From dmccully at mail.nih.gov  Sat Oct 17 21:04:43 2015
From: dmccully at mail.nih.gov (McCully, Dwayne (NIH/NIAMS) [C])
Date: Sat, 17 Oct 2015 19:04:43 +0000
Subject: [Rd] R 3.2.2 - make check and install package hang
In-Reply-To: <432A8E6B26DC62439F0201C069BE2B673F0E70F9@msgb06.nih.gov>
References: <432A8E6B26DC62439F0201C069BE2B673F0E70F9@msgb06.nih.gov>
Message-ID: <432A8E6B26DC62439F0201C069BE2B673F0E72F4@msgb06.nih.gov>

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?


./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 ---

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[Rd] R 3.2.2 - make check and install package hang
McCully, Dwayne (NIH/NIAMS