Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
Just some feedback for the record. Since version R-devel_2009-01-20.tar.gz with Matrix_0.999375-18.tar.gz included I am able again to compile and install R on FreeBSD 8.0-CURRENT out of the box. Many thanks to Martin Maechler and Brian Ripley for the help and work, Rainer Hurling Am 11.01.2009 23:13 (UTC+1) schrieb Rainer Hurling: Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix package. At this point the following break occured: begin installing recommended package Matrix * Installing *source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include-fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c amd_global.c -o amd_global.o make: don't know how to make amd_l_1.o. Stop *** Error code 2 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src/AMD. *** Error code 1 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src. ERROR: compilation failed for package 'Matrix' * Removing '/usr/local/R-devel/library/Matrix' *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel. Please note, that on FreeBSD there is a BSD 'make' as default. If I want to use gmake instead, I explicitly have to set it. Unfortunately this does not work within building the whole R-devel system. With R-2.8.1 I have no problems installing and using R. When I want to build the (external) Matrix package I have to set an environment variable to gmake, found at /usr/local/bin/gmake and all works well. Now my question: Is it possible to change the configure/build of the integrated Matrix package on R-devel? For all other packages there is no need to do so (at least for FreeBSD ;-) Please let me know if I can help. Thanks in advance, Rainer Hurling __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
On Tue, 13 Jan 2009, Prof Brian Ripley wrote: I've discovered that Mac OS still has a FreeBSD make with which I can reproduce this. So I am working with Martin on a patch for the next Matrix update. Meanwhile, if there is an issue with building R-devel with GNU make under FreeBSD (e.g. env MAKE=gmake ./configure env MAKE=gmake make ) we would like to know what it is (see the inline comment in my first reply). This may be a bit late (I finally managed to update to the latest stable FreeBSD release 7.1) but just to report that version _ platform x86_64-unknown-freebsd7.1 arch x86_64 os freebsd7.1 system x86_64, freebsd7.1 status Under development (unstable) major 2 minor 9.0 year 2009 month 01 day19 svn rev47650 language R version.string R version 2.9.0 Under development (unstable) (2009-01-19 r47650) builds fine with # ./configure MAKE=gmake CC=gcc44 F77=gfortran44 FC=gfortran44 CXX=g++44 OBJC=gcc44 R_BROWSER=/usr/local/bin/firefox3 # gmake and passes # gmake check the development version of gcc44 is # gcc44 -v Using built-in specs. Target: x86_64-portbld-freebsd7.1 Configured with: ./..//gcc-4.4-20090116/configure --disable-nls --with-system-zlib --with-libiconv-prefix=/usr/local --with-gmp=/usr/local --program-suffix=44 --libdir=/usr/local/lib/gcc-4.4.0 --with-gxx-include-dir=/usr/local/lib/gcc-4.4.0/include/c++/ --disable-libgcj --prefix=/usr/local --mandir=/usr/local/man --infodir=/usr/local/info/gcc44 --build=x86_64-portbld-freebsd7.1 Thread model: posix gcc version 4.4.0 20090116 (experimental) (GCC) h. -- +--- | Hiroyuki Kawakatsu | Business School, Dublin City University | Dublin 9, Ireland. Tel +353 (0)1 700 7496 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
Matrix has already been updated to be complatible with the FreeBSD make: you will get the update via tools/rsync-recommended. On Tue, 20 Jan 2009, Hiroyuki Kawakatsu wrote: On Tue, 13 Jan 2009, Prof Brian Ripley wrote: I've discovered that Mac OS still has a FreeBSD make with which I can reproduce this. So I am working with Martin on a patch for the next Matrix update. Meanwhile, if there is an issue with building R-devel with GNU make under FreeBSD (e.g. env MAKE=gmake ./configure env MAKE=gmake make ) we would like to know what it is (see the inline comment in my first reply). This may be a bit late (I finally managed to update to the latest stable FreeBSD release 7.1) but just to report that version _ platform x86_64-unknown-freebsd7.1 arch x86_64 os freebsd7.1 system x86_64, freebsd7.1 status Under development (unstable) major 2 minor 9.0 year 2009 month 01 day19 svn rev47650 language R version.string R version 2.9.0 Under development (unstable) (2009-01-19 r47650) builds fine with # ./configure MAKE=gmake CC=gcc44 F77=gfortran44 FC=gfortran44 CXX=g++44 OBJC=gcc44 R_BROWSER=/usr/local/bin/firefox3 # gmake and passes # gmake check the development version of gcc44 is # gcc44 -v Using built-in specs. Target: x86_64-portbld-freebsd7.1 Configured with: ./..//gcc-4.4-20090116/configure --disable-nls --with-system-zlib --with-libiconv-prefix=/usr/local --with-gmp=/usr/local --program-suffix=44 --libdir=/usr/local/lib/gcc-4.4.0 --with-gxx-include-dir=/usr/local/lib/gcc-4.4.0/include/c++/ --disable-libgcj --prefix=/usr/local --mandir=/usr/local/man --infodir=/usr/local/info/gcc44 --build=x86_64-portbld-freebsd7.1 Thread model: posix gcc version 4.4.0 20090116 (experimental) (GCC) h. -- +--- | Hiroyuki Kawakatsu | Business School, Dublin City University | Dublin 9, Ireland. Tel +353 (0)1 700 7496 -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
I've discovered that Mac OS still has a FreeBSD make with which I can reproduce this. So I am working with Martin on a patch for the next Matrix update. Meanwhile, if there is an issue with building R-devel with GNU make under FreeBSD (e.g. env MAKE=gmake ./configure env MAKE=gmake make ) we would like to know what it is (see the inline comment in my first reply). On Mon, 12 Jan 2009, Rainer Hurling wrote: Thank you Brian, for this detailed answer. I think you are right with the new rules. Before contacting the maintainers I will try to collect some more information about the observed failure. Without setting the environment variable MAKE to gmake, I get excatly the same break when installing Matrix under R-2.8.1. So I can test it under 2.8.1. Rainer On 11.01.2009 23:42 (UTC+1), Prof Brian Ripley wrote: You need to take this up with the package maintainers: although recommended packages are distributed with R, they are still contributed packages with separate maintainers. At one point Matrix did work with a non-GNU make (the Solaris one) after suggestions from R-core members on how to remove the obvious GNUisms. It would cetainly be helpful to let the package maintainers know what changes do work. (I presume the issue is amd_i_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDINT -c $ -o $@ amd_l_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDLONG -c $ -o $@ which are new rules since I was able to test.) Unfortunately I can no longer build Matrix (and hence R-devel) on Solaris, as the Sun Studio compilers say some of the C++ code is invalid (and it looks so to me, and I reported it a while back): the file is spqr_front.cpp, so it has not got as far as the point that is giving you trouble. On Sun, 11 Jan 2009, Rainer Hurling wrote: Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix package. At this point the following break occured: begin installing recommended package Matrix * Installing *source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include -fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c amd_global.c -o amd_global.o make: don't know how to make amd_l_1.o. Stop *** Error code 2 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src/AMD. *** Error code 1 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src. ERROR: compilation failed for package 'Matrix' * Removing '/usr/local/R-devel/library/Matrix' *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel. Please note, that on FreeBSD there is a BSD 'make' as default. If I want to use gmake instead, I explicitly have to set it. Unfortunately this does not work within building the whole R-devel system. It would be helpful to know why not. AFAIK GNU make works on other platforms with their own make. With R-2.8.1 I have no problems installing and using R. When I want to build the (external) Matrix package I have to set an environment variable to gmake, found at /usr/local/bin/gmake and all works well. Now my question: Is it possible to change the configure/build of the integrated Matrix package on R-devel? For all other packages there is no need to do so (at least for FreeBSD ;-) Please let me know if I can help. Thanks in advance, Rainer Hurling -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
Thank you Brian, for this detailed answer. I think you are right with the new rules. Before contacting the maintainers I will try to collect some more information about the observed failure. Without setting the environment variable MAKE to gmake, I get excatly the same break when installing Matrix under R-2.8.1. So I can test it under 2.8.1. Rainer On 11.01.2009 23:42 (UTC+1), Prof Brian Ripley wrote: You need to take this up with the package maintainers: although recommended packages are distributed with R, they are still contributed packages with separate maintainers. At one point Matrix did work with a non-GNU make (the Solaris one) after suggestions from R-core members on how to remove the obvious GNUisms. It would cetainly be helpful to let the package maintainers know what changes do work. (I presume the issue is amd_i_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDINT -c $ -o $@ amd_l_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDLONG -c $ -o $@ which are new rules since I was able to test.) Unfortunately I can no longer build Matrix (and hence R-devel) on Solaris, as the Sun Studio compilers say some of the C++ code is invalid (and it looks so to me, and I reported it a while back): the file is spqr_front.cpp, so it has not got as far as the point that is giving you trouble. On Sun, 11 Jan 2009, Rainer Hurling wrote: Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix package. At this point the following break occured: begin installing recommended package Matrix * Installing *source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include -fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c amd_global.c -o amd_global.o make: don't know how to make amd_l_1.o. Stop *** Error code 2 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src/AMD. *** Error code 1 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src. ERROR: compilation failed for package 'Matrix' * Removing '/usr/local/R-devel/library/Matrix' *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel. Please note, that on FreeBSD there is a BSD 'make' as default. If I want to use gmake instead, I explicitly have to set it. Unfortunately this does not work within building the whole R-devel system. It would be helpful to know why not. AFAIK GNU make works on other platforms with their own make. With R-2.8.1 I have no problems installing and using R. When I want to build the (external) Matrix package I have to set an environment variable to gmake, found at /usr/local/bin/gmake and all works well. Now my question: Is it possible to change the configure/build of the integrated Matrix package on R-devel? For all other packages there is no need to do so (at least for FreeBSD ;-) Please let me know if I can help. Thanks in advance, Rainer Hurling __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Package Matrix does not compile in R-devel_2009-01-10
Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix package. At this point the following break occured: begin installing recommended package Matrix * Installing *source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include-fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c amd_global.c -o amd_global.o make: don't know how to make amd_l_1.o. Stop *** Error code 2 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src/AMD. *** Error code 1 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src. ERROR: compilation failed for package 'Matrix' * Removing '/usr/local/R-devel/library/Matrix' *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel. Please note, that on FreeBSD there is a BSD 'make' as default. If I want to use gmake instead, I explicitly have to set it. Unfortunately this does not work within building the whole R-devel system. With R-2.8.1 I have no problems installing and using R. When I want to build the (external) Matrix package I have to set an environment variable to gmake, found at /usr/local/bin/gmake and all works well. Now my question: Is it possible to change the configure/build of the integrated Matrix package on R-devel? For all other packages there is no need to do so (at least for FreeBSD ;-) Please let me know if I can help. Thanks in advance, Rainer Hurling __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package Matrix does not compile in R-devel_2009-01-10
You need to take this up with the package maintainers: although recommended packages are distributed with R, they are still contributed packages with separate maintainers. At one point Matrix did work with a non-GNU make (the Solaris one) after suggestions from R-core members on how to remove the obvious GNUisms. It would cetainly be helpful to let the package maintainers know what changes do work. (I presume the issue is amd_i_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDINT -c $ -o $@ amd_l_%.o: amd_%.c $(INC) $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -I../Include -DDLONG -c $ -o $@ which are new rules since I was able to test.) Unfortunately I can no longer build Matrix (and hence R-devel) on Solaris, as the Sun Studio compilers say some of the C++ code is invalid (and it looks so to me, and I reported it a while back): the file is spqr_front.cpp, so it has not got as far as the point that is giving you trouble. On Sun, 11 Jan 2009, Rainer Hurling wrote: Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix package. At this point the following break occured: begin installing recommended package Matrix * Installing *source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include -fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include-fpic -g -O2 -c amd_global.c -o amd_global.o make: don't know how to make amd_l_1.o. Stop *** Error code 2 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src/AMD. *** Error code 1 Stop in /tmp/Rtmpx5nUS8/R.INSTALL10d63af1/Matrix/src. ERROR: compilation failed for package 'Matrix' * Removing '/usr/local/R-devel/library/Matrix' *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel/src/library/Recommended. *** Error code 1 Stop in /usr/local/R-devel. Please note, that on FreeBSD there is a BSD 'make' as default. If I want to use gmake instead, I explicitly have to set it. Unfortunately this does not work within building the whole R-devel system. It would be helpful to know why not. AFAIK GNU make works on other platforms with their own make. With R-2.8.1 I have no problems installing and using R. When I want to build the (external) Matrix package I have to set an environment variable to gmake, found at /usr/local/bin/gmake and all works well. Now my question: Is it possible to change the configure/build of the integrated Matrix package on R-devel? For all other packages there is no need to do so (at least for FreeBSD ;-) Please let me know if I can help. Thanks in advance, Rainer Hurling __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
