[R] trouble with installing pbatR

[Tena Sakai]

Hello folks,

I am having a problem installing pbatR package.  (My R version is 2.8.1.)

As I execute a command
  > install.packages(lib='/usr/local/apps/R-2.8.1/lib64/R/library', "pbatR")
 it detects lack of rootSolve package and attempts to install it.  But
 cannot seem to compile it, and the rest is aborted.

Any hint as to what I can do?

Thank you in advance for your help.

Tena Sakai
tsakai at gallo.ucsf.edu

Here's the detail:

> install.packages(lib='/usr/local/apps/R-2.8.1/lib64/R/library', "pbatR")
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ŒrootSolve¹

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rootSolve_1.5.tar.gz'
Content type 'application/x-gzip' length 488474 bytes (477 Kb)
opened URL
==================================================
downloaded 477 Kb

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/pbatR_2.2-0.tar.gz'
Content type 'application/x-gzip' length 120576 bytes (117 Kb)
opened URL
==================================================
downloaded 117 Kb

* Installing *source* package 'rootSolve' ...
** libs
gcc -std=gnu99 -I/usr/local/apps/R-2.8.1/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c call_runsteady
.c -o call_runsteady.o
gcc -std=gnu99 -I/usr/local/apps/R-2.8.1/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c call_steady.c
-o call_steady.o
gcc -std=gnu99 -I/usr/local/apps/R-2.8.1/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c call_stsparse.
c -o call_stsparse.o
g77   -fpic  -g -O2 -c dlinpk.f -o dlinpk.o
g77   -fpic  -g -O2 -c lsodes.f -o lsodes.o
lsodes.f: In subroutine `dlsodes':
lsodes.f:1536: warning:
         CALL DSTODE (NEQ, Y, RWORK(LYH), NYH, RWORK(LYH), RWORK(LEWT),
              1
lsodes.f:3468: (continued):
         CALL DSTODE (NEQ, Y, RWORK(LYH), NYH, RWORK(LYH), RWORK(LEWT),
              2
Argument #10 of `dstode' is one type at (2) but is some other type at (1)
[info -f g77 M GLOBALS]
lsodes.f: In subroutine `dprep':
lsodes.f:4980: warning:
         CALL DPREP (NEQ, Y, RWORK(LYH), RWORK(LSAVF), RWORK(LEWT),
              1
lsodes.f:5412: (continued):
         SUBROUTINE DPREP (NEQ, Y, YH, SAVF, EWT, FTEM, IA, JA,
                    2
Argument #10 (named `iwk') of `dprep' is one type at (2) but is some other
type at (1) [info -f g77 M GLOBALS]
g77   -fpic  -g -O2 -c sparsecoeff.f -o sparsecoeff.o
g77   -fpic  -g -O2 -c sparse.f -o sparse.o
g77   -fpic  -g -O2 -c steady.f -o steady.o
steady.f: In subroutine `dsteady':
steady.f:101: 
               Beta = -beta
               ^
Expression at (^) has incorrect data type or rank for its context
steady.f:101: 
               Beta = -beta
                      12
Arithmetic operator at (1) must operate on two scalar (not array)
subexpressions, two function invocations return
ing arithmetic scalars, or a combination of both -- but the subexpression at
(2) is an array
steady.f:106: 
               Beta = -beta
               ^
Expression at (^) has incorrect data type or rank for its context
steady.f:106: 
               Beta = -beta
                      12
Arithmetic operator at (1) must operate on two scalar (not array)
subexpressions, two function invocations return
ing arithmetic scalars, or a combination of both -- but the subexpression at
(2) is an array
make: *** [steady.o] Error 1
ERROR: compilation failed for package 'rootSolve'
** Removing '/usr/local/apps/R-2.8.1/lib64/R/library/rootSolve'
* Installing *source* package 'pbatR' ...
** libs
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c data.cpp -o data.o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c fbatDist.cpp -o fbatDist.
o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c kludge.cpp -o kludge.o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c powerSim.cpp -o powerSim.
o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c random.cpp -o random.o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c sh2win.cpp -o sh2win.o
g++ -I/usr/local/apps/R-2.8.1/lib64/R/include  -I/usr/local/include    -fpic
-g -O2 -c wait.cpp -o wait.o
g++ -shared -L/usr/local/lib64 -o pbatR.so data.o fbatDist.o kludge.o
powerSim.o random.o sh2win.o wait.o   -L/us
r/local/apps/R-2.8.1/lib64/R/lib -lR
** R
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
Loading required package: rootSolve
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
  there is no package called 'rootSolve'
Error: package 'rootSolve' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'pbatR'
** Removing '/usr/local/apps/R-2.8.1/lib64/R/library/pbatR'

The downloaded packages are in
        /tmp/RtmpmWdovn/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(lib = "/usr/local/apps/R-2.8.1/lib64/R/library",  :
  installation of package 'rootSolve' had non-zero exit status
2: In install.packages(lib = "/usr/local/apps/R-2.8.1/lib64/R/library",  :
  installation of package 'pbatR' had non-zero exit status
> 
> exit
Error: object "exit" not found
> q()
Save workspace image? [y/n/c]: n