Error in loading deSolve
praveen.sharma
error on invocation. Is there a way around?
> library(deSolve)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/lib64/R/library/deSolve/libs/
deSolve.so':
/usr/lib64/R/library/deSolve/libs/deSolve.so: undefined symbol:
odeparms_
Error: package/namespace load failed for 'deSolve'
Douglas Bates
<praveen...@ll.mit.edu> wrote:
> I was able to successfully install deSolve, but I get the following
> error on invocation. Is there a way around?
How did you install it? (Compiling the source package or from a binary
package or ...) On what operating system? (It looks like 64-bit
Linux but it would help in any case to have the output of
sessionInfo()
Sharma, Praveen
> install.packages()
Loading Tcl/Tk interface ... done
--- Please select a CRAN mirror for use in this session ---
Warning in install.packages() :
argument 'lib' is missing: using '/usr/lib64/R/library'
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/deSolve_1.5.tar.gz'
Content type 'application/gz' length unknown
opened URL
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downloaded 1.6 Mb
* Installing *source* package 'deSolve' ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c DLLutil.c -o DLLutil.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c R_init_deSolve.c -o R_init_deSolve.o
R_init_deSolve.c: In function `R_init_deSolve':
R_init_deSolve.c:9: warning: passing arg 3 of `R_RegisterCCallable' from incompatible pointer type
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_daspk.c -o call_daspk.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_euler.c -o call_euler.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_lsoda.c -o call_lsoda.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_rk4.c -o call_rk4.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_rkAuto.c -o call_rkAuto.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_rkFixed.c -o call_rkFixed.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c call_zvode.c -o call_zvode.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c daux.f -o daux.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c ddaspk.f -o ddaspk.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c deSolve_utils.c -o deSolve_utils.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c dlinpk.f -o dlinpk.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c dsparsk.f -o dsparsk.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c dvode.f -o dvode.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c errmsg.f -o errmsg.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c ex_Aquaphy.f -o ex_Aquaphy.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c ex_CCL4model.f -o ex_CCL4model.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c ex_ChemicalDAE.c -o ex_ChemicalDAE.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c ex_SCOC.f -o ex_SCOC.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c forcings.c -o forcings.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c opkda1.f -o opkda1.o
opkda1.f: In subroutine `dprep':
opkda1.f:1213: warning:
CALL DPREP (NEQ, Y, RWORK(LYH), RWORK(LSAVF), RWORK(LEWT),
1
opkda1.f:1241: (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]
opkda1.f: In subroutine `dprepi':
opkda1.f:9260: warning:
CALL DPREPI (NEQ, Y, S, RWORK(LYH), RWORK(LSAVF), RWORK(LEWT),
1
opkda1.f:9288: (continued):
SUBROUTINE DPREPI (NEQ, Y, S, YH, SAVR, EWT, RTEM, IA, JA, IC, JC,
2
Argument #13 (named `iwk') of `dprepi' is one type at (2) but is some other type at (1) [info -f g77 M GLOBALS]
g77 -m64 -fpic -O2 -g -pipe -m64 -c opkdmain.f -o opkdmain.o
opkdmain.f: In subroutine `dlsodes':
opkdmain.f:1536: warning:
CALL DSTODE (NEQ, Y, RWORK(LYH), NYH, RWORK(LYH), RWORK(LEWT),
1
opkdmain.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]
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -m64 -c rk_util.c -o rk_util.o
g77 -m64 -fpic -O2 -g -pipe -m64 -c zvode.f -o zvode.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o deSolve.so DLLutil.o R_init_deSolve.o call_daspk.o call_euler.o call_lsoda.o call_rk4.o call_rkAuto.o call_rkFixed.o call_zvode.o daux.o ddaspk.o deSolve_utils.o dlinpk.o dsparsk.o dvode.o errmsg.o ex_Aquaphy.o ex_CCL4model.o ex_ChemicalDAE.o ex_SCOC.o forcings.o opkda1.o opkdmain.o rk_util.o zvode.o -L/usr/lib64/R/lib -lRblas -lg2c -lm -lg2c -lm -L/usr/lib64/R/lib -lR
** R
** data
** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'deSolve'
Formats: text html latex example
DLLfunc text html latex example
DLLres text html latex example
SCOC text html latex example
aquaphy text html latex example
ccl4data text html latex example
ccl4model text html latex example
daspk text html latex example
deSolve text html latex example
diagnostics text html latex example
forcings text html latex example
lsoda text html latex example
lsodar text html latex example
lsode text html latex example
lsodes text html latex example
ode.1D text html latex example
ode.2D text html latex example
ode.3D text html latex example
ode text html latex example
ode.band text html latex example
plot.deSolve text html latex example
rk text html latex example
rk4 text html latex example
rkMethod text html latex example
vode text html latex example
zvode text html latex example
** building package indices ...
* DONE (deSolve)
The downloaded packages are in
'/tmp/RtmpmGZwzH/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning messages:
1: In file.create(f.tg) :
cannot create file '/usr/share/doc/R-2.9.2/html/packages.html', reason 'Permission denied'
2: In tools:::unix.packages.html(.Library) :
cannot create HTML package index
> library(deibrary )
> library(deSolve)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/lib64/R/library/deSolve/libs/deSolve.so':
/usr/lib64/R/library/deSolve/libs/deSolve.so: undefined symbol: odeparms_
Error: package/namespace load failed for 'deSolve'
Sharma, Praveen
>install.packages()
#select the mirror
#select the package - deSolve
# got a successful install --look at the following command
>library()
Packages in library '/usr/lib64/R/library':
base The R Base Package
boot Bootstrap R (S-Plus) Functions (Canty)
class Functions for Classification
cluster Cluster Analysis Extended Rousseeuw et al.
codetools Code Analysis Tools for R
datasets The R Datasets Package
deSolve General solvers for initial value problems of
ordinary differential equations (ODE), partial
differential equations (PDE) and differential
algebraic equations (DAE)
....
Here is sessionInfo
> sessionInfo()
R version 2.9.2 (2009-08-24)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-----Original Message-----
From: mad...@googlegroups.com [mailto:mad...@googlegroups.com] On Behalf Of Douglas Bates
Sent: Thursday, October 22, 2009 2:49 PM
To: mad...@googlegroups.com
Subject: Re: Error in loading deSolve
Douglas Bates
compiled from sources and it doesn't load then that's a bug. They
might be making assumptions about the form of names generated by the
Fortran compiler or something like that but, in any case, it is not a
clean compile if that symbol is referenced and not defined.
I have cc:d the maintainer on this reply.