[Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)

2009-07-23 Thread William Bulley 

I am building from source on RHEL 4 and have run into a
problem while running "make check":

   running code in 'lapack.R' ...make[3]: *** [lapack.Rout] Error 1
   make[3]: Leaving directory `/opt/R/R-2.9.1/tests'
   make[2]: *** [test-Specific] Error 2
   make[2]: Leaving directory `/opt/R/R-2.9.1/tests'
   make[1]: *** [test-all-basics] Error 1
   make[1]: Leaving directory `/opt/R/R-2.9.1/tests'
   make: *** [check] Error 2

I don't know the first thing about R as an application.  The
"./configure" and "make" steps succeeded without error.  I got
a warning about not being able to build "info" and "HTML"
documents.  This is due to an older version (4.5) of makeinfo.
I asked, and our developers think they don't need "info" or
"HTML" documentation.  They are okay with man pages.  However,
there may be other problems from any older libraries or other
missing software.

I asked Kurt Hornik about this.  Here are his comments:

According to Kurt Hornik  on Sun, 07/19/09 at 12:02:
> 
> You have:
> 
> BLAS_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRblas
> LAPACK_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRlapack
> 
> so you really use the BLAS and LAPACK code that comes with R ...
> so I am somewhat clueless on this.
> 
> Perhaps you can ask on the r-devel mailing list whether others
> have had similar problems?

Can anyone shed any light on this problem?  Thanks in advance.

Regards,

web...

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Re: [Rd] maximum supported lag is 350

2009-07-23 Thread Matteo Bertini 

Il 22-07-2009 16:26, Matteo Bertini ha scritto:

I have found a strange error:

 > fit = Arima(flow, c(1,0,1), list(order=c(0,1,1), period=96*7))
Error in makeARIMA(trarma[[1L]], trarma[[2L]], Delta, kappa) :
maximum supported lag is 350

Is in fact quite common to have a lag > 350 using a weekly period in
15min steps = 672 (standard in traffic flow prediction litterature for
example).

Is there any reasons against doing what is suggested in the comment and
avoid the hardcoded limit?

Thanks,
Matteo Bertini



# https://svn.r-project.org/R/trunk/src/library/stats/src/arima.c
SEXP getQ0(SEXP sPhi, SEXP sTheta)
{

[8<]

/* This is the limit using an int index. We could use
size_t and get more on a 64-bit system,
but there seems no practical need. */
if(r > 350) error(_("maximum supported lag is 350"));



Can someone review this analysis?
I can propose a patch to fix the problem if it is ok.

As I can see from the code:

/* NB: nrbar could overflow */
int r = max(p, q + 1);
size_t np = r * (r + 1) / 2, nrbar = np * (np - 1) / 2;

where we want

nrbar <= SIZE_MAX/2

considering that:

np = r * (r + 1) / 2 < (r + 1)^2 / 2 = r2

and

nrbar = np * (np - 1) / 2 < np^2 / 2 < r2^2 / 2

we have a protective:

nrbar < (r + 1)^4 / 8

and we can check for:

(r + 1)^4 / 8 <= SIZE_MAX/2

mat...@zarathustra:~/Documents/src$ cat size_max.c
#include 
#include 
#include 

#define MAX_LAG (int)(sqrt(sqrt(8)) * sqrt(sqrt(SIZE_MAX/2)) - 1)

int main(void) {
int r;
size_t np, nrbar;
printf("MAX_LAG = %d\n", MAX_LAG);
for (r=MAX_LAG-5; rbut perhaps I was missing some detail given the overflow occurs at 
SIZE_MAX/2


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Re: [Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)

2009-07-23 Thread William Bulley 
According to William Bulley  on Thu, 07/23/09 at 11:34:
> 
> I am building from source on RHEL 4 and have run into a
> problem while running "make check":
> 
>running code in 'lapack.R' ...make[3]: *** [lapack.Rout] Error 1
>make[3]: Leaving directory `/opt/R/R-2.9.1/tests'
>make[2]: *** [test-Specific] Error 2
>make[2]: Leaving directory `/opt/R/R-2.9.1/tests'
>make[1]: *** [test-all-basics] Error 1
>make[1]: Leaving directory `/opt/R/R-2.9.1/tests'
>make: *** [check] Error 2

Maybe some additional detail would be useful...   Ah-hem...   :-)

linux% uname -a 
  
Linux host 2.4.21-57.ELsmp #1 SMP Wed Apr 23 01:31:01 EDT 2008 x86_64 x86_64 
x86_64 GNU/Linux

I ran ./configure (see attached files) followed by make and make test.

I have attached the output of a couple of files to help debug this one.

I hope these will be useful.  If not, I can send more details, just ask.

Regards,

web...

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PACKAGE = R
VERSION = 2.9.1

abs_top_srcdir = /opt/R/R-2.9.1
abs_top_builddir = /opt/R/R-2.9.1

include $(top_srcdir)/share/make/vars.mk

AR = ar
ACLOCAL = aclocal
AUTOCONF = autoconf
AUTOMAKE = automake
AUTOHEADER = autoheader
AWK = gawk
BITMAP_LIBS = -ljpeg -lpng -lz -ltiff
BLAS_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRblas
BUILDDIR_IS_SRCDIR = yes
BUILD_CC = 
BUILD_R = 
CC = gcc -std=gnu99
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
DEFS = -DHAVE_CONFIG_H 
DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude="*.o" 
--exclude="*$(SHLIB_EXT)"
DVIPS = /usr/bin/dvips
DYLIB_EXT = .so
DYLIB_LD = gcc -std=gnu99
DYLIB_LDFLAGS = -shared
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C = 
ECHO_N = -n
ECHO_T = 
FFLAGS = -g -O2
FLIBS =  -lg2c -lm
FPICFLAGS = -fpic
F77 = g77
GETWD = /bin/pwd
GZIP = --best
INSTALL = /usr/bin/install -c
INSTALL_DATA = ${INSTALL} -m 644
INSTALL_PROGRAM = ${INSTALL}
INSTALL_SCRIPT = ${INSTALL}
INSTALL_DIR = ${INSTALL} -d
JAVA = 
JAVA_HOME = 
JAVA_LD_LIBRARY_PATH = 
JAVA_LIBS = 
JAVAC = /usr/bin/javac
LATEX = /usr/bin/latex
LDFLAGS = -L/usr/local/lib64
LIBINTL= 
LIBM = -lm
LIBR = 
LIBS =  -ldl -lm
LIBnn = lib64
LIBTOOL = $(SHELL) $(top_builddir)/libtool
LN_S = ln -s
MAIN_CFLAGS = 
MAIN_FFLAGS = 
MAIN_LD = gcc -std=gnu99
MAIN_LDFLAGS = -Wl,--export-dynamic  # -Wl,-bE:$(top_builddir)/etc/R.exp
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
MAKEINDEX = /usr/bin/makeindex
## need this for bootstrapping
MKINSTALLDIRS = /bin/sh $(top_srcdir)/src/scripts/mkinstalldirs.in
PERL = /usr/local/bin/perl
OBJC = 
OBJCFLAGS = -g -O2
R_ARCH = 
R_FRAMEWORK_DIR = $(prefix)/R.framework
R_GZIPCMD = /bin/gzip
## needed for AIX only
# R_HOME = $(top_builddir)
R_MODULES = X11
R_OSTYPE = unix
R_PKGS = $(R_PKGS_BASE)  $(R_PKGS_RECOMMENDED)
R_PLATFORM = x86_64-unknown-linux-gnu
R_XTRA_CFLAGS = 
R_XTRA_CPPFLAGS =  -I. -I$(top_builddir)/src/include -I$(top_srcdir)/src/include
R_XTRA_FFLAGS = 
R_XTRA_LIBS = 
RANLIB = ranlib
READLINE_LIBS = -lreadline -lncurses 
SED = /bin/sed
SHELL = /bin/sh
SHLIB_EXT = .so
SHLIB_CFLAGS = 
SHLIB_FFLAGS = 
SHLIB_LD = gcc -std=gnu99
SHLIB_LDFLAGS = -shared
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
STRIP_LIBS = strip --strip-unneeded
STRIP_STATIC_LIBS = strip --strip-debug
TAR = tar
USE_NLS = yes
X_CFLAGS =  -I/usr/X11R6/include
X_LIBS =  -L/usr/X11R6/lib64 -lX11 -lXt -lXmu
X_PRE_LIBS =  -lSM -lICE
X_EXTRA_LIBS = 
YACC = bison -y

ALL_CFLAGS = $(R_XTRA_CFLAGS) $(MAIN_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(CPPFLAGS) $(DEFS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(MAIN_FFLAGS) $(FFLAGS)
ALL_OBJCFLAGS = $(R_XTRA_OBJCFLAGS) $(MAIN_OBJCFLAGS) $(OBJCFLAGS)
ALL_CFLAGS_LO = $(R_XTRA_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)

.SUFFIXES:
.SUFFIXES: .c .f .m .d .o

.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo "making $@ from $<"
@gcc -std=gnu99 -MM $(ALL_CPPFLAGS) $< > $@
.f.o:
$(F77) $(ALL_FFLAGS) -c $< -o $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
@echo "making $@ from $<"
@gcc -E -M $(ALL_CPPFLAGS) $< > $@

prefix = /usr/local
exec_prefix = ${prefix}
datarootdir = ${prefix}/share
## only used for installing 'R'.
bindir = ${exec_prefix}/bin
## not used
datadir = ${datarootdir}
## used for 'rhome' and installation of standalone Rmath
libdir = ${exec_prefix}/${LIBnn}
## used for man page
mandir = ${datarootdir}/man
## used for installation of standalone Rmath headers
includedir = ${prefix

Re: [Rd] Building a package with BLAS under Windows

2009-07-23 Thread Markus Jochmann 

Solved it myself: The single precision and complex BLAS routines were not
installed.
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