Re: [Rd] Using custom R_LIBS with R CMD install
On 08.02.2012 21:05, Hadley Wickham wrote:
2012/2/8 Uwe Ligges:
On 08.02.2012 19:36, Hadley Wickham wrote:
I wonder it works that far. It won't for me on Windows nor Linux, because
system2 passes the whole thing shQuoted to the shell. Hence it is highly
shell dependent what happens with the ill formed command.
Well I was using the env argument to system2, which claims to be
cross-platform (at least for R and make). This command:
R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/
is ok, isn't it?
You haven't said you were using the env argument, have you? If so, I missed
that part. I assumed you were specifying the above as the "command"
argument.
Hmmm, former message not quoted, as we ask in the posting guide. Where is
the reproducible example?
We seem to be having a bit of a communication breakdown. This is the
code that I run from the command line (on mac os x):
R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/
# Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/
# * installing to library ‘/Users/hadley/R’
# ERROR: dependency ‘ascii’ is not available for package ‘rapport’
But:
ls /Users/hadley/R-dev/
# HandyStuff animation biOps mcmcTools mvbutils quantreg testthat
# SparseMascii ggplot2mturkr nstest scales whisker
It's hard to provide a reproducible example because it depends on
exactly what package you have installed where, but I had hoped that
this would at least illustrate my problem - R CMD install doesn't seem
to be respecting R_LIBS. I'm trying to understand whether this is a
bug, or something I don't understand correctly about R CMD INSTALL.
That's right, then you want (under Linux alikes):
system2("R", "CMD INSTALL package_version.tar.gz", env="R_LIBS=lib")
obviously.
Under Windows, you have to construct the shell command:
"set R_LIBS=lib& R CMD INSTALL package_version.tar.gz"
To clarify, system2 doesn't work in windows?
It does.
> The system2
documentation has: " On Windows, ‘env’ is currently only supported for
commands such as ‘R’ and ‘make’ which accept environment variables on
their command line."
Yes, but "R CMD INSTALL" does not accept those variables in the command
line. This could perhaps be improved given someone finds some time to do it.
Uwe
Hadley
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Re: [Rd] Using custom R_LIBS with R CMD install
>> >> To clarify, system2 doesn't work in windows? > > It does. > >> The system2 >> >> documentation has: " On Windows, ‘env’ is currently only supported for >> commands such as ‘R’ and ‘make’ which accept environment variables on >> their command line." > > Yes, but "R CMD INSTALL" does not accept those variables in the command > line. This could perhaps be improved given someone finds some time to do it. Ok, so R does, but R CMD INSTALL does not. That was the source of my confusion - thanks for clearing that up! However, is there a reason that system2 doesn't use the more general technique of Sys.setenv? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] FORTRAN compilation error
I should also have explained that I was using the default Makeconf file in R-2.14.1\etc\i386. it is reproduced below. I've tried it on other packages and it inserts a z in front of the object files. Dave #-*- Makefile -*- # $(R_HOME}/etc$(R_ARCH)/Makeconf # Hand-edited version for gnuwin32. ifdef DEBUG DLLFLAGS= DEBUGFLAG=-gdwarf-2 else DLLFLAGS=-s DEBUGFLAG= endif DLLFLAGS+= -static-libgcc LINKFLAGS+= -static-libgcc ## Things which are substituted by fixed/Makefile (and also -O3 -> -O2) WIN = 32 BINPREF = # SYMPAT = 's/^.* [BCDRT] _/ /p' for 32-bit # SYMPAT = 's/^.* [BCDRT] / /p' for 64-bit SYMPAT = 's/^.* [BCDRT] _/ /p' IMPDIR = bin/i386 # flags for multilib builds, for compilers, dlltool and windres M_ARCH = DT_ARCH = RC_ARCH = # Used by packages tcltk and tkrplot TCL_HOME = $(R_HOME)/Tcl LOCAL_SOFT = d:/RCompile/CRANpkg/extralibs/local ifneq ($(strip $(LOCAL_SOFT)),) LOCAL_CPPFLAGS = -I"$(LOCAL_SOFT)/include" LOCAL_LIBS = -L"$(LOCAL_SOFT)/lib$(R_ARCH)" -L"$(LOCAL_SOFT)/lib" endif DLLTOOL = $(BINPREF)dlltool --as $(BINPREF)as $(DT_ARCH) DLLTOOLFLAGS = -k NM = $(BINPREF)nm RESCOMP = $(BINPREF)windres $(RC_ARCH) ## MAIN_LD needs to be set by the package LINKER = $(MAIN_LD) ## as a default DLL = $(CC) ## Things defined in Renviron on Unix SED = sed TAR = tar ## Things defined in MkRules CAT = cat CP = cp MKDIR = mkdir RM = rm -f SORT = sort ## For use in packages GRAPHAPP_LIB = -lRgraphapp TCL_VERSION = 85 ZLIB_LIBS = -lRzlib AR = $(BINPREF)ar ## Used by packages 'maps' and 'mapdata' AWK = gawk BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas C_VISIBILITY = CC = $(BINPREF)gcc $(M_ARCH) CFLAGS = -O3 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=core2 CPICFLAGS = CPPFLAGS = CXX = $(BINPREF)g++ $(M_ARCH) CXXCPP = $(CXX) -E CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=core2 CXXPICFLAGS = DYLIB_EXT = .dll DYLIB_LD = $(DLL) DYLIB_LDFLAGS = -shared DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) ECHO = echo ECHO_C = ECHO_N = -n ECHO_T = FC = $(BINPREF)gfortran $(M_ARCH) FCFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 # additional libs needed when linking with $(FC), e.g. on Solaris FCLIBS = F77 = $(BINPREF)gfortran $(M_ARCH) F77_VISIBILITY = FFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 FLIBS = -lgfortran FCPICFLAGS = FPICFLAGS = FOUNDATION_CPPFLAGS = FOUNDATION_LIBS = JAR = JAVA = JAVAC = JAVAH = # JAVA_HOME = # JAVA_LD_LIBRARY_PATH = JAVA_LIBS = -L"$(JAVA_HOME)/bin/client" -ljvm -ljvm-w32 JAVA_CPPFLAGS = -I"$(JAVA_HOME)/../include" -I"$(JAVA_HOME)/../include/win32" LAPACK_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRlapack ## we only need this is if it is external, as otherwise link to R LIBINTL= LIBM = -lm LIBR = -L"$(R_HOME)/$(IMPDIR)" -lR LIBS = -lm ## needed by R CMD config LIBnn = lib LIBTOOL = LDFLAGS = ## needed to build applications linking to static libR # MAIN_LD = # MAIN_LDFLAGS = # MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) # don't have this: would 'mkdir -p' do? # MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs OBJC = $(CC) OBJCFLAGS = -O2 OBJC_LIBS = -lobjc OBJCXX = R_ARCH = /i386 RANLIB = $(BINPREF)ranlib SAFE_FFLAGS = -O3 -ffloat-store SED = sed ## it seems some makes (but not ours) get upset if SHELL is set. # SHELL = /bin/sh SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = $(CXX) ## ideally -shared -static-libstdc++, but not for gcc 4.2.1 SHLIB_CXXLDFLAGS = -shared SHLIB_EXT = .dll SHLIB_FCLD = $(FC) ## ideally -shared -static-libgfortran, but not for gcc 4.2.1 SHLIB_FCLDFLAGS = -shared SHLIB_FFLAGS = SHLIB_LD = $(CC) SHLIB_LDFLAGS = -shared SHLIB_LIBADD = SHLIB_LINK = $(SHLIB_LD) -Wl,--export-all-symbols $(SHLIB_LDFLAGS) $(LDFLAGS) # not implemented in current toolchain SHLIB_OPENMP_CFLAGS = SHLIB_OPENMP_CXXFLAGS = SHLIB_OPENMP_FCFLAGS = SHLIB_OPENMP_FFLAGS = STRIP_LIBS = $(BINPREF)strip --strip-unneeded STRIP_STATIC_LIBS = $(BINPREF)strip --strip-debug TCLTK_CPPFLAGS = -I "$(TCL_HOME)/include" -DWin32 TCLTK_LIBS = -L"$(TCL_HOME)/bin" -ltcl$(TCL_VERSION) -ltk$(TCL_VERSION) STATIC_LIBR = R_XTRA_CFLAGS = R_XTRA_CPPFLAGS = -I"$(R_HOME)/include" 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) $($*-CPPFLAGS) $(CLINK_CPPFLAGS) $(LOCAL_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 = $(LOCAL_LIBS) $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR) $(LIBINTL) .SUFFIXES: .SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o .a .def .dll .exe .rc .c.o: $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@ .c.d: @echo "making $@ from $<" @$(CC) -std=gnu99 -MM $(ALL_CPPFLAGS) $< > $@ .cc.o: $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@ .cpp.o:
Re: [Rd] FORTRAN compilation error
On Feb 9, 2012, at 9:54 AM, David L Lorenz wrote: > > I should also have explained that I was using the default Makeconf file in > R-2.14.1\etc\i386. it is reproduced below. I've tried it on other packages > and it inserts a z in front of the object files. I'm not talking about R Makeconf, but the one in your package (in src). What are your settings there? And what are the files? Thanks, Simon > Dave > > #-*- Makefile -*- > # $(R_HOME}/etc$(R_ARCH)/Makeconf > > # Hand-edited version for gnuwin32. > > ifdef DEBUG > DLLFLAGS= > DEBUGFLAG=-gdwarf-2 > else > DLLFLAGS=-s > DEBUGFLAG= > endif > > DLLFLAGS+= -static-libgcc > LINKFLAGS+= -static-libgcc > > ## Things which are substituted by fixed/Makefile (and also -O3 -> -O2) > WIN = 32 > BINPREF = > # SYMPAT = 's/^.* [BCDRT] _/ /p' for 32-bit > # SYMPAT = 's/^.* [BCDRT] / /p' for 64-bit > SYMPAT = 's/^.* [BCDRT] _/ /p' > IMPDIR = bin/i386 > # flags for multilib builds, for compilers, dlltool and windres > M_ARCH = > DT_ARCH = > RC_ARCH = > # Used by packages tcltk and tkrplot > TCL_HOME = $(R_HOME)/Tcl > LOCAL_SOFT = d:/RCompile/CRANpkg/extralibs/local > > ifneq ($(strip $(LOCAL_SOFT)),) > LOCAL_CPPFLAGS = -I"$(LOCAL_SOFT)/include" > LOCAL_LIBS = -L"$(LOCAL_SOFT)/lib$(R_ARCH)" -L"$(LOCAL_SOFT)/lib" > endif > > DLLTOOL = $(BINPREF)dlltool --as $(BINPREF)as $(DT_ARCH) > DLLTOOLFLAGS = -k > NM = $(BINPREF)nm > RESCOMP = $(BINPREF)windres $(RC_ARCH) > ## MAIN_LD needs to be set by the package > LINKER = $(MAIN_LD) > ## as a default > DLL = $(CC) > > ## Things defined in Renviron on Unix > SED = sed > TAR = tar > > ## Things defined in MkRules > CAT = cat > CP = cp > MKDIR = mkdir > RM = rm -f > SORT = sort > > ## For use in packages > GRAPHAPP_LIB = -lRgraphapp > TCL_VERSION = 85 > ZLIB_LIBS = -lRzlib > > AR = $(BINPREF)ar > ## Used by packages 'maps' and 'mapdata' > AWK = gawk > BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas > C_VISIBILITY = > CC = $(BINPREF)gcc $(M_ARCH) > CFLAGS = -O3 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=core2 > CPICFLAGS = > CPPFLAGS = > CXX = $(BINPREF)g++ $(M_ARCH) > CXXCPP = $(CXX) -E > CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=core2 > CXXPICFLAGS = > DYLIB_EXT = .dll > DYLIB_LD = $(DLL) > DYLIB_LDFLAGS = -shared > DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) > ECHO = echo > ECHO_C = > ECHO_N = -n > ECHO_T = > FC = $(BINPREF)gfortran $(M_ARCH) > FCFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > # additional libs needed when linking with $(FC), e.g. on Solaris > FCLIBS = > F77 = $(BINPREF)gfortran $(M_ARCH) > F77_VISIBILITY = > FFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > FLIBS = -lgfortran > FCPICFLAGS = > FPICFLAGS = > FOUNDATION_CPPFLAGS = > FOUNDATION_LIBS = > JAR = > JAVA = > JAVAC = > JAVAH = > # JAVA_HOME = > # JAVA_LD_LIBRARY_PATH = > JAVA_LIBS = -L"$(JAVA_HOME)/bin/client" -ljvm -ljvm-w32 > JAVA_CPPFLAGS = -I"$(JAVA_HOME)/../include" -I"$(JAVA_HOME)/../include/win32" > LAPACK_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRlapack > ## we only need this is if it is external, as otherwise link to R > LIBINTL= > LIBM = -lm > LIBR = -L"$(R_HOME)/$(IMPDIR)" -lR > LIBS = -lm > ## needed by R CMD config > LIBnn = lib > LIBTOOL = > LDFLAGS = > ## needed to build applications linking to static libR > # MAIN_LD = > # MAIN_LDFLAGS = > # MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) > # don't have this: would 'mkdir -p' do? > # MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs > OBJC = $(CC) > OBJCFLAGS = -O2 > OBJC_LIBS = -lobjc > OBJCXX = > R_ARCH = /i386 > RANLIB = $(BINPREF)ranlib > SAFE_FFLAGS = -O3 -ffloat-store > SED = sed > ## it seems some makes (but not ours) get upset if SHELL is set. > # SHELL = /bin/sh > SHLIB_CFLAGS = > SHLIB_CXXFLAGS = > SHLIB_CXXLD = $(CXX) > ## ideally -shared -static-libstdc++, but not for gcc 4.2.1 > SHLIB_CXXLDFLAGS = -shared > SHLIB_EXT = .dll > SHLIB_FCLD = $(FC) > ## ideally -shared -static-libgfortran, but not for gcc 4.2.1 > SHLIB_FCLDFLAGS = -shared > SHLIB_FFLAGS = > SHLIB_LD = $(CC) > SHLIB_LDFLAGS = -shared > SHLIB_LIBADD = > SHLIB_LINK = $(SHLIB_LD) -Wl,--export-all-symbols $(SHLIB_LDFLAGS) $(LDFLAGS) > # not implemented in current toolchain > SHLIB_OPENMP_CFLAGS = > SHLIB_OPENMP_CXXFLAGS = > SHLIB_OPENMP_FCFLAGS = > SHLIB_OPENMP_FFLAGS = > STRIP_LIBS = $(BINPREF)strip --strip-unneeded > STRIP_STATIC_LIBS = $(BINPREF)strip --strip-debug > TCLTK_CPPFLAGS = -I "$(TCL_HOME)/include" -DWin32 > TCLTK_LIBS = -L"$(TCL_HOME)/bin" -ltcl$(TCL_VERSION) -ltk$(TCL_VERSION) > > STATIC_LIBR = > > R_XTRA_CFLAGS = > R_XTRA_CPPFLAGS = -I"$(R_HOME)/include" > 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) $($*-CPPFLAGS) > $(CLINK_CPPFLAGS) $(LOCAL_CPPFLAGS) > ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS
Re: [Rd] FORTRAN compilation error
Simon, It was not clear that I needed any makefiles in src. I have seen no documentation anywhere that I needed a makefile in src. The FORTRAN source compiles just fine by hand, so the error is not in the code. It is just one single source code file with one subroutine. The problem appears to be the z that is inserted in from the the object file name when the .dll is created. Thanks. Dave From: Simon Urbanek To: David L Lorenz Cc: r-devel@r-project.org Date: 02/09/2012 09:24 AM Subject: Re: [Rd] FORTRAN compilation error On Feb 9, 2012, at 9:54 AM, David L Lorenz wrote: > > I should also have explained that I was using the default Makeconf file in R-2.14.1\etc\i386. it is reproduced below. I've tried it on other packages and it inserts a z in front of the object files. I'm not talking about R Makeconf, but the one in your package (in src). What are your settings there? And what are the files? Thanks, Simon > Dave > > #-*- Makefile -*- > # $(R_HOME}/etc$(R_ARCH)/Makeconf > > # Hand-edited version for gnuwin32. > > ifdef DEBUG > DLLFLAGS= > DEBUGFLAG=-gdwarf-2 > else > DLLFLAGS=-s > DEBUGFLAG= > endif > > DLLFLAGS+= -static-libgcc > LINKFLAGS+= -static-libgcc > > ## Things which are substituted by fixed/Makefile (and also -O3 -> -O2) > WIN = 32 > BINPREF = > # SYMPAT = 's/^.* [BCDRT] _/ /p' for 32-bit > # SYMPAT = 's/^.* [BCDRT] / /p' for 64-bit > SYMPAT = 's/^.* [BCDRT] _/ /p' > IMPDIR = bin/i386 > # flags for multilib builds, for compilers, dlltool and windres > M_ARCH = > DT_ARCH = > RC_ARCH = > # Used by packages tcltk and tkrplot > TCL_HOME = $(R_HOME)/Tcl > LOCAL_SOFT = d:/RCompile/CRANpkg/extralibs/local > > ifneq ($(strip $(LOCAL_SOFT)),) > LOCAL_CPPFLAGS = -I"$(LOCAL_SOFT)/include" > LOCAL_LIBS = -L"$(LOCAL_SOFT)/lib$(R_ARCH)" -L"$(LOCAL_SOFT)/lib" > endif > > DLLTOOL = $(BINPREF)dlltool --as $(BINPREF)as $(DT_ARCH) > DLLTOOLFLAGS = -k > NM = $(BINPREF)nm > RESCOMP = $(BINPREF)windres $(RC_ARCH) > ## MAIN_LD needs to be set by the package > LINKER = $(MAIN_LD) > ## as a default > DLL = $(CC) > > ## Things defined in Renviron on Unix > SED = sed > TAR = tar > > ## Things defined in MkRules > CAT = cat > CP = cp > MKDIR = mkdir > RM = rm -f > SORT = sort > > ## For use in packages > GRAPHAPP_LIB = -lRgraphapp > TCL_VERSION = 85 > ZLIB_LIBS = -lRzlib > > AR = $(BINPREF)ar > ## Used by packages 'maps' and 'mapdata' > AWK = gawk > BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas > C_VISIBILITY = > CC = $(BINPREF)gcc $(M_ARCH) > CFLAGS = -O3 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=core2 > CPICFLAGS = > CPPFLAGS = > CXX = $(BINPREF)g++ $(M_ARCH) > CXXCPP = $(CXX) -E > CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=core2 > CXXPICFLAGS = > DYLIB_EXT = .dll > DYLIB_LD = $(DLL) > DYLIB_LDFLAGS = -shared > DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) > ECHO = echo > ECHO_C = > ECHO_N = -n > ECHO_T = > FC = $(BINPREF)gfortran $(M_ARCH) > FCFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > # additional libs needed when linking with $(FC), e.g. on Solaris > FCLIBS = > F77 = $(BINPREF)gfortran $(M_ARCH) > F77_VISIBILITY = > FFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > FLIBS = -lgfortran > FCPICFLAGS = > FPICFLAGS = > FOUNDATION_CPPFLAGS = > FOUNDATION_LIBS = > JAR = > JAVA = > JAVAC = > JAVAH = > # JAVA_HOME = > # JAVA_LD_LIBRARY_PATH = > JAVA_LIBS = -L"$(JAVA_HOME)/bin/client" -ljvm -ljvm-w32 > JAVA_CPPFLAGS = -I"$(JAVA_HOME)/../include" -I"$(JAVA_HOME)/../include/win32" > LAPACK_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRlapack > ## we only need this is if it is external, as otherwise link to R > LIBINTL= > LIBM = -lm > LIBR = -L"$(R_HOME)/$(IMPDIR)" -lR > LIBS = -lm > ## needed by R CMD config > LIBnn = lib > LIBTOOL = > LDFLAGS = > ## needed to build applications linking to static libR > # MAIN_LD = > # MAIN_LDFLAGS = > # MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) > # don't have this: would 'mkdir -p' do? > # MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs > OBJC = $(CC) > OBJCFLAGS = -O2 > OBJC_LIBS = -lobjc > OBJCXX = > R_ARCH = /i386 > RANLIB = $(BINPREF)ranlib > SAFE_FFLAGS = -O3 -ffloat-store > SED = sed > ## it seems some makes (but not ours) get upset if SHELL is set. > # SHELL = /bin/sh > SHLIB_CFLAGS = > SHLIB_CXXFLAGS = > SHLIB_CXXLD = $(CXX) > ## ideally -shared -static-libstdc++, but not for gcc 4.2.1 > SHLIB_CXXLDFLAGS = -shared > SHLIB_EXT = .dll > SHLIB_FCLD = $(FC) > ## ideally -shared -static-libgfortran, but not for gcc 4.2.1 > SHLIB_FCLDFLAGS = -shared > SHLIB_FFLAGS = > SHLIB_LD = $(CC) > SHLIB_LDFLAGS = -shared > SHLIB_LIBADD = > SHLIB_LINK = $(SHLIB_LD) -Wl,--export-all-symbols $(SHLIB_LDFLAGS) $(LDFLAGS) > # not implemented in current toolchain > SHLIB_OPENMP_CFLAGS = > SHLIB_OPENMP_CXXFLAGS = > SHLIB_OPENMP_FCFLAGS = > SHLIB_OPENMP_FFLAGS = > STRIP_LIBS = $(BINPREF)strip --strip-unneeded > STRIP_STATIC_LIBS = $(BINPREF)strip
Re: [Rd] FORTRAN compilation error
David, On Feb 9, 2012, at 10:48 AM, David L Lorenz wrote: > > Simon, > It was not clear that I needed any makefiles in src. I have seen no > documentation anywhere that I needed a makefile in src. You don't - I thought you are using one to modify the object list. Simple output of ls -l in your src would have been very helpful with your first e-mail ;). > The FORTRAN source compiles just fine by hand, so the error is not in the > code. It is just one single source code file with one subroutine. > The problem appears to be the z that is inserted in from the the object > file name when the .dll is created. Actually, I think I now see the problem - you have incompatible "make" on your PATH that does not come form the R tools (easy way to tell is that our make is case-sensitive while yours is not - hence the warning). Please make sure you have Rtools on your PATH *before* any other tools. Cheers, Simon > > > From: Simon Urbanek > To: David L Lorenz > Cc: r-devel@r-project.org > Date: 02/09/2012 09:24 AM > Subject: Re: [Rd] FORTRAN compilation error > > > > > On Feb 9, 2012, at 9:54 AM, David L Lorenz wrote: > > > > > I should also have explained that I was using the default Makeconf file in > > R-2.14.1\etc\i386. it is reproduced below. I've tried it on other packages > > and it inserts a z in front of the object files. > > I'm not talking about R Makeconf, but the one in your package (in src). What > are your settings there? And what are the files? > > Thanks, > Simon > > > > > Dave > > > > #-*- Makefile -*- > > # $(R_HOME}/etc$(R_ARCH)/Makeconf > > > > # Hand-edited version for gnuwin32. > > > > ifdef DEBUG > > DLLFLAGS= > > DEBUGFLAG=-gdwarf-2 > > else > > DLLFLAGS=-s > > DEBUGFLAG= > > endif > > > > DLLFLAGS+= -static-libgcc > > LINKFLAGS+= -static-libgcc > > > > ## Things which are substituted by fixed/Makefile (and also -O3 -> -O2) > > WIN = 32 > > BINPREF = > > # SYMPAT = 's/^.* [BCDRT] _/ /p' for 32-bit > > # SYMPAT = 's/^.* [BCDRT] / /p' for 64-bit > > SYMPAT = 's/^.* [BCDRT] _/ /p' > > IMPDIR = bin/i386 > > # flags for multilib builds, for compilers, dlltool and windres > > M_ARCH = > > DT_ARCH = > > RC_ARCH = > > # Used by packages tcltk and tkrplot > > TCL_HOME = $(R_HOME)/Tcl > > LOCAL_SOFT = d:/RCompile/CRANpkg/extralibs/local > > > > ifneq ($(strip $(LOCAL_SOFT)),) > > LOCAL_CPPFLAGS = -I"$(LOCAL_SOFT)/include" > > LOCAL_LIBS = -L"$(LOCAL_SOFT)/lib$(R_ARCH)" -L"$(LOCAL_SOFT)/lib" > > endif > > > > DLLTOOL = $(BINPREF)dlltool --as $(BINPREF)as $(DT_ARCH) > > DLLTOOLFLAGS = -k > > NM = $(BINPREF)nm > > RESCOMP = $(BINPREF)windres $(RC_ARCH) > > ## MAIN_LD needs to be set by the package > > LINKER = $(MAIN_LD) > > ## as a default > > DLL = $(CC) > > > > ## Things defined in Renviron on Unix > > SED = sed > > TAR = tar > > > > ## Things defined in MkRules > > CAT = cat > > CP = cp > > MKDIR = mkdir > > RM = rm -f > > SORT = sort > > > > ## For use in packages > > GRAPHAPP_LIB = -lRgraphapp > > TCL_VERSION = 85 > > ZLIB_LIBS = -lRzlib > > > > AR = $(BINPREF)ar > > ## Used by packages 'maps' and 'mapdata' > > AWK = gawk > > BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas > > C_VISIBILITY = > > CC = $(BINPREF)gcc $(M_ARCH) > > CFLAGS = -O3 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=core2 > > CPICFLAGS = > > CPPFLAGS = > > CXX = $(BINPREF)g++ $(M_ARCH) > > CXXCPP = $(CXX) -E > > CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=core2 > > CXXPICFLAGS = > > DYLIB_EXT = .dll > > DYLIB_LD = $(DLL) > > DYLIB_LDFLAGS = -shared > > DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) > > ECHO = echo > > ECHO_C = > > ECHO_N = -n > > ECHO_T = > > FC = $(BINPREF)gfortran $(M_ARCH) > > FCFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > > # additional libs needed when linking with $(FC), e.g. on Solaris > > FCLIBS = > > F77 = $(BINPREF)gfortran $(M_ARCH) > > F77_VISIBILITY = > > FFLAGS = -O3 $(DEBUGFLAG) -mtune=core2 > > FLIBS = -lgfortran > > FCPICFLAGS = > > FPICFLAGS = > > FOUNDATION_CPPFLAGS = > > FOUNDATION_LIBS = > > JAR = > > JAVA = > > JAVAC = > > JAVAH = > > # JAVA_HOME = > > # JAVA_LD_LIBRARY_PATH = > > JAVA_LIBS = -L"$(JAVA_HOME)/bin/client" -ljvm -ljvm-w32 > > JAVA_CPPFLAGS = -I"$(JAVA_HOME)/../include" > > -I"$(JAVA_HOME)/../include/win32" > > LAPACK_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRlapack > > ## we only need this is if it is external, as otherwise link to R > > LIBINTL= > > LIBM = -lm > > LIBR = -L"$(R_HOME)/$(IMPDIR)" -lR > > LIBS = -lm > > ## needed by R CMD config > > LIBnn = lib > > LIBTOOL = > > LDFLAGS = > > ## needed to build applications linking to static libR > > # MAIN_LD = > > # MAIN_LDFLAGS = > > # MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) > > # don't have this: would 'mkdir -p' do? > > # MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs > > OBJC = $(CC) > > OBJCFLAGS = -O2 > > OBJC_LIBS = -lobjc > > OBJCXX = > > R_ARCH = /i386
[Rd] na.omit option in prcomp: formula interface only
This is a wishlist/request for discussion about the behaviour of the na.action option in prcomp, specifically the fact that it only applies to the formula interface. I had a question from a friend (who is smart and careful and generally R's TFM, although like all of us he misses things sometimes) asking why the na.action= argument didn't seem to be doing anything in prcomp (i.e. one gets an "Error in svd(x, nu=0): infinite or missing values in 'x'"). Some poking later, I realized that na.action only applied to the formula interface (so I told him to try prcomp(~.,data=x,...) instead). Sufficiently careful reading of the help page, with hindsight, revealed that na.action only appears in the arguments for the formula method, not the default (on the other hand, 'scale.' only appears in the default formula, but it *does* work with prcomp.formula as well, because prcomp.formula passes ... through to prcomp.default ...) Would it be reasonable to (at least) add a sentence to the documentation saying that na.action applies only to the formula interface or (possibly) to add some NA-processing machinery to prcomp.default to allow it to handle na.action as well? (I can appreciate from looking at stats:::prcomp.formula that the NA-processing is not completely trivial ...) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
