kjblack@gmail.com
2005-Jan-10 15:22 UTC
[Rd] Problem with compiling - Freebsd on AMD64 (PR#7489)
Full_Name: Kelly Black
Version: 2.0.1
OS: FreeBSD 5.3 on AMD64
Submission from: (NULL) (149.106.32.93)
I downloaded R-2.0.1 from the R website, ran configure then make and got an
error. I will paste a copy of the output from the makefile below. The problem
was when the makefile tried to run the R binary. When I came across the error I
reran configure, but this time with the following arguments:
./configure FFLAGS="-g" CFLAGS="-g" CXXFLAGS="-g"
This time when I ran make it compiled with no problems. I tried the same thing
again only with all of the flags set to "-O" and again it compiled
with no
problems. When I ran it with the flags set to "-g -O2" it had the same
error. A
copy of the output from gdb can be found at
http://blackk.union.edu/~black/freebsd/R-error.txt, but the output isn't
very
helpful.
The system used is a laptop, Compaq Presario (amd64), under FreeBSD 5.3 compiled
for the amd64 architecture.
Output from make with flags "-O2"
black@compaqlaptop$ pwd
/tmp/R-2.0.1/src/library/base
black@compaqlaptop$ make
echo "building package 'base'"
building package 'base'
/usr/local/bin/bash ../../../src/scripts/mkinstalldirs ../../../library/base/R
(f=${TMPDIR:-/tmp}/R$$; cat `LC_COLLATE=C ls ./R/*.R ./R/unix/*.R` >>
${f};
/usr/local/bin/bash ../../../tools/move-if-change ${f} all.R)
all.R is unchanged
/usr/local/bin/bash ../../../tools/copy-if-change all.R
../../../library/base/R/base ${f}
../../../library/base/R/base is unchanged
for f in COPYRIGHTS INDEX SOURCES; do if test -f ./${f}; then
/usr/bin/install -c -m 644 ./${f} ../../../library/base; fi; done
if test -f DESCRIPTION; then /usr/bin/install -c -m 644 DESCRIPTION
../../../library/base; (tmp="Built: R 2.0.1; "; if test -d ./src;
then
tmp="${tmp}x86_64-unknown-freebsd5.3"; fi; tmp="${tmp}; `date`;
unix"; echo
"${tmp}") >> ../../../library/base/DESCRIPTION; fi
/usr/local/bin/bash ../../../src/scripts/mkinstalldirs
../../../library/base/demo
for f in `ls -d ./demo/* | sed -e '/CVS/d' -e '/00Index/d'`; do
/usr/bin/install -c -m 644 ${f} ../../../library/base/demo; done
/usr/local/bin/bash ../../../src/scripts/mkinstalldirs
../../../library/base/man
(f=${TMPDIR:-/tmp}/R$$; for rdfile in ./man/*.Rd ./man/unix/*.Rd; do echo
"%
--- Source file: ${rdfile} ---"; cat ${rdfile}; echo '\eof'; done
>> ${f};
/usr/local/bin/bash ../../../tools/move-if-change ${f}
../../../library/base/man/base.Rd)
rm -f ../../../library/base/man/base.Rd.gz
/usr/bin/gzip ../../../library/base/man/base.Rd
/usr/bin/install -c -m 644 ./inst/CITATION ../../../library/base
/usr/bin/install -c -m 644 all.R ../../../library/base/R/base
cat ./makebasedb.R | R_DEFAULT_PACKAGES=NULL LC_COLLATE=C ../../../bin/R
--vanilla --slave > /dev/null
Floating point exception (core dumped)
*** Error code 136
Stop in /tmp/R-2.0.1/src/library/base.
Prof Brian Ripley
2005-Jan-10 16:02 UTC
[Rd] Problem with compiling - Freebsd on AMD64 (PR#7489)
In what sense is this a bug in R? If changing your compiler optimization leads to a segfault, it looks very like a compiler bug. So what was the compiler? [R does work using AMD64 on Linux, but only correctly with gcc >= 3.3.3.] BTW gdb output with "-g -O2" (the R default) ought to be informative, so was this with -O? On Mon, 10 Jan 2005 kjblack@gmail.com wrote:> Full_Name: Kelly Black > Version: 2.0.1 > OS: FreeBSD 5.3 on AMD64 > Submission from: (NULL) (149.106.32.93) > > > I downloaded R-2.0.1 from the R website, ran configure then make and got > an error. I will paste a copy of the output from the makefile below. The > problem was when the makefile tried to run the R binary. When I came > across the error I reran configure, but this time with the following > arguments: > > ./configure FFLAGS="-g" CFLAGS="-g" CXXFLAGS="-g" > > This time when I ran make it compiled with no problems. I tried the same thing > again only with all of the flags set to "-O" and again it compiled with no > problems. When I ran it with the flags set to "-g -O2" it had the same error. A > copy of the output from gdb can be found at > http://blackk.union.edu/~black/freebsd/R-error.txt, but the output isn't very > helpful. > > The system used is a laptop, Compaq Presario (amd64), under FreeBSD 5.3 compiled > for the amd64 architecture. > > Output from make with flags "-O2" > > black@compaqlaptop$ pwd > /tmp/R-2.0.1/src/library/base > black@compaqlaptop$ make > echo "building package 'base'" > building package 'base' > /usr/local/bin/bash ../../../src/scripts/mkinstalldirs ../../../library/base/R > (f=${TMPDIR:-/tmp}/R$$; cat `LC_COLLATE=C ls ./R/*.R ./R/unix/*.R` >> ${f}; > /usr/local/bin/bash ../../../tools/move-if-change ${f} all.R) > all.R is unchanged > /usr/local/bin/bash ../../../tools/copy-if-change all.R > ../../../library/base/R/base ${f} > ../../../library/base/R/base is unchanged > for f in COPYRIGHTS INDEX SOURCES; do if test -f ./${f}; then > /usr/bin/install -c -m 644 ./${f} ../../../library/base; fi; done > if test -f DESCRIPTION; then /usr/bin/install -c -m 644 DESCRIPTION > ../../../library/base; (tmp="Built: R 2.0.1; "; if test -d ./src; then > tmp="${tmp}x86_64-unknown-freebsd5.3"; fi; tmp="${tmp}; `date`; unix"; echo > "${tmp}") >> ../../../library/base/DESCRIPTION; fi > /usr/local/bin/bash ../../../src/scripts/mkinstalldirs > ../../../library/base/demo > for f in `ls -d ./demo/* | sed -e '/CVS/d' -e '/00Index/d'`; do > /usr/bin/install -c -m 644 ${f} ../../../library/base/demo; done > /usr/local/bin/bash ../../../src/scripts/mkinstalldirs > ../../../library/base/man > (f=${TMPDIR:-/tmp}/R$$; for rdfile in ./man/*.Rd ./man/unix/*.Rd; do echo "% > --- Source file: ${rdfile} ---"; cat ${rdfile}; echo '\eof'; done >> ${f}; > /usr/local/bin/bash ../../../tools/move-if-change ${f} > ../../../library/base/man/base.Rd) > rm -f ../../../library/base/man/base.Rd.gz > /usr/bin/gzip ../../../library/base/man/base.Rd > /usr/bin/install -c -m 644 ./inst/CITATION ../../../library/base > /usr/bin/install -c -m 644 all.R ../../../library/base/R/base > cat ./makebasedb.R | R_DEFAULT_PACKAGES=NULL LC_COLLATE=C ../../../bin/R > --vanilla --slave > /dev/null > Floating point exception (core dumped) > *** Error code 136 > > Stop in /tmp/R-2.0.1/src/library/base. > > ______________________________________________ > R-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >-- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Peter Dalgaard
2005-Jan-10 16:11 UTC
[Rd] Problem with compiling - Freebsd on AMD64 (PR#7489)
kjblack@gmail.com writes:> Full_Name: Kelly Black > Version: 2.0.1 > OS: FreeBSD 5.3 on AMD64 > Submission from: (NULL) (149.106.32.93) > > > I downloaded R-2.0.1 from the R website, ran configure then make and got an > error. I will paste a copy of the output from the makefile below. The problem > was when the makefile tried to run the R binary. When I came across the error I > reran configure, but this time with the following arguments: > > ./configure FFLAGS="-g" CFLAGS="-g" CXXFLAGS="-g" > > This time when I ran make it compiled with no problems. I tried the same thing > again only with all of the flags set to "-O" and again it compiled with no > problems. When I ran it with the flags set to "-g -O2" it had the same error. A > copy of the output from gdb can be found at > http://blackk.union.edu/~black/freebsd/R-error.txt, but the output isn't very > helpful.Indeed... This sounds like a compiler error, so information about the GCC version used is crucial. Switching compilers or running with less than optimal optimization is your best chance, unless you can pinpoint exactly what is getting miscompiled so that a workaround can be found. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907