From arnaud.gaboury at gmail.com  Sat Oct 17 23:43:37 2015
From: arnaud.gaboury at gmail.com (arnaud gaboury)
Date: Sat, 17 Oct 2015 23:43:37 +0200
Subject: [Rd] R 3.2.2 - make check and install package hang
In-Reply-To: <432A8E6B26DC62439F0201C069BE2B673F0E72F4@msgb06.nih.gov>
References: <432A8E6B26DC62439F0201C069BE2B673F0E70F9@msgb06.nih.gov>
	<432A8E6B26DC62439F0201C069BE2B673F0E72F4@msgb06.nih.gov>
Message-ID: <CAK1hC9s6--YC0mOsp50aeCDk2yxtf3GSaYksGjVpQfhOXK69BQ@mail.gmail.com>

On Sat, Oct 17, 2015 at 9:04 PM, McCully, Dwayne (NIH/NIAMS) [C]
<dmccully at mail.nih.gov> wrote:
> Hello Everyone,
>
> After trying several ways to compile R 3.2.2 without luck, I?m reaching out for help.
> The ?make check? does not hanges for some reason and when
> trying to install a package it cannot list the download sites (see below).
>
> What could be the problem?

Maybe your exisiting environment variable. Is R already installed? If
yes, please post output of the followning command in a R session:

> Sys.getenv()




>
>
> ./configure --enable-R-shlib --enable-BLAS-shlib
>
> hostname = test
> uname -m = x86_64
> uname -r = 2.6.32-573.7.1.el6.x86_64
> uname -s = Linux
> uname -v = #1 SMP Thu Sep 10 13:42:16 EDT 2015
> OS: Red Hat 6.7
>
> configuring Java ...
> Java interpreter : /usr/bin/java
> Java version     : 1.7.0_85
> Java home path   : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre
> Java compiler    : /usr/bin/javac
> Java headers gen.: /usr/bin/javah
> Java archive tool: /usr/bin/jar
>
> trying to compile and link a JNI program
> detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
> detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
> make[2]: Entering directory `/tmp/Rjavareconf.lcq59l'
> gcc -std=gnu99 -I/home/dmccully/R-3.2.2/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include/linux -I/usr/local/include    -fpic  -g -O2  -c conftest.c -o conftest.o
> gcc -std=gnu99 -shared -L/home/dmccully/R-3.2.2/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/lib/amd64/server -ljvm -L/home/dmccully/R-3.2.2/lib -lR
> make[2]: Leaving directory `/tmp/Rjavareconf.lcq59l'
>
>
> JAVA_HOME        : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre
> Java library path: $(JAVA_HOME)/lib/amd64/server
> JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
> Updating Java configuration in /home/dmccully/R-3.2.2
> Done.
>
> make[1]: Leaving directory `/home/dmccully/R-3.2.2'
> [root at test R-3.2.2]# pwd
> /home/dmccully/R-3.2.2
> [root at test R-3.2.2]# make check
> make[1]: Entering directory `/home/dmccully/R-3.2.2/tests'
> make[2]: Entering directory `/home/dmccully/R-3.2.2/tests'
> make[3]: Entering directory `/home/dmccully/R-3.2.2/tests/Examples'
> Testing examples for package ?base?
>
>
>> install.packages("ggplot2")
> --- Please select a CRAN mirror for use in this session ---
>
>         [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



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[Rd] R 3.2.2 - make check and install package hang
arnaud gaboury