#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’ }}} -- Comment: Please remember to preview and use WikiFormatting, and to cc the maintainer(s). -- Ticket URL: <http://trac.macports.org/ticket/25327#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS