strider711
asked on
trouble with R installation under Linux
I sent the following message to R-dev and R-help but not get an answer...
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/
/usr/local/lib/R/modules//
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.
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/
/usr/local/lib/R/modules//
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.
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ASKER
1. removed my "binary gfortran"
2. used yum install gcc-gfortran
then everything is fine.
The reason I did not use pre-build R is I am not able to install the perl(File::Copy) although I updated perl....