1<br> libxshmfence.so.1 => /usr/lib/64/libxshmfence.so.1<br> libdrm.so.2 => /usr/lib/xorg/amd64/libdrm.so.<wbr>2<br> libglapi.so.0 => /usr/lib/amd64/libglapi.so.0<br> libxcb-glx.so.0 => /usr/lib/amd64/libxcb-glx.so.0<br> libdevinfo.so.1 => /lib/64/libdevinfo.so.1<br> libnvpair.so.1 => /lib/64/libnvpair.so.1<br> libsec.so.1 => /lib/64/libsec.so.1<br> libgen.so.1 => /lib/64/libgen.so.1<br> libavl.so.1 => /lib/64/libavl.so.1<br> libidmap.so.1 => /usr/lib/64/libidmap.so.1<br> libuutil.so.1 => /lib/64/libuutil.so.1<br> libcurses.so.1 => /lib/64/libcurses.so.1<br> libXevie.so.1 => /usr/lib/64/libXevie.so.1<br> libXss.so.1 => /usr/lib/64/libXss.so.1</span><br></div><div><br></div><div>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:<br><span style="font-family:monospace,monospace"><br>dsend@oi-dev:/projects/oi-<wbr>userland/components/<wbr>scientific/gdl/build/amd64/<wbr>src$ ldd gdl <br> libdl.so.1 => /usr/lib/64/libdl.so.1<br> libncurses.so.5 => /usr/lib/64/libncurses.so.5<br> libform.so.1 => /usr/lib/64/libform.so.1<br> libreadline.so.6 => /usr/lib/64/libreadline.so.6<br> libhistory.so.6 => /usr/lib/64/libhistory.so.6<br> libz.so.1 => /usr/lib/64/libz.so.1<br> libpng16.so.16 => /usr/lib/64/libpng16.so.16<br> <b>libgsl.so.19 => /usr/lib/64/libgsl.so.19</b><br> <b> libgslcblas.so.0 => /usr/lib/64/libgslcblas.so.0</b><br> libplplotd.so.11 => /usr/lib/64/libplplotd.so.11<br> libplplotcxxd.so.10 => /usr/lib/64/libplplotcxxd.so.<wbr>10</span><br><br><br></div><div>and boom! <span style="font-family:monospace,monospace"><b>libgslcblas.so<span class="m_-6539132618753477155gmail-"> </span></b></span>appears as expected and tests pass.<br></div><div><br></div><div>I ran out of ideas why this happens. Maybe I spent too much time on this problem and cannot see anything right now.<br></div><div>Maybe I'm missing something obvious so another pair of eyes would be great :) <br>Any ideas?<br><br></div><div>You can find the component package files here: <a href="https://github.com/dsendkowski/oi-userland/tree/gdl" target="_blank">https://github.com/<wbr>dsendkowski/oi-userland/tree/<wbr>gdl<br></a><br></div><div><br></div><div><br></div><div>regards,<br></div><div>Darek<br><br></div><div><br><br><br></div><div><br><br><br><br></div></div>
</blockquote></div><br></div>