Hey Jean-Pierre, On Thursday, January 14, 2016 at 1:17:48 AM UTC-8, Jean-Pierre Flori wrote: > > > > On Thursday, January 14, 2016 at 10:04:52 AM UTC+1, Jean-Pierre Flori > wrote: >> >> I see >> >> #if (defined(Win32) || defined(Win64))/* R instance as a global */Rstart >> Rp;#endif >> in src/rinterface/_rinterface.c. >> That sounds fishy for Cygwin. >> >> >> It looks like: http://trac.sagemath.org/ticket/16089 >> And that the cygwin patch was ill porte here: >> http://trac.sagemath.org/ticket/19638 >> >> Note sure why: >> * the linking to readline was removed, maybe R does it properly now >> without handholding. >> * this change in the patch is either not enough or too much: >> -#if defined(Win32) || defined(Win64) >> +#if defined(Win32) || defined(Win64) || defined(__CYGWIN__) >> Rp->R_Interactive = rtruefalse; >> #else >> R_Interactive = rtruefalse; >> >> Try to remove it first. >> If that's not sufficient the numerous try instead to perform the same >> change for all #if around R_Interactive stuff. >> > Looking at the code of the previous version we shipped, I'd say the > "remove the change" solution should be the right one. >
That did now work for me. Here was the change I made: Travis@apricot ~/sage/build/pkgs/rpy2/patches $ git diff diff --git a/build/pkgs/rpy2/patches/cygwin.patch b/build/pkgs/rpy2/patches/ cygwin.patch index 90641d4..959c70e 100644 --- a/build/pkgs/rpy2/patches/cygwin.patch +++ b/build/pkgs/rpy2/patches/cygwin.patch @@ -58,15 +58,6 @@ diff -ru rpy2-2.7.4.orig/rpy/rinterface/_rinterface.c rpy2-2.7.4/rpy/rinterface/ void win32CallBack() { /* called during i/o, eval, graphics in ProcessEvents */ -@@ -1489,7 +1489,7 @@ - } else { - rtruefalse = FALSE; - } --#if defined(Win32) || defined(Win64) -+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__) - Rp->R_Interactive = rtruefalse; - #else - R_Interactive = rtruefalse; @@ -3749,7 +3749,7 @@ } The log file is attached. Best, Travis -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Found local metadata for rpy2-2.7.5 Using cached file /home/Travis/sage/upstream/rpy2-2.7.5.tar.gz rpy2-2.7.5 ==================================================== Setting up build directory for rpy2-2.7.5 Finished set up **************************************************** Host system: CYGWIN_NT-6.3-WOW apricot 2.3.1(0.291/5/3) 2015-11-14 12:42 i686 Cygwin **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.9.3/lto-wrapper.exe Target: i686-pc-cygwin Configured with: /cygdrive/i/szsz/tmpp/gcc/gcc-4.9.3-1.i686/src/gcc-4.9.3/configure --srcdir=/cygdrive/i/szsz/tmpp/gcc/gcc-4.9.3-1.i686/src/gcc-4.9.3 --prefix=/usr --exec-prefix=/usr --localstatedir=/var --sysconfdir=/etc --docdir=/usr/share/doc/gcc --htmldir=/usr/share/doc/gcc/html -C --build=i686-pc-cygwin --host=i686-pc-cygwin --target=i686-pc-cygwin --without-libiconv-prefix --without-libintl-prefix --libexecdir=/usr/lib --enable-shared --enable-shared-libgcc --enable-static --enable-version-specific-runtime-libs --enable-bootstrap --enable-__cxa_atexit --with-dwarf2 --with-arch=i686 --with-tune=generic --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-threads=posix --enable-libatomic --enable-libgomp --disable-libitm --enable-libquadmath --enable-libquadmath-support --enable-libssp --enable-libada --enable-libjava --enable-libgcj-sublibs --disable-java-awt --disable-symvers --with-ecj-jar=/usr/share/java/ecj.jar --with-gnu-ld --with-gnu-as --with-cloog-include=/usr/include/cloog-isl --without-libiconv-prefix --without-libintl-prefix --with-system-zlib --enable-linker-build-id Thread model: posix gcc version 4.9.3 (GCC) **************************************************** patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" /home/Travis/sage/local/lib/R/bin/R CMD config --ldflags /home/Travis/sage/local/lib/R/bin/R CMD config --cppflags Compilation parameters for rpy2's C components: include_dirs = ['/home/Travis/sage/local/lib/R//include'] library_dirs = ['/home/Travis/sage/local/lib', '/home/Travis/sage/local/lib/R//lib'] libraries = ['R', 'bz2', 'z', 'rt', 'dl', 'm', 'iconv'] extra_link_args = ['-Wl,--large-address-aware', '-Wl,--stack=0xA00000', '-fopenmp', '-Wl,-rpath,/home/Travis/sage/local/lib'] running install running bdist_egg running egg_info writing requirements to rpy2.egg-info/requires.txt writing rpy2.egg-info/PKG-INFO writing top-level names to rpy2.egg-info/top_level.txt writing dependency_links to rpy2.egg-info/dependency_links.txt R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" reading manifest file 'rpy2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README' anywhere in distribution warning: no previously-included files matching '*patch*' found anywhere in distribution warning: no previously-included files matching '*diff*' found anywhere in distribution warning: no previously-included files matching '.hg' found anywhere in distribution warning: no files found matching 'MANIFEST' warning: no files found matching 'README' warning: no files found matching 'MPL_LICENSE' warning: no files found matching 'GPL_LICENSE' warning: no files found matching 'LGPL_LICENSE' no previously-included directories found matching 'dist' warning: no files found matching 'doc/source/rpy2_logo.png' writing manifest file 'rpy2.egg-info/SOURCES.txt' installing library code to build/bdist.cygwin-2.3.1-i686/egg running build_clib building 'r_utils' library creating build creating build/temp.cygwin-2.3.1-i686-2.7 creating build/temp.cygwin-2.3.1-i686-2.7/rpy creating build/temp.cygwin-2.3.1-i686-2.7/rpy/rinterface gcc -I/usr/include/ncurses -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -I./rpy/rinterface -I/home/Travis/sage/local/lib/R//include -c ./rpy/rinterface/r_utils.c -o build/temp.cygwin-2.3.1-i686-2.7/./rpy/rinterface/r_utils.o ./rpy/rinterface/r_utils.c: In function 'externallymanaged_vector': ./rpy/rinterface/r_utils.c:236:3: warning: implicit declaration of function 'malloc' [-Wimplicit-function-declaration] ExternallyManagedVector *extvector = malloc(sizeof(ExternallyManagedVector)); ^ ./rpy/rinterface/r_utils.c:236:40: warning: incompatible implicit declaration of built-in function 'malloc' ExternallyManagedVector *extvector = malloc(sizeof(ExternallyManagedVector)); ^ ar rc build/temp.cygwin-2.3.1-i686-2.7/libr_utils.a build/temp.cygwin-2.3.1-i686-2.7/./rpy/rinterface/r_utils.o running install_lib running build_py creating build/lib.cygwin-2.3.1-i686-2.7 creating build/lib.cygwin-2.3.1-i686-2.7/rpy2 copying ./rpy/rpy_classic.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2 copying ./rpy/tests.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2 copying ./rpy/tests_rpy_classic.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2 copying ./rpy/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2 creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike copying ./rpy/rlike/container.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike copying ./rpy/rlike/functional.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike copying ./rpy/rlike/indexing.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike copying ./rpy/rlike/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_container.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_functional.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_indexing.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rlike/tests creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface copying ./rpy/rinterface/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Device.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/tests creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/constants.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/conversion.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/environments.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/functions.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/help.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/language.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/methods.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/numpy2ri.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/packages.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/packages_utils.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/pandas2ri.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/robject.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/vectors.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects copying ./rpy/robjects/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testArray.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFormula.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFunction.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testHelp.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testLanguage.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testMethods.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPackages.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRObject.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRobjects.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testVector.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/tests creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/dplyr.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/ggplot2.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/grid.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/robjects/lib/tests creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive copying ./rpy/interactive/packages.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive copying ./rpy/interactive/process_revents.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive copying ./rpy/interactive/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive/tests copying ./rpy/interactive/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/interactive/tests creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython copying ./rpy/ipython/ggplot.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython copying ./rpy/ipython/html.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython copying ./rpy/ipython/rmagic.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython copying ./rpy/ipython/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython creating build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/__init__.py -> build/lib.cygwin-2.3.1-i686-2.7/rpy2/ipython/tests running build_ext building 'rpy2.rinterface._rinterface' extension gcc -I/usr/include/ncurses -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/home/Travis/sage/local/lib/R//include -I/home/Travis/sage/local/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o build/temp.cygwin-2.3.1-i686-2.7/./rpy/rinterface/_rinterface.o In file included from ./rpy/rinterface/_rinterface.c:122:0: ./rpy/rinterface/embeddedr.c: In function 'SexpObject_clear': ./rpy/rinterface/embeddedr.c:48:12: warning: unused variable 'res' [-Wunused-variable] SEXP res = rpy2_remove(Rf_mkString(name_buf), ^ In file included from ./rpy/rinterface/_rinterface.c:125:0: ./rpy/rinterface/sexp.c: In function 'Sexp_init': ./rpy/rinterface/sexp.c:738:13: warning: unused variable 'copy' [-Wunused-variable] PyObject *copy = Py_True; ^ In file included from ./rpy/rinterface/_rinterface.c:58:0: ./rpy/rinterface/_rinterface.c: At top level: ./rpy/rinterface/_rinterface.h:203:44: warning: 'PyRinterface_IsInitialized' declared 'static' but never defined [-Wunused-function] static PyRinterface_IsInitialized_RETURN PyRinterface_IsInitialized PyRinterface_IsInitialized_PROTO; ^ ./rpy/rinterface/_rinterface.h:204:38: warning: 'PyRinterface_FindFun' declared 'static' but never defined [-Wunused-function] static PyRinterface_FindFun_RETURN PyRinterface_FindFun PyRinterface_FindFun_PROTO; ^ ./rpy/rinterface/_rinterface.h:205:20: warning: 'embeddedR_isInitialized' defined but not used [-Wunused-variable] static PyObject *embeddedR_isInitialized; ^ In file included from ./rpy/rinterface/_rinterface.c:128:0: ./rpy/rinterface/sequence.c:2168:1: warning: 'ComplexVectorSexp_AsSexp' defined but not used [-Wunused-function] ComplexVectorSexp_AsSexp(PyObject *pyfloat) { ^ In file included from ./rpy/rinterface/_rinterface.c:58:0: ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ShowFiles': ./rpy/rinterface/_rinterface.h:72:5: warning: 'gstate' may be used uninitialized in this function [-Wmaybe-uninitialized] PyGILState_Release(gstate); \ ^ ./rpy/rinterface/_rinterface.c:837:20: note: 'gstate' was declared here PyGILState_STATE gstate; ^ ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_WriteConsoleEx': ./rpy/rinterface/_rinterface.c:383:10: warning: 'consolecallback' may be used uninitialized in this function [-Wmaybe-uninitialized] result = PyEval_CallObject(consolecallback, arglist); ^ In file included from ./rpy/rinterface/_rinterface.c:58:0: ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_CleanUp': ./rpy/rinterface/_rinterface.h:72:5: warning: 'gstate' may be used uninitialized in this function [-Wmaybe-uninitialized] PyGILState_Release(gstate); \ ^ ./rpy/rinterface/_rinterface.c:985:20: note: 'gstate' was declared here PyGILState_STATE gstate; ^ gcc -shared -Wl,--enable-auto-image-base -L/home/Travis/sage/local/lib -Wl,-rpath,/home/Travis/sage/local/lib -L/home/Travis/sage/local/lib -Wl,-rpath,/home/Travis/sage/local/lib build/temp.cygwin-2.3.1-i686-2.7/./rpy/rinterface/_rinterface.o -L/home/Travis/sage/local/lib -L/home/Travis/sage/local/lib/R//lib -L/home/Travis/sage/local/lib/python2.7/config -L/home/Travis/sage/local/lib -Lbuild/temp.cygwin-2.3.1-i686-2.7 -Wl,-R/home/Travis/sage/local/lib -Wl,-R/home/Travis/sage/local/lib/R//lib -lR -lbz2 -lz -lrt -ldl -lm -liconv -lpython2.7 -lr_utils -o build/lib.cygwin-2.3.1-i686-2.7/rpy2/rinterface/_rinterface.dll -Wl,--large-address-aware -Wl,--stack=0xA00000 -fopenmp -Wl,-rpath,/home/Travis/sage/local/lib build/temp.cygwin-2.3.1-i686-2.7/./rpy/rinterface/_rinterface.o: In function `EmbeddedR_init': /home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5/src/./rpy/rinterface/_rinterface.c:1399: undefined reference to `rl_completer_word_break_characters' /home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5/src/./rpy/rinterface/_rinterface.c:1400: undefined reference to `rl_completer_word_break_characters' /home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5/src/./rpy/rinterface/_rinterface.c:1402: undefined reference to `rl_basic_word_break_characters' /home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5/src/./rpy/rinterface/_rinterface.c:1403: undefined reference to `rl_basic_word_break_characters' collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 real 0m5.125s user 0m2.626s sys 0m1.804s ************************************************************************ Error installing package rpy2-2.7.5 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the relevant part of the log file /home/Travis/sage/logs/pkgs/rpy2-2.7.5.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/home/Travis/sage/local/var/tmp/sage/build/rpy2-2.7.5' && '/home/Travis/sage/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************