Hello, I'm trying to build Sage 8.4.beta1 (following the develop branch from git) on Arch Linux, and it fails when trying to build the rpy2-2.8.2.p0 package. I'm attaching the corresponding log file.
Please, let me know if any further information can be helpful to solve the issue. Thanks, Nico. -- 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 [email protected]. To post to this group, send email to [email protected]. 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 rpy2-2.8.2.p0 Attempting to download package rpy2-2.8.2.tar.gz from mirrors https://mirror.koddos.net/sagemath/spkg/upstream/rpy2/rpy2-2.8.2.tar.gz [......................................................................] rpy2-2.8.2.p0 ==================================================== Setting up build directory for rpy2-2.8.2.p0 Finished extraction Applying patches from ../patches... Applying ../patches/cygwin.patch patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c Hunk #1 succeeded at 1156 (offset -6 lines). Hunk #2 succeeded at 3750 (offset 1 line). Hunk #3 succeeded at 3760 (offset 1 line). Hunk #4 succeeded at 3770 (offset 1 line). Hunk #5 succeeded at 3780 (offset 1 line). patching file setup.py Hunk #1 succeeded at 200 (offset 40 lines). **************************************************** Host system: Linux pc-sirolli 4.17.2-1-ARCH #1 SMP PREEMPT Sat Jun 16 11:08:59 UTC 2018 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.1.1/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp Thread model: posix gcc version 8.1.1 20180531 (GCC) **************************************************** Installing rpy2-2.8.2.p0 Warning: This package has a badly-behaved setup.py which outputs more than the package name for 'setup.py --name'; using the last line as the package name: rpy2 Installing package rpy2 using pip2 Ignoring indexes: https://pypi.python.org/simple Processing /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src Running setup.py (path:/tmp/pip-mXHN6p-build/setup.py) egg_info for package from file:///home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src Running command python setup.py egg_info R version 3.4.4 (2018-03-15) -- "Someone to Lean On" /home/nico/appz/sage/local/lib/R/bin/R CMD config --ldflags /home/nico/appz/sage/local/lib/R/bin/R CMD config --cppflags Compilation parameters for rpy2's C components: include_dirs = ['/home/nico/appz/sage/local/lib/R//include'] library_dirs = ['/home/nico/appz/sage/local/lib', '/home/nico/appz/sage/local/lib/R//lib'] libraries = ['readline', 'R', 'pcre', 'lzma', 'bz2', 'z', 'tirpc', 'rt', 'dl', 'm', 'icuuc', 'icui18n'] extra_link_args = ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-rpath,/home/nico/appz/sage/local/lib'] running egg_info creating pip-egg-info/rpy2.egg-info writing requirements to pip-egg-info/rpy2.egg-info/requires.txt writing pip-egg-info/rpy2.egg-info/PKG-INFO writing top-level names to pip-egg-info/rpy2.egg-info/top_level.txt writing dependency_links to pip-egg-info/rpy2.egg-info/dependency_links.txt writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt' R version 3.4.4 (2018-03-15) -- "Someone to Lean On" reading manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' 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 'pip-egg-info/rpy2.egg-info/SOURCES.txt' Source in /tmp/pip-mXHN6p-build has version 2.8.2, which satisfies requirement rpy2==2.8.2 from file:///home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src Installing collected packages: rpy2 Running setup.py install for rpy2: started Running command /home/nico/appz/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-mXHN6p-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-jlSPdN-record/install-record.txt --single-version-externally-managed --compile R version 3.4.4 (2018-03-15) -- "Someone to Lean On" /home/nico/appz/sage/local/lib/R/bin/R CMD config --ldflags /home/nico/appz/sage/local/lib/R/bin/R CMD config --cppflags Compilation parameters for rpy2's C components: include_dirs = ['/home/nico/appz/sage/local/lib/R//include'] library_dirs = ['/home/nico/appz/sage/local/lib', '/home/nico/appz/sage/local/lib/R//lib'] libraries = ['readline', 'R', 'pcre', 'lzma', 'bz2', 'z', 'tirpc', 'rt', 'dl', 'm', 'icuuc', 'icui18n'] extra_link_args = ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-rpath,/home/nico/appz/sage/local/lib'] running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2 copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2 creating build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests creating build/lib.linux-x86_64-2.7/rpy2/rinterface copying ./rpy/rinterface/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests creating build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/language.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/robject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/packages_utils.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/environments.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/conversion.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/vectors.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/methods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/constants.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/functions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/packages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects creating build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/tidyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/grid.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/grdevices.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_grdevices.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests creating build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/process_revents.py -> build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/packages.py -> build/lib.linux-x86_64-2.7/rpy2/interactive creating build/lib.linux-x86_64-2.7/rpy2/interactive/tests copying ./rpy/interactive/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/interactive/tests creating build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/ipython copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython creating build/lib.linux-x86_64-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests running build_clib building 'r_utils' library creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/rpy creating build/temp.linux-x86_64-2.7/rpy/rinterface gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./rpy/rinterface -I/home/nico/appz/sage/local/lib/R//include -c ./rpy/rinterface/r_utils.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o ./rpy/rinterface/r_utils.c: In function 'externallymanaged_vector': ./rpy/rinterface/r_utils.c:230:40: warning: implicit declaration of function 'malloc' [-Wimplicit-function-declaration] ExternallyManagedVector *extvector = malloc(sizeof(ExternallyManagedVector)); ^~~~~~ ./rpy/rinterface/r_utils.c:230:40: warning: incompatible implicit declaration of built-in function 'malloc' ./rpy/rinterface/r_utils.c:230:40: note: include '<stdlib.h>' or provide a declaration of 'malloc' ./rpy/rinterface/r_utils.c:26:1: +#include <stdlib.h> ./rpy/rinterface/r_utils.c:230:40: ExternallyManagedVector *extvector = malloc(sizeof(ExternallyManagedVector)); ^~~~~~ ar rc build/temp.linux-x86_64-2.7/libr_utils.a build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o running build_ext R version 3.4.4 (2018-03-15) -- "Someone to Lean On" building 'rpy2.rinterface._rinterface' extension gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/home/nico/appz/sage/local/lib/R//include -I/home/nico/appz/sage/local/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o In file included from /home/nico/appz/sage/local/include/python2.7/Python.h:8, from ./rpy/rinterface/_rinterface.c:49: /home/nico/appz/sage/local/include/python2.7/pyconfig.h:1223: warning: "_POSIX_C_SOURCE" redefined #define _POSIX_C_SOURCE 200112L In file included from /usr/include/signal.h:25, from ./rpy/rinterface/_rinterface.c:45: /usr/include/features.h:265: note: this is the location of the previous definition # define _POSIX_C_SOURCE 200809L In file included from ./rpy/rinterface/_rinterface.c:98: ./rpy/rinterface/embeddedr.h:6:27: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] extern const unsigned int const RPY_R_INITIALIZED; ^~~~~ ./rpy/rinterface/embeddedr.h:7:27: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] extern const unsigned int const RPY_R_BUSY; ^~~~~ In file included from ./rpy/rinterface/_rinterface.c:116: ./rpy/rinterface/embeddedr.c:5:20: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] const unsigned int const RPY_R_INITIALIZED = 0x01; ^~~~~ ./rpy/rinterface/embeddedr.c:6:20: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] const unsigned int const RPY_R_BUSY = 0x02; ^~~~~ In file included from ./rpy/rinterface/_rinterface.c:52: ./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:831:20: note: 'gstate' was declared here PyGILState_STATE gstate; ^~~~~~ In file included from /home/nico/appz/sage/local/include/python2.7/Python.h:131, from ./rpy/rinterface/_rinterface.c:49: ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_WriteConsoleEx': /home/nico/appz/sage/local/include/python2.7/ceval.h:15:5: warning: 'consolecallback' may be used uninitialized in this function [-Wmaybe-uninitialized] PyEval_CallObjectWithKeywords(func, arg, (PyObject *)NULL) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./rpy/rinterface/_rinterface.c:339:9: note: 'consolecallback' was declared here void *consolecallback; ^~~~~~~~~~~~~~~ ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ChooseFile': ./rpy/rinterface/_rinterface.c:790:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy((char *)buf, path_str, (l>len-1)?len-1:l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./rpy/rinterface/_rinterface.c:789:9: note: length computed here int l=strlen(path_str); ^~~~~~~~~~~~~~~~ ./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ReadConsole': ./rpy/rinterface/_rinterface.c:583:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy((char *)buf, input_str, (l>len-1)?len-1:l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./rpy/rinterface/_rinterface.c:582:9: note: length computed here int l=strlen(input_str); ^~~~~~~~~~~~~~~~~ In file included from ./rpy/rinterface/_rinterface.c:52: ./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:979:20: note: 'gstate' was declared here PyGILState_STATE gstate; ^~~~~~ gcc -pthread -shared -L/home/nico/appz/sage/local/lib -Wl,-rpath,/home/nico/appz/sage/local/lib -L/home/nico/appz/sage/local/lib -Wl,-rpath,/home/nico/appz/sage/local/lib build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o -L/home/nico/appz/sage/local/lib -L/home/nico/appz/sage/local/lib/R//lib -L/home/nico/appz/sage/local/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R/home/nico/appz/sage/local/lib -Wl,-R/home/nico/appz/sage/local/lib/R//lib -lreadline -lR -lpcre -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n -lpython2.7 -lr_utils -o build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so -Wl,--export-dynamic -fopenmp -Wl,-rpath,/home/nico/appz/sage/local/lib building 'rpy2.rinterface._rpy_device' extension gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I/home/nico/appz/sage/local/lib/R//include -Irpy/rinterface -I/home/nico/appz/sage/local/include/python2.7 -c ./rpy/rinterface/_rpy_device.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/_rpy_device.o gcc -pthread -shared -L/home/nico/appz/sage/local/lib -Wl,-rpath,/home/nico/appz/sage/local/lib -L/home/nico/appz/sage/local/lib -Wl,-rpath,/home/nico/appz/sage/local/lib build/temp.linux-x86_64-2.7/./rpy/rinterface/_rpy_device.o -L/home/nico/appz/sage/local/lib -L/home/nico/appz/sage/local/lib/R//lib -L/home/nico/appz/sage/local/lib -Lbuild/temp.linux-x86_64-2.7 -Wl,-R/home/nico/appz/sage/local/lib -Wl,-R/home/nico/appz/sage/local/lib/R//lib -lreadline -lR -lpcre -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n -lpython2.7 -lr_utils -o build/lib.linux-x86_64-2.7/rpy2/rinterface/_rpy_device.so -Wl,--export-dynamic -fopenmp -Wl,-rpath,/home/nico/appz/sage/local/lib running install_lib creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2 creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/tests copying build/lib.linux-x86_64-2.7/rpy2/ipython/tests/test_rmagic.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/tests copying build/lib.linux-x86_64-2.7/rpy2/ipython/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/tests copying build/lib.linux-x86_64-2.7/rpy2/ipython/rmagic.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython copying build/lib.linux-x86_64-2.7/rpy2/ipython/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython copying build/lib.linux-x86_64-2.7/rpy2/ipython/html.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython copying build/lib.linux-x86_64-2.7/rpy2/ipython/ggplot.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/tests copying build/lib.linux-x86_64-2.7/rpy2/interactive/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/tests copying build/lib.linux-x86_64-2.7/rpy2/interactive/packages.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive copying build/lib.linux-x86_64-2.7/rpy2/interactive/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive copying build/lib.linux-x86_64-2.7/rpy2/interactive/process_revents.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests/test_dplyr.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests/test_grdevices.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests/test_ggplot2.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/grdevices.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/grid.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tidyr.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/ggplot2.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib copying build/lib.linux-x86_64-2.7/rpy2/robjects/lib/dplyr.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testPandasConversions.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testHelp.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testLanguage.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testArray.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testPackages.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testNumpyConversions.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testDataFrame.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testEnvironment.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testFormula.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testRObject.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testFunction.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testRobjects.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testVector.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/tests/testMethods.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests copying build/lib.linux-x86_64-2.7/rpy2/robjects/packages.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/functions.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/constants.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/methods.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/vectors.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/help.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/numpy2ri.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/pandas2ri.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/conversion.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/environments.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/packages_utils.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/robject.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects copying build/lib.linux-x86_64-2.7/rpy2/robjects/language.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface copying build/lib.linux-x86_64-2.7/rpy2/rinterface/_rpy_device.so -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface copying build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpExtPtr.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpSymbol.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpClosure.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpVector.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_Device.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpVectorNumeric.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_Sexp.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_SexpEnvironment.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/tests/test_EmbeddedR.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests copying build/lib.linux-x86_64-2.7/rpy2/rinterface/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike creating /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests copying build/lib.linux-x86_64-2.7/rpy2/rlike/tests/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests copying build/lib.linux-x86_64-2.7/rpy2/rlike/tests/test_functional.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests copying build/lib.linux-x86_64-2.7/rpy2/rlike/tests/test_container.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests copying build/lib.linux-x86_64-2.7/rpy2/rlike/tests/test_indexing.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests copying build/lib.linux-x86_64-2.7/rpy2/rlike/indexing.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike copying build/lib.linux-x86_64-2.7/rpy2/rlike/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike copying build/lib.linux-x86_64-2.7/rpy2/rlike/functional.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike copying build/lib.linux-x86_64-2.7/rpy2/rlike/container.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike copying build/lib.linux-x86_64-2.7/rpy2/__init__.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2 copying build/lib.linux-x86_64-2.7/rpy2/rpy_classic.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2 copying build/lib.linux-x86_64-2.7/rpy2/tests.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2 copying build/lib.linux-x86_64-2.7/rpy2/tests_rpy_classic.py -> /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2 byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/tests/test_rmagic.py to test_rmagic.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/rmagic.py to rmagic.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/html.py to html.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/ipython/ggplot.py to ggplot.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/packages.py to packages.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/interactive/process_revents.py to process_revents.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests/test_dplyr.py to test_dplyr.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests/test_grdevices.py to test_grdevices.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tests/test_ggplot2.py to test_ggplot2.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/grdevices.py to grdevices.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/grid.py to grid.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/tidyr.py to tidyr.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/ggplot2.py to ggplot2.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/lib/dplyr.py to dplyr.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testPandasConversions.py to testPandasConversions.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testHelp.py to testHelp.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testLanguage.py to testLanguage.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testArray.py to testArray.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testPackages.py to testPackages.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testNumpyConversions.py to testNumpyConversions.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testDataFrame.py to testDataFrame.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testEnvironment.py to testEnvironment.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testFormula.py to testFormula.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testRObject.py to testRObject.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testFunction.py to testFunction.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testRobjects.py to testRobjects.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testVector.py to testVector.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/tests/testMethods.py to testMethods.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/packages.py to packages.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/functions.py to functions.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/constants.py to constants.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/methods.py to methods.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/vectors.py to vectors.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/help.py to help.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/numpy2ri.py to numpy2ri.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/pandas2ri.py to pandas2ri.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/conversion.py to conversion.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/environments.py to environments.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/packages_utils.py to packages_utils.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/robject.py to robject.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/robjects/language.py to language.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpExtPtr.py to test_SexpExtPtr.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpSymbol.py to test_SexpSymbol.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpClosure.py to test_SexpClosure.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpVector.py to test_SexpVector.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_Device.py to test_Device.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpVectorNumeric.py to test_SexpVectorNumeric.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_Sexp.py to test_Sexp.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_SexpEnvironment.py to test_SexpEnvironment.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/tests/test_EmbeddedR.py to test_EmbeddedR.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests/test_functional.py to test_functional.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests/test_container.py to test_container.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/tests/test_indexing.py to test_indexing.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/indexing.py to indexing.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/functional.py to functional.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rlike/container.py to container.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/__init__.py to __init__.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/rpy_classic.py to rpy_classic.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/tests.py to tests.pyc byte-compiling /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2/tests_rpy_classic.py to tests_rpy_classic.pyc running install_egg_info 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 reading manifest file 'rpy2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' 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' Copying rpy2.egg-info to /home/nico/appz/sage/local/lib/python2.7/site-packages/rpy2-2.8.2-py2.7.egg-info running install_scripts writing list of installed files to '/tmp/pip-jlSPdN-record/install-record.txt' Running setup.py install for rpy2: finished with status 'done' Removing source in /tmp/pip-mXHN6p-build Successfully installed rpy2-2.8.2 Cleaning up... real 1m52.700s user 0m7.616s sys 0m0.774s No record that 'rpy2' was ever installed; skipping uninstall Copying package files from temporary location /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/inst to /home/nico/appz/sage/local Successfully installed rpy2-2.8.2.p0 Deleting temporary build directory /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0 Finished installing rpy2-2.8.2.p0.spkg Found local metadata for rpy2-2.8.2.p0 Using cached file /home/nico/appz/sage/upstream/rpy2-2.8.2.tar.gz rpy2-2.8.2.p0 ==================================================== Setting up build directory for rpy2-2.8.2.p0 Finished extraction Applying patches from ../patches... Applying ../patches/cygwin.patch patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c Hunk #1 succeeded at 1156 (offset -6 lines). Hunk #2 succeeded at 3750 (offset 1 line). Hunk #3 succeeded at 3760 (offset 1 line). Hunk #4 succeeded at 3770 (offset 1 line). Hunk #5 succeeded at 3780 (offset 1 line). patching file setup.py Hunk #1 succeeded at 200 (offset 40 lines). **************************************************** Host system: Linux pc-sirolli 4.17.14-arch1-1-ARCH #1 SMP PREEMPT Thu Aug 9 11:56:50 UTC 2018 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto Thread model: posix gcc version 8.2.0 (GCC) **************************************************** Warning: No files to uninstall for 'rpy2' Uninstalling existing 'rpy2' Installing rpy2-2.8.2.p0 /home/nico/appz/sage/local/lib/R//bin/exec/R: error while loading shared libraries: libicuuc.so.61: cannot open shared object file: No such file or directory Traceback (most recent call last): File "setup.py", line 331, in <module> ri_ext = getRinterface_ext() File "setup.py", line 234, in getRinterface_ext if rexec.version[0] == 'development' or \ File "setup.py", line 160, in version universal_newlines = True) File "/home/nico/appz/sage/local/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '('/home/nico/appz/sage/local/lib/R/bin/R', '--version')' returned non-zero exit status 127 Error: could not determine package name ******************************************************************************** Error installing rpy2-2.8.2.p0 ******************************************************************************** real 0m0.525s user 0m0.240s sys 0m0.052s ************************************************************************ Error installing package rpy2-2.8.2.p0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /home/nico/appz/sage/logs/pkgs/rpy2-2.8.2.p0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0 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/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0' && '/home/nico/appz/sage/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************ Found local metadata for rpy2-2.8.2.p0 Using cached file /home/nico/appz/sage/upstream/rpy2-2.8.2.tar.gz rpy2-2.8.2.p0 ==================================================== Setting up build directory for rpy2-2.8.2.p0 Finished extraction Applying patches from ../patches... Applying ../patches/cygwin.patch patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c Hunk #1 succeeded at 1156 (offset -6 lines). Hunk #2 succeeded at 3750 (offset 1 line). Hunk #3 succeeded at 3760 (offset 1 line). Hunk #4 succeeded at 3770 (offset 1 line). Hunk #5 succeeded at 3780 (offset 1 line). patching file setup.py Hunk #1 succeeded at 200 (offset 40 lines). **************************************************** Host system: Linux pc-sirolli 4.17.14-arch1-1-ARCH #1 SMP PREEMPT Thu Aug 9 11:56:50 UTC 2018 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto Thread model: posix gcc version 8.2.0 (GCC) **************************************************** No record that 'rpy2' was ever installed; skipping uninstall Installing rpy2-2.8.2.p0 /home/nico/appz/sage/local/lib/R//bin/exec/R: error while loading shared libraries: libicuuc.so.61: cannot open shared object file: No such file or directory Traceback (most recent call last): File "setup.py", line 331, in <module> ri_ext = getRinterface_ext() File "setup.py", line 234, in getRinterface_ext if rexec.version[0] == 'development' or \ File "setup.py", line 160, in version universal_newlines = True) File "/home/nico/appz/sage/local/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '('/home/nico/appz/sage/local/lib/R/bin/R', '--version')' returned non-zero exit status 127 Error: could not determine package name ******************************************************************************** Error installing rpy2-2.8.2.p0 ******************************************************************************** real 0m3.778s user 0m0.374s sys 0m0.108s ************************************************************************ Error installing package rpy2-2.8.2.p0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /home/nico/appz/sage/logs/pkgs/rpy2-2.8.2.p0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0 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/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0' && '/home/nico/appz/sage/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************ Found local metadata for rpy2-2.8.2.p0 Using cached file /home/nico/appz/sage/upstream/rpy2-2.8.2.tar.gz rpy2-2.8.2.p0 ==================================================== Setting up build directory for rpy2-2.8.2.p0 Finished extraction Applying patches from ../patches... Applying ../patches/cygwin.patch patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c Hunk #1 succeeded at 1156 (offset -6 lines). Hunk #2 succeeded at 3750 (offset 1 line). Hunk #3 succeeded at 3760 (offset 1 line). Hunk #4 succeeded at 3770 (offset 1 line). Hunk #5 succeeded at 3780 (offset 1 line). patching file setup.py Hunk #1 succeeded at 200 (offset 40 lines). **************************************************** Host system: Linux pc-sirolli 4.17.14-arch1-1-ARCH #1 SMP PREEMPT Thu Aug 9 11:56:50 UTC 2018 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto Thread model: posix gcc version 8.2.0 (GCC) **************************************************** No record that 'rpy2' was ever installed; skipping uninstall Installing rpy2-2.8.2.p0 /home/nico/appz/sage/local/lib/R//bin/exec/R: error while loading shared libraries: libicuuc.so.61: cannot open shared object file: No such file or directory Traceback (most recent call last): File "setup.py", line 331, in <module> ri_ext = getRinterface_ext() File "setup.py", line 234, in getRinterface_ext if rexec.version[0] == 'development' or \ File "setup.py", line 160, in version universal_newlines = True) File "/home/nico/appz/sage/local/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '('/home/nico/appz/sage/local/lib/R/bin/R', '--version')' returned non-zero exit status 127 Error: could not determine package name ******************************************************************************** Error installing rpy2-2.8.2.p0 ******************************************************************************** real 0m4.187s user 0m0.284s sys 0m0.125s ************************************************************************ Error installing package rpy2-2.8.2.p0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /home/nico/appz/sage/logs/pkgs/rpy2-2.8.2.p0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /home/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0 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/nico/appz/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0' && '/home/nico/appz/sage/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
