[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Mark Kimpel
mwkimpel at gmail.com
Thu Jul 16 04:00:01 CEST 2009
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.ulrich at 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<mwkimpel at 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
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