Package: stimfit Version: 0.10.9-1 Severity: serious Justification: fails to build from source
Per http://lists.debian.org/debian-devel-announce/2011/02/msg00011.html, gcc now normally invokes ld with an option that directs it to consider only libraries that explicitly appear on the command line. This change affects stimfit as currently packaged, as it uses BLAS symbols without directly linking against libblas. Previously, stimfit's use of LAPACK would have sufficed to bring libbblas to the linker's attention as a potential library of interest, but now that arrangement merely informs the resulting error message: /bin/bash ./libtool --tag=CXX --mode=link g++ -O2 -g -g -O2 -fPIC -I/usr/lib/wx/include/gtk2-unicode-release-2.8 -I/usr/include/wx-2.8 -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D__WXGTK__ -pthread -Wall -llapack -L/usr/lib/python2.6 -lpython2.6 -Wl,-rpath,/usr/lib/stimfit -avoid-version -o stimfit stimfit-channel.o stimfit-section.o stimfit-recording.o stimfit-core.o stimfit-fitlib.o stimfit-measlib.o stimfit-asciilib.o stimfit-cfslib.o stimfit-hdf5lib.o cfs.o stimfit-abflib.o stimfit-atflib.o stimfit-axglib.o stimfit-hekalib.o stimfit-abffiles.o stimfit-csynch.o stimfit-filedesc.o stimfit-FileReadCache.o stimfit-FileIO.o stimfit-abfheadr.o stimfit-abfhwave.o stimfit-Oldheadr.o stimfit-abfutil.o stimfit-msbincvt.o stimfit-unix.o stimfit-abferror.o stimfit-axatffio32.o stimfit-fileio2.o stimfit-ProtocolReaderABF2.o stimfit-SimpleStringCache.o stimfit-abf2headr.o stimfit-AxoGraph_ReadWrite.o stimfit-fileUtils.o stimfit-stringUtils.o stimfit-byteswap.o lm.o Axb.o misc.o lmlec.o lmbc.o stimfit-app.o stimfit-doc.o stimfit-stfcheckbox.o stimfit-copygrid.o stimfit-graph.o stimfit-printout.o stimfit-parentframe.o stimfit-childframe.o stimfit-view.o stimfit-table.o stimfit-zoom.o stimfit-cursorsdlg.o stimfit-eventdlg.o stimfit-fitseldlg.o stimfit-smalldlgs.o stimfit-funclib.o stimfit-usrdlg.o -pthread -lwx_baseu-2.8 -lwx_gtk2u_core-2.8 -lwx_gtk2u_adv-2.8 -lwx_gtk2u_aui-2.8 -lwx_baseu_net-2.8 ./src/stfswig/libstf.la -lfftw3 -lhdf5 -lhdf5_hl ./src/app/libstimfit.a libtool: link: g++ -O2 -g -g -O2 -fPIC -I/usr/lib/wx/include/gtk2-unicode-release-2.8 -I/usr/include/wx-2.8 -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D__WXGTK__ -pthread -Wall -Wl,-rpath -Wl,/usr/lib/stimfit -o .libs/stimfit stimfit-channel.o stimfit-section.o stimfit-recording.o stimfit-core.o stimfit-fitlib.o stimfit-measlib.o stimfit-asciilib.o stimfit-cfslib.o stimfit-hdf5lib.o cfs.o stimfit-abflib.o stimfit-atflib.o stimfit-axglib.o stimfit-hekalib.o stimfit-abffiles.o stimfit-csynch.o stimfit-filedesc.o stimfit-FileReadCache.o stimfit-FileIO.o stimfit-abfheadr.o stimfit-abfhwave.o stimfit-Oldheadr.o stimfit-abfutil.o stimfit-msbincvt.o stimfit-unix.o stimfit-abferror.o stimfit-axatffio32.o stimfit-fileio2.o stimfit-ProtocolReaderABF2.o stimfit-SimpleStringCache.o stimfit-abf2headr.o stimfit-AxoGraph_ReadWrite.o stimfit-fileUtils.o stimfit-stringUtils.o stimfit-byteswap.o lm.o Axb.o misc.o lmlec.o lmbc.o stimfit-app.o stimfit-doc.o stimfit-stfcheckbox.o stimfit-copygrid.o s timfit-graph.o stimfit-printout.o stimfit-parentframe.o stimfit-childframe.o stimfit-view.o stimfit-table.o stimfit-zoom.o stimfit-cursorsdlg.o stimfit-eventdlg.o stimfit-fitseldlg.o stimfit-smalldlgs.o stimfit-funclib.o stimfit-usrdlg.o -pthread -llapack -L/usr/lib/python2.6 -lpython2.6 -lwx_baseu-2.8 -lwx_gtk2u_core-2.8 -lwx_gtk2u_adv-2.8 -lwx_gtk2u_aui-2.8 -lwx_baseu_net-2.8 ./src/stfswig/.libs/libstf.so /usr/lib/libfftw3.so /usr/lib/libhdf5.so /usr/lib/libhdf5_hl.so ./src/app/libstimfit.a -pthread -Wl,-rpath -Wl,/build/buildd-stimfit_0.10.9-1-i386-5rQxiX/stimfit-0.10.9/debian/tmp/usr/lib/stimfit /usr/bin/ld: misc.o: undefined reference to symbol 'dgemm_' /usr/bin/ld: note: 'dgemm_' is defined in DSO //usr/lib/libblas.so.3gf so try adding it to the linker command line //usr/lib/libblas.so.3gf: could not read symbols: Invalid operation collect2: ld returned 1 exit status make[3]: *** [stimfit] Error 1 [Taken from https://buildd.debian.org/fetch.cgi?pkg=stimfit&arch=i386&ver=0.10.9-1&stamp=1301667138&file=log&as=raw ] Could you please link stimfit directly against libblas and double check that you won't need to list any other libraries? Thanks! -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
