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.
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
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