Opened 13 years ago
Closed 13 years ago
#1943 closed defect (fixed)
[with spkg] Sage 2.10.1.rc0: rpy fails to build on OSX 10.4
Reported by: | mabshoff | Owned by: | mabshoff |
---|---|---|---|
Priority: | blocker | Milestone: | sage-2.10.1 |
Component: | packages: standard | Keywords: | |
Cc: | Merged in: | ||
Authors: | Reviewers: | ||
Report Upstream: | Work issues: | ||
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
Robert Bradshaw reported the following:
running build_ext building '_rpy2061' extension C compiler: gcc -g -Wall -I/Users/robert/sage/sage-2.10.1.rc0/local/ include -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/ creating build/temp.macosx-10.3-i386-2.5 creating build/temp.macosx-10.3-i386-2.5/src compile options: '-DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ - DRPY_SHNAME=_rpy2061 -DINIT_RPY=init_rpy2061 -UPRE_2_2 -I/Users/ robert/sage/sage-2.10.1.rc0/local/lib/R/include -Isrc -I/Users/robert/ sage/sage-2.10.1.rc0/local/lib/python2.5/site-packages/numpy/core/ include -I/Users/robert/sage/sage-2.10.1.rc0/local/include/python2.5 -c' gcc: src/io2061.c src/io2061.c: In function ‘RPy_ReadConsole’: src/io2061.c:131: warning: pointer targets in passing argument 1 of ‘snprintf’ differ in signedness src/io2061.c: At top level: /Users/robert/sage/sage-2.10.1.rc0/local/lib/python2.5/site-packages/ numpy/core/include/numpy/__multiarray_api.h:944: warning: ‘_import_array’ defined but not used gcc: src/R_eval2061.c /Users/robert/sage/sage-2.10.1.rc0/local/lib/python2.5/site-packages/ numpy/core/include/numpy/__multiarray_api.h:944: warning: ‘_import_array’ defined but not used gcc: src/rpymodule2061.c src/rpymodule2061.c:1488: warning: initialization from incompatible pointer type src/rpymodule2061.c:1491: warning: ‘intargfunc’ is deprecated src/rpymodule2061.c:1491: warning: initialization from incompatible pointer type src/rpymodule2061.c:1493: warning: initialization from incompatible pointer type gcc -bundle -undefined dynamic_lookup -L/Users/robert/sage/ sage-2.10.1.rc0/local/lib/ -I/Users/robert/sage/sage-2.10.1.rc0/local/ include -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/ build/ temp.macosx-10.3-i386-2.5/src/rpymodule2061.o build/temp.macosx-10.3- i386-2.5/src/R_eval2061.o build/temp.macosx-10.3-i386-2.5/src/ io2061.o -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/R/bin -L/ Users/robert/sage/sage-2.10.1.rc0/local/lib/R/lib -L/Users/robert/ sage/sage-2.10.1.rc0/local/lib/gcc-lib/i386-apple-darwin8.10.3/4.0.3/ -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/R/bin -L/Users/robert/ sage/sage-2.10.1.rc0/local/lib/R/lib -L/Users/robert/sage/ sage-2.10.1.rc0/local/lib/gcc-lib/i386-apple-darwin8.10.3/4.0.3/ -lR - llapack -lcblas -latlas -lf95 -o build/lib.macosx-10.3-i386-2.5/ _rpy2061.so /usr/bin/ld: warning can't open dynamic library: libRblas.dylib referenced from: /Users/robert/sage/sage-2.10.1.rc0/local/lib/R/lib/ libR.dylib (checking for undefined symbols may be affected) (No such file or directory, errno = 2) /usr/bin/ld: Undefined symbols: _dgemm_ referenced from libR expected to be defined in libRblas.dylib _dsyrk_ referenced from libR expected to be defined in libRblas.dylib _zgemm_ referenced from libR expected to be defined in libRblas.dylib _dcopy_ referenced from libR expected to be defined in libRblas.dylib _dtrsm_ referenced from libR expected to be defined in libRblas.dylib _daxpy_ referenced from libR expected to be defined in libRblas.dylib _dswap_ referenced from libR expected to be defined in libRblas.dylib _ddot_ referenced from libR expected to be defined in libRblas.dylib __g95_sign_r8 referenced from libR expected to be defined in libRblas.dylib _dasum_ referenced from libR expected to be defined in libRblas.dylib _dscal_ referenced from libR expected to be defined in libRblas.dylib _dnrm2_ referenced from libR expected to be defined in libRblas.dylib _drot_ referenced from libR expected to be defined in libRblas.dylib _drotg_ referenced from libR expected to be defined in libRblas.dylib collect2: ld returned 1 exit status /usr/bin/ld: warning can't open dynamic library: libRblas.dylib referenced from: /Users/robert/sage/sage-2.10.1.rc0/local/lib/R/lib/ libR.dylib (checking for undefined symbols may be affected) (No such file or directory, errno = 2) /usr/bin/ld: Undefined symbols: _dgemm_ referenced from libR expected to be defined in libRblas.dylib _dsyrk_ referenced from libR expected to be defined in libRblas.dylib _zgemm_ referenced from libR expected to be defined in libRblas.dylib _dcopy_ referenced from libR expected to be defined in libRblas.dylib _dtrsm_ referenced from libR expected to be defined in libRblas.dylib _daxpy_ referenced from libR expected to be defined in libRblas.dylib _dswap_ referenced from libR expected to be defined in libRblas.dylib _ddot_ referenced from libR expected to be defined in libRblas.dylib __g95_sign_r8 referenced from libR expected to be defined in libRblas.dylib _dasum_ referenced from libR expected to be defined in libRblas.dylib _dscal_ referenced from libR expected to be defined in libRblas.dylib _dnrm2_ referenced from libR expected to be defined in libRblas.dylib _drot_ referenced from libR expected to be defined in libRblas.dylib _drotg_ referenced from libR expected to be defined in libRblas.dylib collect2: ld returned 1 exit status error: Command "gcc -bundle -undefined dynamic_lookup -L/Users/robert/ sage/sage-2.10.1.rc0/local/lib/ -I/Users/robert/sage/sage-2.10.1.rc0/ local/include -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/ build/ temp.macosx-10.3-i386-2.5/src/rpymodule2061.o build/temp.macosx-10.3- i386-2.5/src/R_eval2061.o build/temp.macosx-10.3-i386-2.5/src/ io2061.o -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/R/bin -L/ Users/robert/sage/sage-2.10.1.rc0/local/lib/R/lib -L/Users/robert/ sage/sage-2.10.1.rc0/local/lib/gcc-lib/i386-apple-darwin8.10.3/4.0.3/ -L/Users/robert/sage/sage-2.10.1.rc0/local/lib/R/bin -L/Users/robert/ sage/sage-2.10.1.rc0/local/lib/R/lib -L/Users/robert/sage/ sage-2.10.1.rc0/local/lib/gcc-lib/i386-apple-darwin8.10.3/4.0.3/ -lR - llapack -lcblas -latlas -lf95 -o build/lib.macosx-10.3-i386-2.5/ _rpy2061.so" failed with exit status 1 Error building RPY -- Python interface to R. real 0m2.094s user 0m0.656s sys 0m0.650s sage: An error occurred while installing rpy-1.0.1.p0 Please email sage-devel http://groups.google.com/group/sage-devel explaining the problem and send the relevant part of of /Users/robert/sage/sage-2.10.1.rc0/install.log. Describe your computer, operating system, etc. If you want to try to fix the problem, yourself *don't* just cd to /Users/robert/sage/sage-2.10.1.rc0/spkg/build/rpy-1.0.1.p0 and type 'make'. Instead type "/Users/robert/sage/sage-2.10.1.rc0/sage -sh" in order to set all environment variables correctly, then cd to /Users/robert/sage/sage-2.10.1.rc0/spkg/build/rpy-1.0.1.p0 (When you are done debugging, you can type "exit" to leave the subshell.) Error installing rpy. real 4m44.687s user 2m17.993s sys 1m33.051s sage: An error occurred while installing r-2.6.1.p13 Please email sage-devel http://groups.google.com/group/sage-devel explaining the problem and send the relevant part of of /Users/robert/sage/sage-2.10.1.rc0/install.log. Describe your computer, operating system, etc. If you want to try to fix the problem, yourself *don't* just cd to /Users/robert/sage/sage-2.10.1.rc0/spkg/build/r-2.6.1.p13 and type 'make'.
Cheers,
Michael
Change History (3)
comment:1 Changed 13 years ago by
- Summary changed from Sage 2.10.1.rc0: rpy fails to build on OSX 10.4 to [with spkg] Sage 2.10.1.rc0: rpy fails to build on OSX 10.4
comment:2 Changed 13 years ago by
The rpy test now also passes on OSX 10.4
comment:3 Changed 13 years ago by
- Resolution set to fixed
- Status changed from new to closed
Merged in Sage 2.10.1.rc1
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A working r.spkg can be found at
http://sage.math.washington.edu/home/mabshoff/release-cycles-2.10.1/rc1/r-2.6.1.p14.spkg
It builds fine on linux, OSX 10.5 & 10.4. I have also tested it on linux and OSX 10.5, but am waiting for the OSX 10.4 build to finish.
Cheers,
Michael