R devel - Jan 2009 - 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

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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at 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

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
day            19
svn rev        47650
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

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