2010/11/23 Moreland Gibbs <[email protected]>: > Hi > I am new to Fink, so if this is not the appropriate place for this please > let me know. > > > > I have installed Fink 0.29.16 on my mac (iMac 2.4 GHz Core 2 Duo, OS 10.6.5) > and have been trying to install the the mol bio package EMBOSS 6.3.1-3 using > Fink Commander 0.5.5, and via command line.
Fink Commander runs the command-line tools, so any failures are normally the same. > The Fink installation side as far as I can tell all went well. > However, when I try to build the EMBOSS package it fails towards the end of > the compilation process (output is shown below). > The issue appears to be with a JAVA component requirement. Based on what I > read in support lists, I have installed and updated Apple SDK for 10.6. Did > not work. Also downloaded and installed javadeveloper_10.6_10m3261 from > Apple developer site. > If anyone give pointers on how to solve this problem so I can get EMBOSS > running, I would greatly appreciate it. > Cheers in advance > Moreland > > The following package will be installed or updated: > emboss-nucleus6-dev > The following 3 additional packages will be installed: > emboss-ajax6-shlibs emboss-nucleus6-shlibs emboss-plplot3-shlibs > Do you want to continue? [Y/n] > Setting runtime build-lock... > dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-emboss-6.3.1-3 > /sw/src/fink.build > dpkg-deb: building package `fink-buildlock-emboss-6.3.1-3' in > `/sw/src/fink.build/fink-buildlock-emboss-6.3.1-3_2010.11.24-15.03.44_darwin-i386.deb'. > Installing build-lock package... > /sw/bin/dpkg-lockwait -i > /sw/src/fink.build/fink-buildlock-emboss-6.3.1-3_2010.11.24-15.03.44_darwin-i386.deb > Selecting previously deselected package fink-buildlock-emboss-6.3.1-3. > (Reading database ... 6919 files and directories currently installed.) > Unpacking fink-buildlock-emboss-6.3.1-3 (from > .../fink-buildlock-emboss-6.3.1-3_2010.11.24-15.03.44_darwin-i386.deb) ... > Setting up fink-buildlock-emboss-6.3.1-3 (2010.11.24-15.03.44) ... > gzip -dc /sw/src/EMBOSS-6.3.1.tar.gz | /sw/bin/tar -xf - --no-same-owner > --no-same-permissions > [ -r /sw/fink/dists/stable/main/finkinfo/sci/emboss-6.3.1-3.patch ] > patch -p1 < /sw/fink/dists/stable/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... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > 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) awk > 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 ... 6920 files and directories currently installed.) > Removing fink-buildlock-emboss-6.3.1-3 ... > Failed: phase compiling: emboss-6.3.1-3 failed > The emboss package needs to be fixed to look for Java in the proper location. -- Alexander K. Hansen akh AT finkproject DOT org Fink User Liaison and Documenter ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. 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