Looks like it is easy enough to backport my change. The question is: is it worth fixing an older and confusingly-packaged form of this same program, vs just killing off that old mess? I had initially not simply deleted 6.3.1-3 because I was still working on getting the 6.3.1-102 overhaul to build cleanly and consistently. A user also seemed to want it because he preferred an inconsistent/unpredictable build-result (due to uncontrolled detection/use of database back-ends) rather than forcing dependencies on databases he did not want. dan On Wed, 15 Dec 2010 16:25:16 -0600, Bradley Hartman Bakken wrote: Hello, > > Despite having installed Apple's new Java Developer Package, the EMBOSS suite fails to compile. I pasted fink's chatter below. I believe the problem is this: the 'emboss-ajax6-shlibs' package isn't looking in the proper place for the Javaos directory. Earlier today, Daniel Macks successfully fixed this issue in the EMBOSS 6.3.1-102 (for 10.6/x84_64) package, so he may have some insight on the fix that's needed. > > Many thanks! And do let me know if you need any system information from me. > > Fink 0.29.17 > Mac OS X 10.6.5 > Intel Core 2 Duo > > Cheers, > Bradley > > - - - > > [ -r /sw/fink/dists/unstable/main/finkinfo/sci/emboss-6.3.1-3.patch ] > patch -p1 < /sw/fink/dists/unstable/main/finkinfo/sci/emboss-6.3.1-3.patch > patching file README.fixes > patching file ajax/acd/Makefile.in > patching file ajax/ajaxdb/Makefile.in > patching file ajax/core/Makefile.in > patching file ajax/graphics/Makefile.in > patching file configure > patching file m4/mysql.m4 > patching file nucleus/Makefile.in > patching file plplot/Makefile.in > /sw/bin/autoreconf -fi > libtoolize: putting auxiliary files in `.'. > libtoolize: copying file `./ltmain.sh' > libtoolize: putting macros in `m4'. > libtoolize: copying file `m4/libtool.m4' > libtoolize: copying file `m4/ltoptions.m4' > libtoolize: copying file `m4/ltsugar.m4' > libtoolize: copying file `m4/ltversion.m4' > libtoolize: copying file `m4/lt~obsolete.m4' > libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and > libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. > ./configure --prefix=/sw --with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home --with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home/include --disable-dependency-tracking --libdir=/sw/lib/EMBOSS --docdir=/sw/share/EMBOSS > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... ./install-sh -c -d > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking build system type... i386-apple-darwin10.5.0 > checking host system type... i386-apple-darwin10.5.0 > checking how to print strings... printf > checking for style of include used by make... GNU > checking for gcc... gcc > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking dependency style of gcc... none > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld > checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands " ="... yes > checking how to convert i386-apple-darwin10.5.0 file names to i386-apple-darwin10.5.0 format... func_convert_file_noop > checking how to convert i386-apple-darwin10.5.0 file names to toolchain format... func_convert_file_noop > checking for /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for ar... ar > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /usr/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... no > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes > checking dynamic linker characteristics... darwin10.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > checking for gawk... (cached) gawk > checking for gcc... (cached) gcc > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc accepts -g... (cached) yes > checking for gcc option to accept ISO C89... (cached) none needed > checking dependency style of gcc... (cached) none > checking how to run the C preprocessor... gcc -E > checking for inline... inline > checking whether byte ordering is bigendian... no > checking whether ln -s works... yes > checking whether make sets $(MAKE)... (cached) yes > checking for X... libraries , headers > checking for gethostbyname... yes > checking for connect... yes > checking for remove... yes > checking for shmat... yes > checking for IceConnectionNumber in -lICE... yes > checking for dirent.h that defines DIR... yes > checking for library containing opendir... none required > checking for ANSI C header files... (cached) yes > checking for unistd.h... (cached) yes > checking TargetConfig.h usability... yes > checking TargetConfig.h presence... yes > checking for TargetConfig.h... yes > checking for an ANSI C-conforming const... yes > checking for pid_t... yes > checking for size_t... yes > checking whether struct tm is in sys/time.h or time.h... time.h > checking whether getpgrp requires zero arguments... yes > checking for strftime... yes > checking vfork.h usability... no > checking vfork.h presence... no > checking for vfork.h... no > checking for fork... yes > checking for vfork... yes > checking for working fork... yes > checking for working vfork... (cached) yes > checking for vprintf... yes > checking for _doprnt... no > checking for memmove... yes > checking X11/Xlib.h usability... yes > checking X11/Xlib.h presence... yes > checking for X11/Xlib.h... yes > checking for socket in -lc... yes > checking for main in -lm... yes > checking if docroot is given... no > checking if gcc profiling is selected... no > checking if java include directory given... yes > Java directory /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home exists > checking for javac... yes > checking if java OS include directory given... yes > Javaos directory /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home/include does not exist > make > make: *** No targets specified and no makefile found. Stop. > ### execution of make failed, exit code 2 > Removing runtime build-lock... > Removing build-lock package... > /sw/bin/dpkg-lockwait -r fink-buildlock-emboss-6.3.1-3 > (Reading database ... 40395 files and directories currently installed.) > Removing fink-buildlock-emboss-6.3.1-3 ... > Updating the list of locally available binary packages. > Scanning dists/unstable/main/binary-darwin-i386 > New package: dists/unstable/main/binary-darwin-i386/sci/emboss-libajax6-dev_6.3.1-102_darwin-i386.deb > New package: dists/unstable/main/binary-darwin-i386/sci/emboss-libajax6-shlibs_6.3.1-102_darwin-i386.deb > New package: dists/unstable/main/binary-darwin-i386/sci/emboss-libnucleus6-dev_6.3.1-102_darwin-i386.deb > New package: dists/unstable/main/binary-darwin-i386/sci/emboss-libnucleus6-shlibs_6.3.1-102_darwin-i386.deb > New package: dists/unstable/main/binary-darwin-i386/sci/emboss_6.3.1-102_darwin-i386.deb > Failed: phase compiling: emboss-6.3.1-3 failed > > ------------------------------------------------------------------------------ > Lotusphere 2011 > Register now for Lotusphere 2011 and learn how > to connect the dots, take your collaborative environment > to the next level, and enter the era of Social Business. > http://p.sf.net/sfu/lotusphere-d2d > _______________________________________________ > Fink-devel mailing list > Fink-devel@lists.sourceforge.net > http://news.gmane.org/gmane.os.apple.fink.devel > Subscription management: > https://lists.sourceforge.net/lists/listinfo/fink-devel > >
-- Daniel Macks dma...@netspace.org ------------------------------------------------------------------------------ Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d _______________________________________________ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
