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Steve Dutky

2005-Feb-07 17:56 UTC

[Rd] Problems encountered/fixed making CrossCompileBuild

Dear All:

I encountered and apparently overcame problems following Yan 
and Rossini?s procedure for  "Building Microsoft Windows 
Versions of R and R packages under Intel Linux" 
(http://cran.r-project.org/doc/contrib/cross-build.pdf):  I 
have successfully cross-compiled R packages for Windows on a 
FreeBSD 4.10 i386 system.

My  revisions to Makefile-rcb (http://cran.r-
project.org/doc/contrib/Makefile-rcb ) follow here:

1. created makevar MAKE initialized to gmake.  Replaced all 
direct references to make with $(MAKE).

2. updated  makevar MINGW_CROSS = mingw-cross4 to point to 
http://www.stats.ox.ac.uk/pub/Rtools/mingw-cross4.tar.bz2 , 
replacing original reference to mingw-cross2.

3. updated MkRules HEADER=$(CROSSDIR)/i586-mingw32/include , 
replacing  original reference to <snip>/mingw32/include. 

4. reset LinuxFresh = YES
Yan and Rossini imply that linuxR: is an optional step if R 
is already installed.  I ran afoul of steps in 
$(WINR)/<snip>/gnuwin32/MakePkg referencing symbols in the 
tools package in the system's version of R.  Happily, these 
ran successfully against $(LINUXR)/R/bin/R.

I hope some of this turns useful to others attempting this.

Thanks, Steve Dutky 
Sdutky@terpalum.umd.edu

Revised Makefile-rcb:

############################ -*- Mode: Makefile -*- 
###########################
## Makefile-rcb --- Makefile for R cross-building
##
## Author          : Jun Yan (University of Iowa) 
<jyan@stat.uiowa.edu>
##                   A.J. Rossini (UW - Seattle) 
<rossini@u.washington.edu>
## Last modified   : 10/11/2004
## Provisionally revised 2/1/2004 S Dutky 
<sdutky@terpalum.umd.edu>
##############################################################
#################
MAKE =  /usr/local/bin/gmake
SHELL = /bin/sh
WGET = wget --passive-ftp
BINS = \*.so \*.dll \*.RData \*.rda \*.zip \*.rds \*.pdf \*.ps

#### define directories

## the current directory where all the following cross-
building happens
RCB := $(shell pwd)
## the directory where the downloaded sources are stored
DOWNDIR = $(RCB)/downloads
## the directory where the cross-tools are installed
CROSSDIR = $(RCB)/cross-tools
## the directory where R sources are unpacked for cross-
building
WINR = $(RCB)/WinR
## the dirECTOry where R for Linux will be compiled and 
installed
LINUXR = $(RCB)/LinuxR

## the directory where package sources are stored
PKGDIR = $(RCB)/pkgsrc
## the directory where the built packages for windows are to 
be stored
WINRLIBS = $(RCB)/WinRlibs

## current versions
R = R-2.0.0
## snapshot R is only available at 
ftp://ftp.stat.math.ethz.ch/Software/R
ifeq ($(findstring devel, $(R)), devel)
RURL = ftp://ftp.stat.math.ethz.ch/Software/R
REXT = tar.gz
else
RURL = http://cran.us.r-project.org/src/base/R-2
REXT = tar.gz
endif

R_TCL_URL = http://www.murdoch-sutherland.com/Rtools/R_Tcl.zip

#MINGW_CROSS = mingw-cross2 now:
MINGW_CROSS = mingw-cross4

## R_EXE
LinuxFresh = YES
ifeq ($(strip $(LinuxFresh)),YES)
R_EXE = $(LINUXR)/R/bin/R
else
R_EXE = R
endif

default: 
	@echo "syntax:"
	@echo "make <target>"
	@echo "No <Target> Specified.  Should be one of:"
	@echo " "
	@echo "-------------------"
	@echo "down     : downloads files"
	@echo "xtools   : unpack cross compilers"
	@echo "prepsrc  : unpack and prepare source code"
	@echo "mkrules  : patch source code for cross-compile"
	@echo "R        : cross-compile R"
	@echo " "
	@echo "(or to run all at once (trusting, aren't 
you?))"
	@echo " "
	@echo "CrossCompileBuild"
	@echo " "
	@echo "(To build packages or bundles, steps above 
have to be run"
	@echo " first to get a working build of R, which is 
required!)"
	@echo " "
	@echo "pkg-NAME_VER    : cross-build package NAME_VER"
	@echo "bundle-NAME_VER : cross-build packages in 
bundle NAME_VER"
	@echo " "
	@echo "(For example, put geepack_0.2-7.tar.gz and 
VR_7.1-10.tar.gz"
	@echo " in subdirectory pkgsrc, then do"
	@echo " "
	@echo " make pkg-geepack_0.2-7"
	@echo " make bundle-VR_7.1-10)"
	@echo "-------------------"
	@echo " "

buildR: clean prepsrc mkrules R

#### steps described in the document

down:
	mkdir -p $(DOWNDIR); \
	cd $(DOWNDIR); \
	$(WGET) $(RURL)/$(R).$(REXT) -O $(R).tgz; \
	$(WGET) $(R_TCL_URL); \
	$(WGET) http://www.stats.ox.ac.uk/pub/Rtools/
$(MINGW_CROSS).tar.bz2; \

downR:
	mkdir -p $(DOWNDIR); \
	cd $(DOWNDIR); \
	$(WGET) $(RURL)/$(R).$(REXT) -O $(R).tgz; \

downRTcl:
	mkdir -p $(DOWNDIR); \
	cd $(DOWNDIR); \
	$(WGET) $(R_TCL_URL);\

downXtools:
	mkdir -p $(DOWNDIR); \
	cd $(DOWNDIR); \
	$(WGET) http://www.stats.ox.ac.uk/pub/Rtools/
$(MINGW_CROSS).tar.bz2; \

linuxR:
	mkdir -p $(LINUXR); \
	cd $(LINUXR); \
	tar zxf $(DOWNDIR)/$(R).tgz; \
	cd $(LINUXR)/$(R); \
	./configure; \
	$(MAKE); \
	$(MAKE) prefix=$(LINUXR)/R install; \

xtools:
	mkdir -p $(RCB)/cross-tools; \
	cd $(CROSSDIR); \
	tar jxf $(DOWNDIR)/$(MINGW_CROSS).tar.bz2; \

prepsrc:
	mkdir -p $(WINR); \
	cd $(WINR); \
	rm -rf $(R); \
	tar zxf $(DOWNDIR)/$(R).tgz; \
	cd $(WINR)/$(R); \
	unzip $(DOWNDIR)/R_Tcl.zip

mkrules:
	cd $(WINR)/$(R)/src/gnuwin32/; \
	cp MkRules MkRules.orig; \
	sed 's|^BUILD=MINGW|BUILD=CROSS|; 
s|^HEADER=.*$$|HEADER=$(CROSSDIR)/i586-mingw32/include|; 
s|^R_EXE=.*$$|R_EXE=$(R_EXE)|; s|# R_EXE=R|R_EXE=$(R_EXE)|' 
MkRules.orig > MkRules

R:
	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
	cd $(WINR)/$(R)/src/gnuwin32/; \
	$(MAKE); \
	cd $(RCB)/WinR; \
	tar zcf Win-$(R).tgz $(R)

pkg-%:
	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
	export mypkg=`echo $* | cut -d'_' -f1,1`; \
	cd $(PKGDIR); \
	rm -rf $$mypkg; \
	tar zxf $*.tar.gz; \
	echo -------$$mypkg------; \
	cd $(WINR)/$(R)/src/gnuwin32/; \
	$(MAKE) PKGDIR=$(PKGDIR) RLIB=$(WINRLIBS) STAMP=no 
pkg-$$mypkg; \
	mkdir -p $(WINRLIBS); \
	cd $(WINRLIBS); \
	rm -rf $$mypkg.zip; \
	zip -rl $$mypkg.zip $$mypkg -x $(BINS);\
	zip -r9 $$mypkg.zip $$mypkg -i $(BINS);\
	rm -rf $$mypkg

#### this section no longer works as of R-2.0.0
# bundle-%:
# 	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
# 	cd $(PKGDIR); \
# 	tar zxf $*.tar.gz; \
# 	export mybundle=`echo $* | cut -d'_' -f1,1`; \
# 	echo -------$$mybundle------; \
# 	cd $(WINR)/$(R)/src/gnuwin32/; \
# 	$(MAKE) PKGDIR=$(PKGDIR) RLIB=$(WINRLIBS) STAMP=no 
bundle-$$mybundle; \
# 	mkdir -p $(WINRLIBS); \
# 	cd $(WINRLIBS); \
# 	ls $(PKGDIR)/$$mybundle/; \
# 	echo $(PKGDIR)/$$mybundle/DESCRIPTION; \
# 	grep "^Contains:" $(PKGDIR)/$$mybundle/DESCRIPTION | 
sed -e 's/Contains: //'; \
# 	export incl=`grep "^Contains:" $(PKGDIR)/
$$mybundle/DESCRIPTION | sed -e 's/Contains: //'`; \
# 	echo ------$$incl------; \
# 	for pkg in $$incl; do \
# 	(rm -rf $$pkg.zip; \
# 	 zip -rl $$pkg.zip $$pkg -x $(BINS); \
# 	 zip -r9 $$pkg.zip $$pkg -i $(BINS); \
# 	 rm -rf $$pkg); \
# 	done; 
bundle-%:
	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
	cd $(WINR)/$(R)/src/library;\
	tar zxf $(PKGDIR)/$*.tar.gz; \
	export mybundle=`echo $* | cut -d'_' -f1,1`; \
	echo -------$$mybundle------; \
	cd $(WINR)/$(R)/src/gnuwin32/; \
	$(R_EXE) CMD perl XINSTALL --unsafe --
docs=normal ../library/$${mybundle} || exit 1; \
	mkdir -p $(WINRLIBS); \
	ls $(WINR)/$(R)/src/library/$$mybundle/; \
	echo $(PKGDIR)/$$mybundle/DESCRIPTION; \
	grep "^Contains:" $(WINR)/$(R)/src/library/
$$mybundle/DESCRIPTION | sed -e 's/Contains: //'; \
	export incl=`grep "^Contains:" $(WINR)/
$(R)/src/library/$$mybundle/DESCRIPTION | sed -
e 's/Contains: //'`; \
	echo ------$$incl------; \
	cd $(WINR)/$(R)/library; \
	for pkg in $$incl; do \
	(rm -rf $$pkg.zip; \
	 zip -rl $(WINRLIBS)/$$pkg.zip $$pkg -x $(BINS); \
	 zip -r9 $(WINRLIBS)/$$pkg.zip $$pkg -i $(BINS); \
	 rm -rf $$pkg); \
	done; \
	rm -rf $(WINR)/$(R)/src/library/$${mybundle}; \


#### other targets that may be useful

pkgclean-%:
	cd $(PKGDIR); \
	rm -rf $*


recommended:
	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
	cd $(WINR)/$(R)/src/gnuwin32/; \
	$(MAKE) recommended

# dist-recommended:
# 	mkdir -p $(WINRLIBS); \
# 	cd $(WINR)/$(R)/src/gnuwin32/; \
# 	$(MAKE) dist-recommended; \
# 	mv Recommended.zip $(WINRLIBS)/

clean:
	rm -rf $(WINR)

#### not tested
# rinstaller:
# 	export 
PATH=$(CROSSDIR)/bin:$(CROSSDIR)/mingw32/bin:$(PATH); \
# 	cd $(WINR)/$(R)/src/gnuwin32/; \
# 	$(MAKE) rinstaller


CrossCompileBuild :
	$(MAKE) down
	$(MAKE) xtools 
	$(MAKE) prepsrc
	$(MAKE) mkrules
	$(MAKE) R

Jake Bowers

2005-Feb-07 22:11 UTC

head link

[Rd] R-patched Make Check Fails on reg-tests-1.R on linux and OS X

Dear Developers,

I've been playing around with compiling R on my Debian Linux machine (dual
Athlon 1.4ghz) and my OS X machine (dual G5). I'm emailing now because
reg-tests-1.R fails during make check on my debian machine using gcc-3.4,
and on my OS X machine using gcc-3.3. I am using r-patched updated via svn
today (Updated to revision 33075.)

Here are some details:

**Using gcc-3.4 on debian:
gcc-3.4 (GCC) 3.4.4 20041218 (prerelease) (Debian 3.4.3-6)

wes:/home/temp/R/r-patched/tests# tail
reg-tests-1.Rout.fail>
> ## automatic row.names can be number-like, MM, 2004-11-26
> d0 <- data.frame(x=1:3, y=pi*2:0)
> row.names(d0)[3] <- c("01.00")
> write.table(d0, (tf <- tempfile()))
> d <- read.table(tf)
> ## gave error ("duplicate row.names") in 2.0.1
> stopifnot(all.equal(d,d0))
> unlink(tf)
**Using gcc-3.3 on debian works fine (passes all make check).
gcc (GCC) 3.3.5 (Debian 1:3.3.5-5)

**Using gcc-3.3 on OS X.
gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1671)

More info on my OS X build:
./configure --with-blas='-framework vecLib' --with-lapack --with-aqua
--with-x --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
--enable-R-shlib TCLTK_LIBS='-framework Tcl -framework Tk'
TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.Framework/Headers
-I/Library/Frameworks/Tk.Framework/Headers' --with-recommended

g77 is version 3.4 downloaded from hpc.sf.net.
GNU Fortran (GCC) 3.4.2

 echo $PATH
/usr/local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin:/sw/bin:/sw/sbin:/usr/local/pvm3/lib:/usr/local/pvm3/bin/DARWIN

and, to prevent it from using stuff in the fink directory:

CPPFLAGS='-I/usr/local/include'

Here is the output where make check fails:

running regression tests
running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout] Error
1
make[2]: *** [test-Reg] Error 2
make[1]: *** [test-all-basics] Error 1
make: *** [check-all] Error 2

sphere:~/TEMP/R/r-patched/tests jwbowers$ tail
reg-tests-1.Rout.fail>
>
> ## automatic row.names can be number-like, MM, 2004-11-26
> d0 <- data.frame(x=1:3, y=pi*2:0)
> row.names(d0)[3] <- c("01.00")
> write.table(d0, (tf <- tempfile()))
> d <- read.table(tf)
> ## gave error ("duplicate row.names") in 2.0.1
> stopifnot(all.equal(d,d0))
> unlink(tf)
Should I be very concerned about this? I tend to mostly use my OS X
machine since the Linux box is about 4 years old.

I hope this information is helpful --- I'm sorry if this is something
obvious! (I found some posts from last summer about problems with gcc-3.4,
which might explain the problems with gcc-3.4 on linux, but I didn't find
anything obvious about gcc-3.3 on the Mac).

Thanks so much for all of your work!!

Best,

Jake

Jake Bowers
Assistant Professor
Dept of Political Science
University of Michigan
http://www.umich.edu/~jwbowers

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