At installation of dev-lang/R some environment variables are generated and stored in /usr/lib/R/etc/Makeconf. This results in problems building the rJava R-package http://www.rforge.net/rJava/ JAVA_LIBS and JAVA_LD_LIBRARY_PATH contain absolute references (part of Makeconf concerning JAVA) JAR = /etc/java-config-2/current-system-vm/bin/jar JAVA = /etc/java-config-2/current-system-vm/jre/bin/java JAVAC = /etc/java-config-2/current-system-vm/bin/javac JAVAH = /etc/java-config-2/current-system-vm/bin/javah JAVA_HOME = /etc/java-config-2/current-system-vm JAVA_LD_LIBRARY_PATH = /usr/opt/sun-jdk-1.5.0.11/jre/lib/amd64/server:/usr/opt/sun-jdk-1.5.0.11/jre/lib/amd64:/usr/opt/sun-j dk-1.5.0.11/jre/../lib/amd64: JAVA_LIBS = -L/usr/opt/sun-jdk-1.5.0.11/jre/lib/amd64/server -L/usr/opt/sun-jdk-1.5.0.11/jre/lib/amd64 -L/usr/opt/sun-jdk-1. 5.0.11/jre/../lib/amd64 -L -ljvm according to the R documentation, Makeconf is generated at configure time. the problem can be circumvented by changing Makeconf: JAVA_LD_LIBRARY_PATH = /etc/java-config-2/current-system-vm/jre/lib/amd64/server:/etc/java-config-2/current-system-vm/jre/li b/amd64:/etc/java-config-2/current-system-vm/../lib/amd64: JAVA_LIBS = -L/etc/java-config-2/current-system-vm/jre/lib/amd64/server -L/etc/java-config-2/current-system-vm/jre/lib/amd64 -L/etc/java-config-2/current-system-vm/jre/../lib/amd64 -ljvm Reproducible: Didn't try Portage 2.1.2.12 (default-linux/amd64/2006.1, gcc-4.1.2, glibc-2.5-r4, 2.6.22-gentoo-r2 x86_64) ================================================================= System uname: 2.6.22-gentoo-r2 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ Gentoo Base System release 1.12.9 Timestamp of tree: Tue, 28 Aug 2007 08:30:01 +0000 app-shells/bash: 3.2_p17 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r4 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.9-r2 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.17 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.21 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="ftp://ftp.uni-kassel.de/pub/linux/gentoo.org/ http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/" LINGUAS="en de" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/haskell" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X alsa amd64 berkdb bitmap-fonts blas cli cracklib crypt cups doc dri fortran gdbm gpm iconv ipv6 isdnlog java jpeg kde lapack midi mudflap ncurses nis nls nptl nptlonly opengl openmp pam pcre pdf perl png ppds pppd python readline reflection session spl ssl svg tcpd truetype-fonts type1-fonts unicode xinerama xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en de" USERLAND="GNU" VIDEO_CARDS="radeon" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Andreas, Thanks for the note. I'll have a look at it. Best, Markus
Created attachment 130995 [details, diff] patch to fix java paths in Makeconf Could you please try the attached patch and let me know if it does the right thing on your machine (it works for me). Thanks, Markus
In >=R-2.6, I added a pkg_config that should take care of it. Every time a java update is performed you should run an ebuild config or whatever tool you use to run the pkg_config in ebuilds. It is a simple call to "R CMD javareconf".
This bug was taken care of some time ago. Closing.
