Nie mogę zainstalować rJava 0.9 na Ubuntu 10.04

Używam R 2.13 z CRAN apt repo dla Ubuntu 10.04, a ja próbuję zainstalować Deducer, który wymaga JGR/rJava, ale rJava nie chce budować/instalować, narzekając na nie można zbudować aplikacji JNI. Próbowałem sudo R CMD javareconf zgodnie z sugestią, ale to tylko doprowadziło do innego błędu dotyczącego rozbrajania konfiguracji. Znalazłem R: rJava package install failing, więc wypróbowałem sugestie tam instalacji r-cran-rjava (ale to 0.8 i Deducer/JGR wydają się nalegać na instalowanie 0.9) i błahy z moim $JAVA_HOME, wszystko bez skutku. Jakieś pomysły?Nie mogę zainstalować rJava 0.9 na Ubuntu 10.04

Oto bardziej kompletny zapis tego, co się stało:

$ sudo aptitude install r-cran-rjava 
... 
$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

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(c('JGR','Deducer')) 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JavaGD_0.5-4.tar.gz' 
Content type 'application/x-gzip' length 102242 bytes (99 Kb) 
opened URL 
================================================== 
downloaded 99 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/iplots_1.1-4.tar.gz' 
Content type 'application/x-gzip' length 330323 bytes (322 Kb) 
opened URL 
================================================== 
downloaded 322 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JGR_1.7-7.tar.gz' 
Content type 'application/x-gzip' length 536564 bytes (523 Kb) 
opened URL 
================================================== 
downloaded 523 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/Deducer_0.4-4.tar.gz' 
Content type 'application/x-gzip' length 5325794 bytes (5.1 Mb) 
opened URL 
================================================== 
downloaded 5.1 Mb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
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 
c hecking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 

Make sure you have Java Development Kit installed and correctly registered in R. 
If in doubt, re-run "R CMD javareconf" as root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 
* installing *source* package ‘JavaGD’ ... 
checking for gcc... gcc 
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 accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -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 
checking for stdlib.h... (cached) yes 
checking for GNU libc compatible malloc... yes 
checking return type of signal handlers... void 
checking for memset... yes 
checking for mkdir... yes 
checking for rmdir... yes 
checking for select... yes 
checking for socket... yes 
checking Java support in R... present: 
interpreter : '/usr/bin/java' 
cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 
ERROR: configuration failed for package ‘JavaGD’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JavaGD’ 
ERROR: dependency ‘rJava’ is not available for package ‘iplots’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/iplots’ 
ERROR: dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ are not available for package ‘JGR’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JGR’ 
ERROR: dependencies ‘rJava’, ‘JGR’ are not available for package ‘Deducer’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Deducer’ 

The downloaded packages are in 
     ‘/tmp/RtmpCSITmm/downloaded_packages’ 
Warning messages: 
1: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'rJava' had non-zero exit status 
2: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JavaGD' had non-zero exit status 
3: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'iplots' had non-zero exit status 
4: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JGR' had non-zero exit status 
5: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'Deducer' had non-zero exit status 
> 


R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

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') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
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 accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 

Make sure you have Java Development Kit installed and correctly registered in R. 
If in doubt, re-run "R CMD javareconf" as root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpTk0ftk/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
> 
$ sudo R CMD javareconf 
Java interpreter : /usr/bin/java 
Java version  : 1.6.0_20 
Java home path : /usr/lib/jvm/java-6-openjdk/jre 
Java compiler : /usr/bin/javac 
Java headers gen.: /usr/bin/javah 
Java archive tool: /usr/bin/jar 
Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib 
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm 
JNI cpp flags : 

Updating Java configuration in /etc/R 
Done. 

$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

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') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
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 accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -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 
c hecking 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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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 : '' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
configure: error: One or more Java configuration variables are not set. 
Make sure R is configured with full Java support (including JDK). Run 
R CMD javareconf 
as root to add Java support to R. 

If you don't have root privileges, run 
R CMD javareconf -e 
to set all Java-related variables and then install rJava. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpsJBxfe/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
>

Źródło

2011-08-20 Yang

Dał ci tę samą poradę kilka razy. Czy istnieje dobry powód, aby nie słuchać tego? Tutaj znowu jest, jeśli go przegapiłeś: "Jeśli masz wątpliwości, ponownie uruchom" R CMD javareconf "jako root." –

Huh? Wyraźnie stwierdziłem, że zrobiłem to w moim pierwotnym pytaniu, a także w zapisie ... – Yang

Przepraszam. Co to było? To, że odwołujesz się do pytania, a następnie przystąpiłeś do instalacji przed wykonaniem poprawek, które zostały zasugerowane. –

Dah, niedługo po wysłaniu znalazłem odpowiedź tutaj:

http://r-interface.blogspot.com/2012/04/install-r-jgr-and-deducer-in-ubuntu.html

Chociaż miałem już zainstalowane Sun Java, Kluczem było uruchomienie update-java-alternatives, aby przełączyć się na Sun Java przed uruchomieniem javareconf:

sudo update-java-alternatives -s java-6-sun 
sudo R CMD javareconf

Źródło

2011-08-20 03:05:12 Yang

Powinno to wszystko działać tak, jak jest dostarczane w Debianie/Ubuntu z opcją Javy skonfigurowaną dla pakietów R i rJava, używając pakietu Java SDK w systemie Ubuntu. Jeśli zdecydujesz się przełączyć na inny Java backend, musisz zrekonfigurować. –

Oto kolejna opcja:

przed uruchomieniem R, to zrobić

export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk/jre/lib/amd64/server

(na ścieżce powyżej substytut położenie danego libjvm.so, jeśli masz inną konfigurację). Aby znaleźć libjvm.so można zrobić

sudo updatedb && locate libjvm.so

Źródło

2011-12-27 05:01:26 DWright

jeden inny (stosunkowo oczywiste) ostrzeżenie: nie rób tego, co zrobiłem i zainstalować zarówno java6 i java7. Doprowadziło to do konfliktu, którego nie mogłem "naprawić" poprzez określenie ścieżek i zmiennych środowiskowych. Usunięcie i ponowna instalacja java6 doprowadziły do pomyślnej instalacji JGR. (to pod ubuntu precyzyjny, na zasadzie PowerBook G4 firmy Apple)

Źródło

2013-02-06 02:41:06

DWright jest right..an alternatywa zamiast eksportować go za każdym razem, niż zacząć R jest zlokalizować ścieżka java

sudo locate libjvm.so

i dodać IR ldpaths

sudo gedit /etc/R/ldpaths 

i.e 
${JAVA_HOME=/usr/java/jdk1.7.0_07/jre}

Źródło

2013-07-22 02:58:09 CocoOS

Nie mogę zainstalować rJava 0.9 na Ubuntu 10.04

Odpowiedz

Powiązane problemy