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
