From hongbinzhang711 at yahoo.com  Wed Jan  6 01:19:22 2010
From: hongbinzhang711 at yahoo.com (Hongbin Zhang)
Date: Tue, 5 Jan 2010 16:19:22 -0800 (PST)
Subject: [Rd] lapack problem on Linux fedora 11
Message-ID: <20224.88995.qm@web62408.mail.re1.yahoo.com>


I need your help to make R works on my linux box, runing fedora 11.

Few things on the machine and steps I did:

1. uname -a shows:
  Linux bagvapp 2.6.29.4-167.fc11.i586 #1 SMP Wed May 27 17:14:37 EDT 2009 i686 athlon i386 GNU/Linux

2. it has a gcc (version 4.4) RedHat's build

3. the g77 comes with the box does not work (R's configure tells it could not compile simple fortran code); so I download and install a binary version of gfortran (version 4.5) and set the LD_LIBRARY_PATH.

4. download R-2.10.1; ./configure --with-readline=no --with-x=no
   (i.e., I did not use --with-blas or --with-lapack as the manuals indicated; the box does have its copy of blas.so and lapack.so under /usr/lib)

5. my test of lapack in R is to run: library(nlme); and then run the example from this package:
     fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
                 data = Loblolly,
                 fixed = Asym + R0 + lrc ~ 1,
                 random = Asym ~ 1,
                 start = c(Asym = 103, R0 = -8.5, lrc = -3.3))

6. here is the error:

+ + + + Error in chol.default((value + t(value))/2) :
  lapack routines cannot be loaded
In addition: Warning message:
In chol.default((value + t(value))/2) :
  unable to load shared library '/usr/local/lib/R/modules//lapack.so':
  /usr/local/lib/R/modules//lapack.so: cannot restore segment prot after reloc: Permission denied

Other things I tried:
        *. remove the -O2 flag while compiling lapack
        *. "ln -s" this linux box's copy of lapack.so
        *. replace the lapack.so with the other .so created by R, namely
             libRlapack.so (why R creates two copies of the .so?)

None of those work.

Help please.

Hongbin



[Rd] lapack problem on Linux fedora 11
Hongbin Zhang