[EMBOSS] Compiling EMBOSS: missing jni.h?

[Sylvain Foisy]

Hi,

I'am trying to build a bioinfo workstation with Xubuntu and of course, I am
trying to compile the latest EMBOSS (5.0 is the latest version of the
pre-built package). I just hit a snag... After invoking make, it compiles
for a while and then crashes with this (sorry for the length):

Making all in ajax
make[1]: Entering directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax'
/bin/bash ../libtool --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"6.0.1\" -DSTDC_HEADERS=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1
-DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
-DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
-DPLD_png=1 -I. 
-DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\"
-DPREFIX=\"/usr/local\" -I../plplot
-DPOSIX_MALLOC_THRESHOLD=10   -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -DLENDIAN
-I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk
-DNO_AUTH  -O2 -MT ajacd.lo -MD -MP -MF
.deps/ajacd.Tpo -c -o ajacd.lo ajacd.c
mkdir .libs
 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1
-DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1
-DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1
-I. -DAJAX_FIXED_ROOT=\"/opt/bioxubuntu/sources/EMBOSS-6.0.1/emboss\"
-DPREFIX=\"/usr/local\" -I../plplot
-DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN
-I/usr/lib/jvm/java-6-openjdk/jre -DHAVE_JAVA -I/usr/lib/jvm/java-6-openjdk
-DNO_AUTH -O2 -MT ajacd.lo -MD -MP -MF
.deps/ajacd.Tpo -c ajacd.c  -fPIC -DPIC -o .libs/ajacd.o
In file included from ajax.h:77,
                 from ajacd.c:41:
ajjava.h:13:17: error: jni.h: No such file or directory
In file included from ajax.h:77,
                 from ajacd.c:41:
ajjava.h:33: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:35: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:38: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:41: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:43: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:45: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:47: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:50: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:52: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:54: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:56: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jint'
ajjava.h:60: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:67: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:71: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:75: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:83: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:87: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:91: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:96: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:101: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:106: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jbyteArray'
ajjava.h:111: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:116: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
ajjava.h:121: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'jboolean'
make[1]: *** [ajacd.lo] Error 1
make[1]: Leaving directory `/opt/bioxubuntu/sources/EMBOSS-6.0.1/ajax'
make: *** [all-recursive] Error 1

Can anyone point me toward a solution? I have openjdk-6-jdk installed via
apt-get but it seems that I am missing something...

Best regards

Sylvain 


==================================================================

Sylvain Foisy, Ph. D.
Chargé de projet / Project Manager
Bio-informatique

Adresse postale:

Laboratoire de genetique et medecine genomique de l'inflammation
Institut de cardiologie de Montreal
5000 Belanger
Montreal, Qc
H1T 1C8

T: 514-376-3330 x.2299 | F: 514-593-2539
M: sylvain.foisy at inflammgen.org
W: http://www.inflammgen.org

==================================================================