From jayoung at fhcrc.org  Thu May 21 23:44:30 2009
From: jayoung at fhcrc.org (Janet Young)
Date: Thu, 21 May 2009 14:44:30 -0700
Subject: [Rd] problems building R-2.9.0 on solaris
Message-ID: <629ED978-FBAC-4DF3-BF24-D63E0736D20B@fhcrc.org>

Hi,

I've successfully updated our linux version of R to 2.9.0 but am  
having trouble on our solaris machine.  I had previously installed  
2.8.1 and earlier versions without trouble.

I'm using R-patched_2009-05-20.tar.gz (I had also tried the 2009-05-10  
version).  Here's some info on our machine (I'm not the sysadmin):
[2] bedrock:/home/jayoung> uname -a
SunOS bedrock 5.10 Generic_118833-36 sun4v sparc SUNW,Sun-Fire-T200

Here's how I have been successfully installing the last few versions  
of R:

setenv LD_LIBRARY_PATH /home/jayoung/mysql/mysql-5.0.45-solaris10- 
sparc-64bit/lib:/opt/SUNWspro/lib:/usr/lib:/usr/openwin/lib
setenv PATH /home/jayoung/mysql/mysql-5.0.45-solaris10-sparc-64bit/lib/ 
bin:/bin:/sbin:/usr/sbin:/etc:/opt/SUNWspro/bin:/usr/ccs/bin
unsetenv R_HOME
./configure --enable-R-shlib R_PAPERSIZE='letter' --prefix='/home/ 
btrask/traskdata'
make
make install

Now, when I do that, configure looks like it completes OK, but during  
"make" it fails.  It also fails if I omit the "--enable-R-shlib"  
during configure.

It fails in a different way if I use my regular environment (i.e.  
start a new terminal, and use the commands as above but omitting the  
two setenv lines) - but that has never worked, so I won't bother you  
with the details of that (unless it seems like useful information to  
someone?). The setenvs I'm using (PATH and LD_LIBRARY_PATH) were given  
to me by the syadmin people here as a suggestion to get R installation  
working.

Below I have pasted the last part of the output from make:

 >>> Building/Updating help pages for package 'tcltk'
      Formats: text html latex example
   TclInterface                      text    html    latex   example
   TkCommands                        text    html    latex   example
   TkWidgetcmds                      text    html    latex   example
   TkWidgets                         text    html    latex   example
   tclServiceMode                    text    html    latex   example
   tcltk-defunct                     text    html    latex
   tcltk-package                     text    html    latex
   tkProgressBar                     text    html    latex   example
   tkStartGUI                        text    html    latex
   tk_choose.dir                     text    html    latex   example
   tk_choose.files                   text    html    latex   example
   tk_messageBox                     text    html    latex
   tk_select.list                    text    html    latex
   tkpager                           text    html    latex
begin installing recommended package VR
ERROR unable to create '/home/jayoung/source_codes/R/R-2.9.0/ 
unpack_solaris3/R-patched/library/MASS'
*** Error code 1
The following command caused the error:
MAKE="make" R_LIBS= ../../../bin/R CMD INSTALL --no-lock -l "../../../ 
library" VR.tgz > VR.ts.out 2>&1 || (cat VR.ts.out && exit 1)
make: Fatal error: Command failed for target `VR.ts'
Current working directory /home/jayoung/source_codes/R/R-2.9.0/ 
unpack_solaris3/R-patched/src/library/Recommended
*** Error code 1
The following command caused the error:
make stamp-recommended
make: Fatal error: Command failed for target `recommended-packages'
Current working directory /home/jayoung/source_codes/R/R-2.9.0/ 
unpack_solaris3/R-patched/src/library/Recommended
*** Error code 1
The following command caused the error:
(cd src/library/Recommended && make)
make: Fatal error: Command failed for target `stamp-recommended'


I'm not sure if this is a bug, or something screwy about the way our  
system is set up (I suspect the latter).  I'd be grateful for any  
ideas you might have to help me figure this out.

thanks in advance,

Janet Young

-------------------------------------------------------------------

Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168,
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung  ...at...  fhcrc.org

http://www.fhcrc.org/labs/trask/



[Rd] problems building R-2.9.0 on solaris
Janet Young