Folks:
I recently updated to El Capitan, and it seemed to have broken StatET.
Specifically, when install rj, I get the following error. Any ideas?
--j
> install.packages(c("rj", "rj.gd"), repos="
http://download.walware.de/rj-2.0";)
Warning: unable to access index for repository
http://download.walware.de/rj-2.0/bin/macosx/mavericks/contrib/3.2
Package which is only available in source form, and may need compilation of
C/C++/Fortran:
‘rj’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘rj’, ‘rj.gd’
trying URL 'http://download.walware.de/rj-2.0/src/contrib/rj_2.0.4-2.tar.gz'
Content type 'application/x-tar' length 346105 bytes (337 KB)
==================================================
downloaded 337 KB
trying URL '
http://download.walware.de/rj-2.0/src/contrib/rj.gd_2.0.0-1.tar.gz'
Content type 'application/x-tar' length 123251 bytes (120 KB)
==================================================
downloaded 120 KB
* installing *source* package ‘rj’ ...
checking R config... found
R_HOME : /Library/Frameworks/R.framework/Resources
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object
files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking Java support in R... ok
JAVA_HOME:
/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre
JAVA : /usr/bin/java
JAVAC : /usr/bin/javac
JAVAH : /usr/bin/javah
JAVA_CPPFLAGS:
-I/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/../include
-I/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/../include/darwin
JAVA_LIBS:
-L/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/server
-ljvm
JAR : /usr/bin/jar
configure: creating ./config.status
config.status: creating src/Makevars
=== configuring in jri
(/private/var/folders/7k/6j77__7n6kz0st6bphc3hn080000gn/T/Rtmpd8ic9z/R.INSTALL1b8d4e197bed/rj/jri)
configure: running /bin/sh ./configure --disable-option-checking
'--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking build system type... i386-apple-darwin15.0.0
checking host system type... i386-apple-darwin15.0.0
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object
files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking whether Java interpreter works... checking whether JNI programs
can be compiled... yes
checking whether JNI programs can be run... configure: error: Cannot run a
simple JNI program - probably your jvm library is in non-standard location
or JVM is unsupported. See config.log for details.
configure: error: ./configure failed for jri
ERROR: configuration failed for package ‘rj’
* removing
‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rj’
ERROR: dependency ‘rj’ is not available for package ‘rj.gd’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/
rj.gd’
The downloaded source packages are in
‘/private/var/folders/7k/6j77__7n6kz0st6bphc3hn080000gn/T/RtmpGoQti6/downloaded_packages’
Warning messages:
1: In install.packages(file.choose(),
"/Library/Frameworks/R.framework/Resources/library/", :
installation of package ‘/Users/jgrn307/Downloads/rj_2.0.4-2.tar.gz’ had
non-zero exit status
2: In install.packages(file.choose(),
"/Library/Frameworks/R.framework/Resources/library/", :
installation of package ‘/Users/jgrn307/Downloads/rj_2.0.4-2.tar.gz’ had
non-zero exit status
3: In install.packages(c("rj", "rj.gd"), repos = "
http://download.walware.de/rj-2.0";) :
installation of package ‘rj’ had non-zero exit status
4: In install.packages(c("rj", "rj.gd"), repos = "
http://download.walware.de/rj-2.0";) :
installation of package ‘rj.gd’ had non-zero exit status
>
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