[R] JGR / linux
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(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
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 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('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
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
also installing the dependency ‘JavaGD’
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -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-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -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
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-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux -Iinclude -fpic -g
-O2 -c
Re: [R] JGR / linux
Your R is way too old: please follow the advice in the posting guide.
I suspect the current JavaJD requires R = 2.7.0 from the errors you are
getting below.
On Tue, 3 Jun 2008, g-h-d wrote:
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(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
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 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('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
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
also installing the dependency ‘JavaGD’
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -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-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -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
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-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
Re: [R] JGR / linux
Thanks.
I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and those
below for JGR and it worked.
...but there are problems with help files e.g. ?matrix generates the
following message:
/tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
g-h-d wrote:
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(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
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 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('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
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
also installing the dependency ‘JavaGD’
trying URL
'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -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-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -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
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-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib
Re: [R] JGR / linux
On 3 June 2008 at 08:42, g-h-d wrote:
| I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and those
| below for JGR and it worked.
|
| ...but there are problems with help files e.g. ?matrix generates the
| following message:
|
| /tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
I think you can ignore that. It's just a warning. The rest of your steps
were very sound.
In particular ...
| g-h-d wrote:
|
| Hi all,
|
| i'm trying to install JGR on linux (see bottom), but it runs into errors.
| The bottom of the sequence below shows JavaJD could not be found
|
| Any suggestion, please?
|
|
| $ sudo apt-get install sun-java6-jdk
|
| $ sudo update-alternatives --config java
|
| There are 5 alternatives which provide `java'.
|
| Selection Alternative
| ---
| 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
| 2 /usr/bin/gij-4.1
| 3 /usr/bin/gij-4.2
| 4 /usr/lib/jvm/java-gcj/jre/bin/java
| + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
... a very good idea to realign what command will default to being 'java' ...
| $sudo R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_03
| Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
| Java compiler : /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
... but given that javareconf also looks after javac and javah, I recommend
doing the same update-alternatives call for 'javah' and 'javac'.
I just re-did that on a Ubuntu 8.04, 32bit, machine and it re-built rJava,
JGR, JavaGD, ... without a hitch.
Dirk
| Java library path:
|
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
| JNI linker flags : -L$(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
| JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
| -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
|
| Updating Java configuration in /etc/R
| Done.
|
| $ sudo R
|
| R version 2.5.1 (2007-06-27)
| Copyright (C) 2007 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('JGR', dep=TRUE)
| Warning in install.packages(JGR, dep = TRUE) :
| 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
| also installing the dependency JavaGD
|
| trying URL
| 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
| Content type 'application/x-gzip' length 86505 bytes
| opened URL
| ==
| downloaded 84Kb
|
| trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
| Content type 'application/x-gzip' length 426244 bytes
| opened URL
| ==
| downloaded 416Kb
|
| * Installing *source* package 'JavaGD' ...
| checking for gcc... gcc-4.2 -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-4.2 -std=gnu99 accepts -g... yes
| checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
| checking how to run the C preprocessor... gcc-4.2 -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
Re: [R] JGR / linux
Dirk Eddelbuettel wrote:
On 3 June 2008 at 08:42, g-h-d wrote:
| I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and
those
| below for JGR and it worked.
|
| ...but there are problems with help files e.g. ?matrix generates the
| following message:
|
| /tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
I think you can ignore that. It's just a warning. The rest of your steps
were very sound.
In particular ...
| g-h-d wrote:
|
| Hi all,
|
| i'm trying to install JGR on linux (see bottom), but it runs into
errors.
| The bottom of the sequence below shows JavaJD could not be found
|
| Any suggestion, please?
|
|
| $ sudo apt-get install sun-java6-jdk
|
| $ sudo update-alternatives --config java
|
| There are 5 alternatives which provide `java'.
|
| Selection Alternative
| ---
| 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
| 2 /usr/bin/gij-4.1
| 3 /usr/bin/gij-4.2
| 4 /usr/lib/jvm/java-gcj/jre/bin/java
| + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
... a very good idea to realign what command will default to being 'java'
...
| $sudo R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_03
| Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
| Java compiler : /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
... but given that javareconf also looks after javac and javah, I
recommend
doing the same update-alternatives call for 'javah' and 'javac'.
I just re-did that on a Ubuntu 8.04, 32bit, machine and it re-built rJava,
JGR, JavaGD, ... without a hitch.
Dirk
| Java library path:
|
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
| JNI linker flags : -L$(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
| JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
| -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
|
| Updating Java configuration in /etc/R
| Done.
|
| $ sudo R
|
| R version 2.5.1 (2007-06-27)
| Copyright (C) 2007 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('JGR', dep=TRUE)
| Warning in install.packages(JGR, dep = TRUE) :
| 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
| also installing the dependency JavaGD
|
| trying URL
| 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
| Content type 'application/x-gzip' length 86505 bytes
| opened URL
| ==
| downloaded 84Kb
|
| trying URL
'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
| Content type 'application/x-gzip' length 426244 bytes
| opened URL
| ==
| downloaded 416Kb
|
| * Installing *source* package 'JavaGD' ...
| checking for gcc... gcc-4.2 -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-4.2 -std=gnu99 accepts -g... yes
| checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none
needed
| checking how to run the C preprocessor... gcc-4.2 -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
Re: [R] JGR / linux
Dirk Eddelbuettel wrote: On 3 June 2008 at 13:44, g-h-d wrote: | | $ sudo apt-get install sun-java6-jdk | | | | $ sudo update-alternatives --config java | | | | There are 5 alternatives which provide `java'. | | | | Selection Alternative | | --- | | 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java | | 2 /usr/bin/gij-4.1 | | 3 /usr/bin/gij-4.2 | | 4 /usr/lib/jvm/java-gcj/jre/bin/java | | + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java | | About the message resulting from calling say ?matrix: the message may be a | warning, but ?matrix just doesnt work, I can't use it (or any other help | command). I see. That appears to be the same at my end. You may want to bring that to the attention of the rosuda.org folks. | About doing the same update-alternatives call for 'javah' and 'javac'. I | actually don't know what you mean exactly. Could you please clarify? Thanks. See what I left from your initial post -- besides running $ sudo update-alternatives --config java it may be prudent to also redirect via $ sudo update-alternatives --config javac $ sudo update-alternatives --config javah as 'R CMD javareconf' checkes for all three. But as you got JGR built, this may not matter. I always found that other java compilers from gij, gcj, ecj, ... would get in the way. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thanks for clarifying. -- View this message in context: http://www.nabble.com/JGR---linux-tp17622071p17635209.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
