ports/108543: math/R (R-2.4.0/R-2.4.1) won't upgrade/install on FreeBSD 6.2-STABLE/RELEASE AMD64

Tue Jan 30 10:00:34 UTC 2007

>Number:         108543
>Category:       ports
>Synopsis:       math/R (R-2.4.0/R-2.4.1)      won't upgrade/install on FreeBSD 6.2-STABLE/RELEASE AMD64
>Confidential:   no
>Severity:       serious
>Priority:       high
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          sw-bug
>Submitter-Id:   current-users
>Arrival-Date:   Tue Jan 30 10:00:33 GMT 2007
>Closed-Date:
>Last-Modified:
>Originator:     O. Hartmann
>Release:        FreeBSD 6.2-STABLE AMD64
>Organization:
FU Berlin
>Environment:
FreeBSD foo.org 6.2-STABLE FreeBSD 6.2-STABLE #74: Mon Jan 29 20:48:33 UTC 2007     root at fooorg:/usr/obj/usr/src/sys/FOO  amd64
>Description:
Upgrading R-2.4.0 to 2.4.1 via 'portupgrade' or newly installation of R-2.4.1 after deletion of the port won't work on FreeBSD 6.2-STABLE AMD64, but works on FreeBSD 6.2-STABLE i386.
I tried reinstalling every dependend port (recompiling), but this did not work. I also recompiled and reinstalled BLAS/LAPACK on AMD64, but it also did not change anything. Below are the last lines of compilation errors. The missing library 'libblas.so.1' is /usr/local/lib/libblas.so.2 and present. I have no idea why the compilation process needs the old library. On i386 everything runs smooth! There is no libblas.so.1, only libblas.so.2 is present and R gets compiled well.

 gfortran42  -fpic  -g -O2 -c xxxpr.f -o xxxpr.o
cc -std=gnu99 -shared -L/usr/local/lib  -o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../appl/*.o ../nmath/*.o ../unix/*.o  2>/de
 v/null|grep -v /ext-` -lblas -L/usr/local/lib/gcc-4.2.0/gcc/x86_64-portbld-freebsd6.2/4.2.0 -L/usr/local/lib/gcc-4.2.0 -lgfortran -lm -lgcc_s       /usr/local/lib/libintl.so /usr/local/lib/libiconv.so -Wl,-rpath -Wl,/usr/local/lib -lreadline -lpcre -lbz2 -lz -lm -liconv
mkdir /usr/ports/math/R/work/R-2.4.1/bin/exec
mkdir /usr/ports/math/R/work/R-2.4.1/lib
cc -std=gnu99      -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H  -fpic  -O2 -fno-strict-aliasing -pipe -march=athlon64 -c Rmain.c -o Rmain.o
cc -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR
/usr/bin/ld: warning: libblas.so.1, needed by /usr/local/lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/local/lib/libR.so: undefined reference to `dasum_'
/usr/local/lib/libR.so: undefined reference to `dscal_'
/usr/local/lib/libR.so: undefined reference to `drot_'
/usr/local/lib/libR.so: undefined reference to `dswap_'
/usr/local/lib/libR.so: undefined reference to `dcopy_'
/usr/local/lib/libR.so: undefined reference to `ddot_'
/usr/local/lib/libR.so: undefined reference to `dgemm_'
/usr/local/lib/libR.so: undefined reference to `dtrsm_'
/usr/local/lib/libR.so: undefined reference to `dsyrk_'
/usr/local/lib/libR.so: undefined reference to `drotg_'
/usr/local/lib/libR.so: undefined reference to `daxpy_'
/usr/local/lib/libR.so: undefined reference to `dnrm2_'
/usr/local/lib/libR.so: undefined reference to `zgemm_'
*** Error code 1

Stop in /usr/ports/math/R/work/R-2.4.1/src/main.
*** Error code 1

Stop in /usr/ports/math/R/work/R-2.4.1/src.
*** Error code 1

Stop in /usr/ports/math/R/work/R-2.4.1.
*** Error code 1

Stop in /usr/ports/math/R.
** Command failed [exit code 1]: /usr/bin/script -qa /tmp/portupgrade.27136.0 env UPGRADE_TOOL=portupgrade UPGRADE_PORT=R-2.4.0 UPGRADE_PORT_VER=2.4.0 make
** Fix the problem and try again.
--->  Build of math/R ended at: Tue, 30 Jan 2007 09:29:50 +0000 (consumed 00:02:33)
--->  Upgrade of math/R ended at: Tue, 30 Jan 2007 09:29:50 +0000 (consumed 00:02:33)
--->  ** Upgrade tasks 1: 0 done, 0 ignored, 0 skipped and 1 failed
--->  Listing the results (+:done / -:ignored / *:skipped / !:failed)
        ! math/R (R-2.4.0)      (linker error)
--->  Packages processed: 0 done, 0 ignored, 0 skipped and 1 failed
--->  Session ended at: Tue, 30 Jan 2007 09:29:50 +0000 (consumed 00:02:43)

>How-To-Repeat:
Try to newly install or simply upgrade R-2.4.0 on FreeBSD 6.2 AMD64 (only a problem on AMD64, not i386).
>Fix:
Not known
>Release-Note:
>Audit-Trail:
>Unformatted: