Hi Mark, The first thing that jumps out to me is that 2.7.1 compiles JRI, while 2.9.1 does not (for some reason, autodetect decides not to compile).
HTH, Josh -- http://www.fosstrading.com On Wed, Jul 15, 2009 at 1:46 PM, Mark Kimpel<mwkim...@gmail.com> wrote: > I have been futzing around for days tying to get rJava to install on > my freshly build Debian Lenny installation. I have R-2.9.1 installed > from source in my R_HOME directory and R-2.7.1 installed via apt-get > install r-recommended. I was tried many different things, but by > accident started up R-2.7.1 as root and viola, successful install. I > immediately exited out of R-2.7.1 and started R-2.9.1 as root and > compilation fails. The file > > The output is voluminous, but is included below. I had originally > thought that my problem had to do with setting environmental > variables, but now it seems not. > > Thanks, > Mark > > mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root > Password: > mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# > /home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R > WARNING: ignoring environment value of R_HOME > > R version 2.9.1 (2009-06-26) > Copyright (C) 2009 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> install.packages('rJava') > Warning in install.packages("rJava") : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz' > Content type 'application/x-gzip' length 240527 bytes (234 Kb) > opened URL > ================================================== > downloaded 234 Kb > > * Installing *source* package ‘rJava’ ... > checking for gcc... gcc -std=gnu99 > 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 gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/wait.h that is POSIX.1 compatible... 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 string.h... (cached) yes > checking sys/time.h usability... yes > checking sys/time.h presence... yes > checking for sys/time.h... yes > checking for unistd.h... (cached) yes > checking for an ANSI C-conforming const... yes > checking whether time.h and sys/time.h may both be included... yes > configure: checking whether gcc -std=gnu99 supports static inline... > yes > checking Java support in R... present: > interpreter : '/usr/bin/java' > archiver : '/usr/bin/jar' > compiler : '/usr/bin/javac' > header prep.: '/usr/bin/javah' > cpp flags : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux' > java libs : '-L$(JAVA_HOME)/lib/amd64/server > -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L > -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm' > checking whether JNI programs can be compiled... yes > checking JNI data types... ok > checking whether JRI should be compiled (autodetect)... no > checking whether debugging output should be enabled... no > checking whether memory profiling is desired... no > checking whether threads support is requested... no > checking whether callbacks support is requested... no > checking whether JNI cache support is requested... no > checking whether JRI is requested... no > configure: creating ./config.status > config.status: creating src/Makevars > config.status: creating R/zzz.R > config.status: creating src/config.h > ** libs > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.1/R-build/lib64/R/include > -I. -I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include > -I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include/linux > -I/usr/local/include -fpic -g -O2 -c Rglue.c -o Rglue.o > In file included from Rglue.c:2: > rJava.h:17:17: error: jni.h: No such file or directory > In file included from Rglue.c:2: > rJava.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘*’ token > rJava.h:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘*’ token > rJava.h:120: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘*’ token > rJava.h:122: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘javaStringClass’ > rJava.h:123: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘javaObjectClass’ > rJava.h:124: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘javaClassClass’ > rJava.h:125: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘javaFieldClass’ > rJava.h:127: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘mid_forName’ > rJava.h:128: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘mid_getName’ > rJava.h:129: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘mid_getType’ > rJava.h:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘mid_getField’ > rJava.h:133: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘clClassLoader’ > rJava.h:134: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘oClassLoader’ > rJava.h:137: error: expected ‘)’ before ‘*’ token > rJava.h:138: error: expected ‘)’ before ‘*’ token > rJava.h:139: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘R1par2jvalue’ > rJava.h:144: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘callToString’ > rJava.h:147: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘createObject’ > rJava.h:148: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘findClass’ > rJava.h:149: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘objectClass’ > rJava.h:151: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newDoubleArray’ > rJava.h:152: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newIntArray’ > rJava.h:153: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newBooleanArrayI’ > rJava.h:154: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newString’ > rJava.h:155: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newCharArrayI’ > rJava.h:156: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newShortArrayI’ > rJava.h:157: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newFloatArrayD’ > rJava.h:158: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newLongArrayD’ > rJava.h:159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newByteArray’ > rJava.h:160: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘newByteArrayI’ > rJava.h:162: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘makeGlobal’ > rJava.h:163: error: expected ‘)’ before ‘*’ token > rJava.h:164: error: expected ‘)’ before ‘*’ token > rJava.h:166: error: expected ‘)’ before ‘*’ token > rJava.h:168: error: expected ‘)’ before ‘*’ token > rJava.h:170: error: expected ‘)’ before ‘*’ token > Rglue.c: In function ‘JRefObjectFinalizer’: > Rglue.c:79: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:79: error: (Each undeclared identifier is reported only once > Rglue.c:79: error: for each function it appears in.) > Rglue.c:79: error: ‘env’ undeclared (first use in this function) > Rglue.c:79: warning: implicit declaration of function ‘getJNIEnv’ > Rglue.c:80: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:80: error: expected ‘;’ before ‘o’ > Rglue.c:95: error: ‘o’ undeclared (first use in this function) > Rglue.c:98: warning: implicit declaration of function ‘releaseGlobal’ > Rglue.c: At top level: > Rglue.c:104: error: expected ‘)’ before ‘*’ token > Rglue.c: In function ‘deserializeSEXP’: > Rglue.c:151: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:151: error: ‘env’ undeclared (first use in this function) > Rglue.c:152: error: ‘clClassLoader’ undeclared (first use in this function) > Rglue.c:152: error: ‘oClassLoader’ undeclared (first use in this function) > Rglue.c:153: error: ‘jbyteArray’ undeclared (first use in this function) > Rglue.c:153: error: expected ‘;’ before ‘ser’ > Rglue.c:154: error: ‘ser’ undeclared (first use in this function) > Rglue.c:155: error: ‘jmethodID’ undeclared (first use in this function) > Rglue.c:155: error: expected ‘;’ before ‘mid’ > Rglue.c:156: error: ‘mid’ undeclared (first use in this function) > Rglue.c:157: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:157: error: expected ‘;’ before ‘res’ > Rglue.c:158: error: ‘res’ undeclared (first use in this function) > Rglue.c:159: error: expected ‘;’ before ‘go’ > Rglue.c:161: error: ‘go’ undeclared (first use in this function) > Rglue.c:173: warning: implicit declaration of function ‘releaseObject’ > Rglue.c: At top level: > Rglue.c:214: error: expected ‘)’ before ‘*’ token > Rglue.c:380: error: expected ‘)’ before ‘*’ token > Rglue.c:390: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘R1par2jvalue’ > Rglue.c: In function ‘RcallMethod’: > Rglue.c:410: error: ‘jvalue’ undeclared (first use in this function) > Rglue.c:410: error: expected ‘;’ before ‘jpar’ > Rglue.c:411: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:411: error: expected ‘;’ before ‘tmpo’ > Rglue.c:412: error: expected ‘;’ before ‘o’ > Rglue.c:414: error: ‘jmethodID’ undeclared (first use in this function) > Rglue.c:414: error: expected ‘;’ before ‘mid’ > Rglue.c:415: error: ‘jclass’ undeclared (first use in this function) > Rglue.c:415: error: expected ‘;’ before ‘cls’ > Rglue.c:416: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:416: error: ‘env’ undeclared (first use in this function) > Rglue.c:424: error: ‘o’ undeclared (first use in this function) > Rglue.c:440: error: ‘cls’ undeclared (first use in this function) > Rglue.c:440: warning: implicit declaration of function ‘findClass’ > Rglue.c:442: warning: implicit declaration of function ‘objectClass’ > Rglue.c:467: warning: implicit declaration of function ‘Rpar2jvalue’ > Rglue.c:467: error: ‘jpar’ undeclared (first use in this function) > Rglue.c:467: error: ‘tmpo’ undeclared (first use in this function) > Rglue.c:471: error: ‘mid’ undeclared (first use in this function) > Rglue.c:475: warning: implicit declaration of function ‘checkExceptionsX’ > Rglue.c:481: warning: implicit declaration of function ‘Rfreejpars’ > Rglue.c:542: error: ‘jlong’ undeclared (first use in this function) > Rglue.c:542: error: expected ‘;’ before ‘r’ > Rglue.c:546: error: ‘r’ undeclared (first use in this function) > Rglue.c:555: error: ‘jshort’ undeclared (first use in this function) > Rglue.c:555: error: expected ‘;’ before ‘r’ > Rglue.c:568: error: ‘jboolean’ undeclared (first use in this function) > Rglue.c:568: error: expected ‘;’ before ‘r’ > Rglue.c:607: error: expected ‘;’ before ‘r’ > Rglue.c:620: warning: implicit declaration of function ‘j2SEXP’ > Rglue.c:620: warning: assignment makes pointer from integer without a cast > Rglue.c: In function ‘RcallSyncMethod’: > Rglue.c:634: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:634: error: expected ‘;’ before ‘o’ > Rglue.c:635: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:635: error: ‘env’ undeclared (first use in this function) > Rglue.c:642: error: ‘o’ undeclared (first use in this function) > Rglue.c:650: error: ‘JNI_OK’ undeclared (first use in this function) > Rglue.c: In function ‘RcreateObject’: > Rglue.c:671: error: ‘jvalue’ undeclared (first use in this function) > Rglue.c:671: error: expected ‘;’ before ‘jpar’ > Rglue.c:672: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:672: error: expected ‘;’ before ‘tmpo’ > Rglue.c:673: error: expected ‘;’ before ‘o’ > Rglue.c:674: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:674: error: ‘env’ undeclared (first use in this function) > Rglue.c:690: error: ‘jpar’ undeclared (first use in this function) > Rglue.c:690: error: ‘tmpo’ undeclared (first use in this function) > Rglue.c:704: error: ‘o’ undeclared (first use in this function) > Rglue.c:704: warning: implicit declaration of function ‘createObject’ > Rglue.c:723: warning: return makes pointer from integer without a cast > Rglue.c: At top level: > Rglue.c:727: error: expected ‘)’ before ‘*’ token > Rglue.c:758: error: expected ‘)’ before ‘*’ token > Rglue.c:770: error: expected ‘)’ before ‘*’ token > Rglue.c: In function ‘RcreateArray’: > Rglue.c:786: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:786: error: ‘env’ undeclared (first use in this function) > Rglue.c:793: error: ‘jbyteArray’ undeclared (first use in this function) > Rglue.c:793: error: expected ‘;’ before ‘a’ > Rglue.c:794: error: ‘a’ undeclared (first use in this function) > Rglue.c:795: warning: implicit declaration of function ‘new_jarrayRef’ > Rglue.c:795: warning: return makes pointer from integer without a cast > Rglue.c:797: error: ‘jcharArray’ undeclared (first use in this function) > Rglue.c:797: error: expected ‘;’ before ‘a’ > Rglue.c:799: warning: return makes pointer from integer without a cast > Rglue.c:801: error: ‘jintArray’ undeclared (first use in this function) > Rglue.c:801: error: expected ‘;’ before ‘a’ > Rglue.c:803: warning: return makes pointer from integer without a cast > Rglue.c:809: error: ‘jfloatArray’ undeclared (first use in this function) > Rglue.c:809: error: expected ‘;’ before ‘a’ > Rglue.c:811: warning: return makes pointer from integer without a cast > Rglue.c:813: error: ‘jlongArray’ undeclared (first use in this function) > Rglue.c:813: error: expected ‘;’ before ‘a’ > Rglue.c:815: warning: return makes pointer from integer without a cast > Rglue.c:817: error: ‘jdoubleArray’ undeclared (first use in this function) > Rglue.c:817: error: expected ‘;’ before ‘a’ > Rglue.c:819: warning: return makes pointer from integer without a cast > Rglue.c:824: error: ‘jobjectArray’ undeclared (first use in this function) > Rglue.c:824: error: expected ‘;’ before ‘a’ > Rglue.c:828: error: ‘jobject’ undeclared (first use in this function) > Rglue.c:828: error: expected ‘;’ before ‘so’ > Rglue.c:829: error: ‘so’ undeclared (first use in this function) > Rglue.c:833: warning: return makes pointer from integer without a cast > Rglue.c:838: error: ‘jbooleanArray’ undeclared (first use in this function) > Rglue.c:838: error: expected ‘;’ before ‘a’ > Rglue.c:840: warning: return makes pointer from integer without a cast > Rglue.c:845: error: ‘jclass’ undeclared (first use in this function) > Rglue.c:845: error: expected ‘;’ before ‘ac’ > Rglue.c:861: error: ‘ac’ undeclared (first use in this function) > Rglue.c:881: error: expected ‘;’ before ‘a’ > Rglue.c:883: error: ‘javaObjectClass’ undeclared (first use in this function) > Rglue.c:888: error: expected ‘;’ before ‘o’ > Rglue.c:893: error: ‘o’ undeclared (first use in this function) > Rglue.c:899: warning: return makes pointer from integer without a cast > Rglue.c:904: error: expected ‘;’ before ‘a’ > Rglue.c:906: warning: return makes pointer from integer without a cast > Rglue.c: In function ‘RpollException’: > Rglue.c:916: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:916: error: ‘env’ undeclared (first use in this function) > Rglue.c:917: error: ‘jthrowable’ undeclared (first use in this function) > Rglue.c:917: error: expected ‘;’ before ‘t’ > Rglue.c:919: error: ‘t’ undeclared (first use in this function) > Rglue.c: In function ‘RclearException’: > Rglue.c:927: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:927: error: ‘env’ undeclared (first use in this function) > Rglue.c: In function ‘RthrowException’: > Rglue.c:948: error: ‘JNIEnv’ undeclared (first use in this function) > Rglue.c:948: error: ‘env’ undeclared (first use in this function) > Rglue.c:949: error: ‘jthrowable’ undeclared (first use in this function) > Rglue.c:949: error: expected ‘;’ before ‘t’ > Rglue.c:960: error: ‘t’ undeclared (first use in this function) > make: *** [Rglue.o] Error 1 > ERROR: compilation failed for package ‘rJava’ > * Removing ‘/usr/local/lib/R/site-library/rJava’ > * Restoring previous ‘/usr/local/lib/R/site-library/rJava’ > > The downloaded packages are in > ‘/tmp/Rtmp0D1hWd/downloaded_packages’ > Warning message: > In install.packages("rJava") : > installation of package 'rJava' had non-zero exit status >> q() > Save workspace image? [y/n/c]: n > mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# R > > R version 2.7.1 (2008-06-23) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> install.packages('rJava') > Warning in install.packages("rJava") : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz' > Content type 'application/x-gzip' length 240527 bytes (234 Kb) > opened URL > ================================================== > downloaded 234 Kb > > * Installing *source* package 'rJava' ... > checking for gcc... gcc -std=gnu99 > 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 gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/wait.h that is POSIX.1 compatible... 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 string.h... (cached) yes > checking sys/time.h usability... yes > checking sys/time.h presence... yes > checking for sys/time.h... yes > checking for unistd.h... (cached) yes > checking for an ANSI C-conforming const... yes > checking whether time.h and sys/time.h may both be included... yes > configure: checking whether gcc -std=gnu99 supports static inline... > yes > checking Java support in R... present: > interpreter : '/usr/bin/java' > archiver : '/usr/bin/jar' > compiler : '/usr/bin/javac' > header prep.: '/usr/bin/javah' > cpp flags : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux' > java libs : '-L$(JAVA_HOME)/lib/amd64/server > -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L > -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm' > checking whether JNI programs can be compiled... yes > checking JNI data types... ok > checking whether JRI should be compiled (autodetect)... yes > checking whether debugging output should be enabled... no > checking whether memory profiling is desired... no > checking whether threads support is requested... no > checking whether callbacks support is requested... no > checking whether JNI cache support is requested... no > checking whether JRI is requested... yes > configure: creating ./config.status > config.status: creating src/Makevars > config.status: creating R/zzz.R > config.status: creating src/config.h > === configuring in jri (/tmp/R.INSTALL.bELNGf/rJava/jri) > configure: running /bin/sh ./configure '--prefix=/usr/local' > --cache-file=/dev/null --srcdir=. > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for gcc... gcc -std=gnu99 > 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 gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking whether Java interpreter works... checking whether JNI > programs can be compiled... yes > checking whether JNI programs can be run... yes > checking JNI data types... ok > checking whether Rinterface.h exports R_CStackXXX variables... yes > checking whether Rinterface.h exports R_SignalHandlers... yes > configure: creating ./config.status > config.status: creating src/Makefile > config.status: creating Makefile > config.status: creating run > config.status: creating src/config.h > ** libs > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c arrayc.c -o arrayc.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c callback.c -o callback.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c callJNI.c -o callJNI.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c fields.c -o fields.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c init.c -o init.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c jri_glue.c -o jri_glue.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c loader.c -o loader.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c Rglue.c -o Rglue.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c rJava.c -o rJava.o > gcc -std=gnu99 -I/usr/share/R/include -I. > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic -g > -O2 -c tools.c -o tools.o > gcc -std=gnu99 -shared -o rJava.so arrayc.o callback.o callJNI.o > fields.o init.o jri_glue.o loader.o Rglue.o rJava.o tools.o > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64/server > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64 > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../lib/amd64 -L > -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm > -L/usr/lib64/R/lib -lR > make -C ../jri/ > make[1]: Entering directory `/tmp/R.INSTALL.bELNGf/rJava/jri' > make -C src JRI.jar > make[2]: Entering directory `/tmp/R.INSTALL.bELNGf/rJava/jri/src' > /usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java > ../RBool.java ../RConsoleOutputStream.java ../Rengine.java > ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java > ../RVector.java > /usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine > gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude > -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux > -I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include > gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK > -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux > -I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include > jri.c: In function ‘jri_getObjectArray’: > jri.c:303: warning: cast from pointer to integer of different size > gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude > -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux > -I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include > gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK > -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include > gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude > -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux > gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK > -DRIF_HAS_RSIGHAND -g -O2 > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux -fpic > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include > -I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux > gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o > globals.o rjava.o -shared > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64/server > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64 > -L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../lib/amd64 -L > -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm > -L/usr/lib64/R/lib -lR > /usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java > ../RBool.java ../RConsoleOutputStream.java ../Rengine.java > ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java > ../RVector.java > /usr/bin/jar fc JRI.jar org libjri.so > make[2]: Leaving directory `/tmp/R.INSTALL.bELNGf/rJava/jri/src' > rm -f libjri.so > cp src/libjri.so libjri.so > /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d > examples examples/rtest2.java > Note: examples/rtest2.java uses or overrides a deprecated API. > Note: Recompile with -Xlint:deprecation for details. > /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d > examples examples/rtest.java > Note: examples/rtest.java uses or overrides a deprecated API. > Note: Recompile with -Xlint:deprecation for details. > make[1]: Leaving directory `/tmp/R.INSTALL.bELNGf/rJava/jri' > ** R > ** inst > ** preparing package for lazy loading > ** help > >>> Building/Updating help pages for package 'rJava' > Formats: text html latex example > accessOp text html latex example > jarray text html latex example > jarrayRef-class text html latex > jcall text html latex example > jcast text html latex example > jcastToArray text html latex example > jcheck text html latex example > jengine text html latex example > jequals text html latex example > jfield text html latex example > jfloat-class text html latex > jfloat text html latex > jinit text html latex example > jmemprof text html latex example > jnew text html latex example > jnull text html latex example > jobjRef-class text html latex > jpackage text html latex example > jreflection text html latex example > jserialize text html latex > jsimplify text html latex example > loader text html latex example > show text html latex > ** building package indices ... > * DONE (rJava) > > The downloaded packages are in > /tmp/RtmplOpZ4F/downloaded_packages >> q() > Save workspace image? [y/n/c]: n > mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > > "The real problem is not whether machines think but whether men do." > -- B. F. Skinner > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
