Well, guess what, rJava also compiles on R-devel (soon to be R-2.10.0). I'll stick with that for my purposes. Thanks for your suggestion. Mark ------------------------------------------------------------ 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 ****************************************************************** On Wed, Jul 15, 2009 at 3:13 PM, Joshua Ulrich<josh.m.ulr...@gmail.com> wrote: > 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
