William Bulley
2009-Jul-23 15:34 UTC
[Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)
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 <Kurt.Hornik at wu.ac.at> 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... -- William Bulley Email: web at umich.edu The information contained in this message may be CONFIDE...{{dropped:6}}
William Bulley
2009-Jul-23 18:54 UTC
[Rd] problem building R 2.9.1 from source on RHEL 4 (x86_64)
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 2Maybe 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 The information contained in this message may be CONFIDENTIAL and is for the intended addressee only. Any unauthorized use, dissemination of the information, or copying of this message is prohibited. If you are not the intended addressee, please notify the sender immediately, and delete this message. -------------- 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 $@