[MacPorts] #25327: gcc-mp-4.3: Internal error compiling R packages

[MacPorts]

#25327: gcc-mp-4.3: Internal error compiling R packages
--------------------------------+-------------------------------------------
 Reporter:  raramayo@…          |       Owner:  macports-tickets@…                   
     Type:  defect              |      Status:  new                                  
 Priority:  Normal              |   Milestone:                                       
Component:  ports               |     Version:  1.9.1                                
 Keywords:                      |        Port:  gcc43 R                              
--------------------------------+-------------------------------------------
Changes (by jmr@…):

 * cc: kjell.konis@…, mww@… (added)
  * keywords:  gcc, Bioconductor =>
  * port:  R => gcc43 R


Old description:

> When trying to upgrade my Bioconductor 'R' packages using MacPorts I run
> into the following:
>
> * installing *source* package ‘IRanges’ ...
> ** libs
> /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
> -I/opt/local/include    -fPIC  -O2 -m32 -c AEbufs.c -o AEbufs.o
> dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
>   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
>   Reason: image not found
> gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
> Please submit a full bug report.
> See <http://gcc.gnu.org/bugs.html> for instructions.
> make: *** [AEbufs.o] Error 1
> ERROR: compilation failed for package ‘IRanges’
> ...
> ...
> ...
>
> * installing *source* package ‘limma’ ...
> ** libs
> /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
> -I/opt/local/include    -fPIC  -O2 -m32 -c normexp.c -o normexp.o
> dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
>   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
>   Reason: image not found
> gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
> Please submit a full bug report.
> See <http://gcc.gnu.org/bugs.html> for instructions.
> make: *** [normexp.o] Error 1
> ERROR: compilation failed for package ‘limma’
> ...
> ...
> ...
>
> * installing *source* package ‘RSQLite’ ...
> checking for gcc... /opt/local/bin/gcc-mp-4.3 -std=gnu99
> checking for C compiler default output file name... rm: a.out.dSYM: is a
> directory
>
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
> ERROR: configuration failed for package ‘RSQLite’
> ...
> ...
> ...
>
> * installing *source* package ‘Biostrings’ ...
> ** libs
> /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
> -I/opt/local/include -I"/Users/raramayo/R/i386-apple-
> darwin9.8.0-library/2.11/IRanges/include"   -fPIC  -O2 -m32 -c
> BAB_class.c -o BAB_class.o
> dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
>   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
>   Reason: image not found
> gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
> Please submit a full bug report.
> See <http://gcc.gnu.org/bugs.html> for instructions.
> make: *** [BAB_class.o] Error 1
> ERROR: compilation failed for package ‘Biostrings’

New description:

 When trying to upgrade my Bioconductor 'R' packages using MacPorts I run
 into the following:
 {{{
 * installing *source* package ‘IRanges’ ...
 ** libs
 /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
 -I/opt/local/include    -fPIC  -O2 -m32 -c AEbufs.c -o AEbufs.o
 dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
   Reason: image not found
 gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
 Please submit a full bug report.
 See <http://gcc.gnu.org/bugs.html> for instructions.
 make: *** [AEbufs.o] Error 1
 ERROR: compilation failed for package ‘IRanges’
 ...
 ...
 ...

 * installing *source* package ‘limma’ ...
 ** libs
 /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
 -I/opt/local/include    -fPIC  -O2 -m32 -c normexp.c -o normexp.o
 dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
   Reason: image not found
 gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
 Please submit a full bug report.
 See <http://gcc.gnu.org/bugs.html> for instructions.
 make: *** [normexp.o] Error 1
 ERROR: compilation failed for package ‘limma’
 ...
 ...
 ...

 * installing *source* package ‘RSQLite’ ...
 checking for gcc... /opt/local/bin/gcc-mp-4.3 -std=gnu99
 checking for C compiler default output file name... rm: a.out.dSYM: is a
 directory

 configure: error: C compiler cannot create executables
 See `config.log' for more details.
 ERROR: configuration failed for package ‘RSQLite’
 ...
 ...
 ...

 * installing *source* package ‘Biostrings’ ...
 ** libs
 /opt/local/bin/gcc-mp-4.3 -std=gnu99 -I/opt/local/lib/R/include
 -I/opt/local/include -I"/Users/raramayo/R/i386-apple-
 darwin9.8.0-library/2.11/IRanges/include"   -fPIC  -O2 -m32 -c BAB_class.c
 -o BAB_class.o
 dyld: Library not loaded: /opt/local/lib/libmpfr.1.dylib
   Referenced from: /opt/local/libexec/gcc/i386-apple-darwin9/4.3.5/cc1
   Reason: image not found
 gcc-mp-4.3: Internal error: Trace/BPT trap (program cc1)
 Please submit a full bug report.
 See <http://gcc.gnu.org/bugs.html> for instructions.
 make: *** [BAB_class.o] Error 1
 ERROR: compilation failed for package ‘Biostrings’
 }}}

--

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Ticket URL: <http://trac.macports.org/ticket/25327#comment:1>
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