[Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)
William Bulley
web at umich.edu
Thu Jul 23 20:54:11 CEST 2009
According to William Bulley <web at umich.edu> 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...
--
William Bulley Email: web at umich.edu
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-------------- next part --------------
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}/include
rhome = ${libdir}/R
rsharedir = ${rhome}/share
rincludedir = ${rhome}/include
rdocdir = ${rhome}/doc
## Overrides for installing R as a framework (MacOS X).
#FW_VERSION =
#rhome = $(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources
#bindir = $(rhome)
#mandir = $(rhome)
Rexecbindir = $(rhome)/bin
Rexecbindir2 = $(rhome)/bin/exec$(R_ARCH)
Rexeclibdir = $(rhome)/lib$(R_ARCH)
## FIXME:
## Alternatively, we could try to set pkglibdir = $(rhome)/lib when
## switching to automake.
## </FIXME>
Rexecmodulesdir = $(rhome)/modules$(R_ARCH)
-------------- next part --------------
# etc/Makeconf. Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
include $(R_SHARE_DIR)/make/vars.mk
AR = ar
BLAS_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRblas
C_VISIBILITY =
CC = gcc -std=gnu99
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++
CXXCPP = g++ -E
CXXFLAGS = -g -O2
CXXPICFLAGS = -fpic
DYLIB_EXT = .so
DYLIB_LD = gcc -std=gnu99
DYLIB_LDFLAGS = -shared
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F77 = g77
F77_VISIBILITY =
FC = g77
FCFLAGS = -g -O2
FFLAGS = -g -O2
FLIBS = -lg2c -lm
FCPICFLAGS = -fpic
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /usr/bin/jar
JAVA =
JAVAC = /usr/bin/javac
JAVAH =
JAVA_HOME =
JAVA_LD_LIBRARY_PATH =
JAVA_LIBS =
JAVA_CPPFLAGS =
LAPACK_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRlapack
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR =
LIBS = -ldl -lm
## needed by R CMD config
LIBnn = lib64
LIBTOOL = $(SHELL) $(R_HOME)/bin/libtool
LDFLAGS = -L/usr/local/lib64
## needed to build applications linking to static libR
MAIN_LD = gcc -std=gnu99
MAIN_LDFLAGS = -Wl,--export-dynamic
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
OBJC =
OBJCFLAGS = -g -O2
OBJC_LIBS =
OBJCXX = g++
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -g -O2 -ffloat-store
SED = /bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++
SHLIB_CXXLDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FCLD = g77
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS =
SHLIB_LD = gcc -std=gnu99
SHLIB_LDFLAGS = -shared
SHLIB_LIBADD =
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
STRIP_LIBS = strip --strip-unneeded
STRIP_STATIC_LIBS = strip --strip-debug
TCLTK_CPPFLAGS =
TCLTK_LIBS =
## for linking to libR.a
STATIC_LIBR = # $(R_HOME)/lib$(R_ARCH)/libR.a $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline -lncurses $(LIBS)
R_XTRA_CFLAGS =
R_XTRA_CPPFLAGS = -I$(R_INCLUDE_DIR)
R_XTRA_CXXFLAGS =
R_XTRA_FFLAGS =
ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CPPFLAGS) $(CLINK_CPPFLAGS)
ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .C .d .f .f90 .f95 .m .mm .M .o
.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo "making $@ from $<"
@gcc -std=gnu99 -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.C.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.C.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
@echo "making $@ from $<"
@gcc -E -M $(ALL_CPPFLAGS) $< > $@
.mm.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
$(F77) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
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