From web at umich.edu  Thu Jul 23 20:54:11 2009
From: web at umich.edu (William Bulley)
Date: Thu, 23 Jul 2009 14:54:11 -0400
Subject: [Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)
Message-ID: <20090723185411.GA80388@dell1>

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 $@


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