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McCully, Dwayne (NIH/NIAMS) [C]

2015-Oct-17 19:04 UTC

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

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 ---

	[[alternative HTML version deleted]]

arnaud gaboury

2015-Oct-17 21:43 UTC

head link

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

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
>


-- 

google.com/+arnaudgabourygabx

Jeroen Ooms

2015-Oct-18 12:14 UTC

head link

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

On Sat, Oct 17, 2015 at 9:04 PM, McCully, Dwayne (NIH/NIAMS) [C]
<dmccully at mail.nih.gov> wrote:> After trying several ways to compile R 3.2.2 without luck, I?m reaching out
for help.
If you are new to R you probably want to use the precompiled binaries.
On CentOS/RHEL these are available through the EPEL repositories (see
http://bit.ly/1xVxGlD for installation instructions)

Once EPEL is installed you can simply do 'yum install R-devel' as you
would do on Fedora.

McCully, Dwayne (NIH/NIAMS) [C]

2015-Oct-19 12:07 UTC

head link

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

Below is the output.   Thanks for the help. 
> Sys.getenv()BASH_FUNC_module()      () { eval
                       
`/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd
                        bash $*` }
COLUMNS                 152
CPATH                   /cm/shared/apps/uge/8.2.1/include
CVS_RSH                 ssh
DISPLAY                 localhost:10.0
EDITOR                  vi
G_BROKEN_FILENAMES      1
HISTCONTROL             ignoredups
HISTSIZE                1000
HOME                    /root
HOSTNAME                test
LANG                    en_US.UTF-8
LD_LIBRARY_PATH        
/cm/shared/apps/R/3.2.1/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/lib/amd64/server:/cm/shared/apps/uge/8.2.1/lib/lx-amd64
LESSOPEN                ||/usr/bin/lesspipe.sh %s
LINES                   48
_LMFILES_              
/cm/local/modulefiles/shared:/cm/shared/modulefiles/uge/8.2.1:/cm/local/modulefiles/cmsh:/cm/local/modulefiles/cmd:/cm/local/modulefiles/cluster-tools/7.1:/cm/shared/modulefiles/cmgui/7.1:/cm/shared/modulefiles/R/3.2.1
LN_S                    ln -s
LOADEDMODULES          
shared:uge/8.2.1:cmsh:cmd:cluster-tools/7.1:cmgui/7.1:R/3.2.1
LOGNAME                 root
LS_COLORS              
rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL                    /var/spool/mail/root
MAKE                    make
MANPATH                
/cm/local/apps/cluster-tools/man:/cm/local/apps/cmd/man:/cm/shared/apps/uge/8.2.1/man:/usr/share/centrifydc/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/man:/cm/local/apps/environment-modules/current/share/man
MINICOM                 -t ansi-generic
MODULEPATH              /cm/local/modulefiles:/cm/shared/modulefiles
MODULESHOME             /cm/local/apps/environment-modules/3.2.10/Modules/3.2.10
MODULE_VERSION          3.2.10
MODULE_VERSION_STACK    3.2.10
NXDIR                   /usr/NX
PAGER                   /usr/bin/less
PATH                   
/cm/shared/apps/R/3.2.1/bin:/cm/shared/apps/cmgui:/cm/local/apps/cluster-tools/bin:/cm/local/apps/cmd/sbin:/cm/local/apps/cmd/bin:/cm/shared/apps/uge/8.2.1/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/share/centrifydc/sbin:/usr/share/centrifydc/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/cm/local/apps/environment-modules/3.2.10/bin:/usr/NX/bin:/opt/dell/srvadmin/bin:/opt/dell/srvadmin/sbin:/root/bin
PWD                     /root
QTDIR                   /usr/lib64/qt-3.3
QTINC                   /usr/lib64/qt-3.3/include
QTLIB                   /usr/lib64/qt-3.3/lib
R_ARCH
R_BROWSER               /usr/bin/firefox
R_BZIPCMD               /usr/bin/bzip2
R_DOC_DIR               /cm/shared/apps/R/3.2.1/lib64/R/doc
R_GZIPCMD               /bin/gzip
R_HOME                  /cm/shared/apps/R/3.2.1/lib64/R
R_INCLUDE_DIR           /cm/shared/apps/R/3.2.1/lib64/R/include
R_LIBS_SITE
R_LIBS_USER             ~/R/x86_64-unknown-linux-gnu-library/3.2
R_PAPERSIZE             a4
R_PDFVIEWER             /usr/bin/xdg-open
R_PLATFORM              x86_64-unknown-linux-gnu
R_PRINTCMD              lpr
R_RD4PDF                times,hyper
R_SESSION_TMPDIR        /tmp/Rtmphn5m15
R_SHARE_DIR             /cm/shared/apps/R/3.2.1/lib64/R/share
R_SYSTEM_ABI            linux,gcc,gxx,gfortran,?
R_TEXI2DVICMD           /usr/bin/texi2dvi
R_UNZIPCMD              /usr/bin/unzip
R_ZIPCMD                /usr/bin/zip
SED                     /bin/sed
SGE_ROOT                /cm/shared/apps/uge/8.2.1
SHELL                   /bin/bash
SHLVL                   1
SSH_ASKPASS             /usr/libexec/openssh/gnome-ssh-askpass
TAR                     /bin/gtar
TERM                    xterm
USER                    root
XAUTHORITY              /root/.xauthtGhzUe

-----Original Message-----
From: arnaud gaboury [mailto:arnaud.gaboury at gmail.com] 
Sent: Saturday, October 17, 2015 5:44 PM
To: McCully, Dwayne (NIH/NIAMS) [C] <dmccully at mail.nih.gov>
Cc: r-devel at r-project.org
Subject: Re: [Rd] R 3.2.2 - make check and install package hang

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
>


-- 

google.com/+arnaudgabourygabx

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