Mailman 3 May 2013 - NumPy-Discussion

numpy.scipy.org page 404s
by Christopher Hanley 05 May '13

05 May '13

Dear Numpy Webmasters, Would it be possible to either redirect numpy.scipy.org to www.numpy.org or to the main numpy github landing page? Currently numpy.scipy.org hits a Github 404 page. As the numpy.scipy.org site still shows up in searches it would be useful to have that address resolve to something more helpful. Thank you for your time and help, Chris

6 14

"Lists" and "Join" function needed
by Bakhtiyor Zokhidov 05 May '13

05 May '13

Hi, I have the following code which represents intersected point of each cell in the given two points, A(x0,y0) and B(x1,y1). def intersected_points(x0, x1, y0, y1): # slope m = (y1 - y0 )/( x1 - x0) # Boundary of the selected points x_ceil = ceil( min (x0, x1 )) x_floor = floor( max(x0, x1)) y_ceil = ceil( min(y0, y1)) y_floor = floor( max(y0, y1)) # calculate all intersected x coordinate ax = [] for x in arange(x_ceil, x_floor + 1, 1): ax.append([ x, m * ( x - x0 ) + y0 ]) # calculate all intersected y coordinate for y in arange(y_ceil, y_floor + 1, 1): ax.append([ ( y - y0 ) * ( 1./m ) + x0, y ]) return ax Sample values: intersected_points(1.5,4.4,0.5,4.1) Output: [[2.0, 1.1206896551724137], [3.0, 2.3620689655172411], [4.0, 3.6034482758620685], [1.9027777777777779, 1.0], [2.7083333333333335, 2.0], [3.5138888888888893, 3.0], [4.3194444444444446, 4.0]] The output I got is unsorted values, so, for each cell coordinates, where line crosses: BUT, The result I want to get should be something in increased orders like: (x0,y0), (x1,y1), (x2,y2), (x3,y3) where x0, y0 - intial, x1,y1 - final point. Other values are intersected line coordinates! Any answers will be appreciated, -- Bakhtiyor Zokhidov

2 2

Error installing numpy 1.7.1
by Francesco Pacchiani 04 May '13

04 May '13

Hello, I want to install numpy 1.7.1 for use with python 3.2.1 and have been blocked by an error during the build process. My OS is Mandriva 2001. I'm installing numpy from source because python2.7 is already installed and seems to be the default, the rpm's don't install anything in python3.2/site-packages. The command used is "python3 setup.py build" and below I have posted the end of the outptut which contains the error message. I understand it is the compilation of _capi.c that posses problems, but have not been able to solve it. The fenv.h file is installed in different directories /usr/include /usr/local/src/numpy-1.7.1/numpy/core/include/numpy/fenv/fenv.h and /usr/local/src/numpy-1.7.1/build/py3k/numpy/core/include/numpy/fenv/fenv.h Using strace, one realizes that there is a call for "build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so" that generates a "No such file or directory". The end of the output of "strace python3 setup.py build" command is posted below as well. Indeed no such library exists, should it? Does anybody understand the problem or have a hint to give. Thanks. Francesco Output after executing: python3 setup.py build creating build/temp.linux-x86_64-3.2/numpy/lib creating build/temp.linux-x86_64-3.2/numpy/lib/src compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-3.2/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.2mu -Ibuild/src.linux-x86_64-3.2/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.2/numpy/core/src/umath -c' gcc: numpy/lib/src/_compiled_base.c gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-3.2/numpy/lib/src/_compiled_base.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.2 -lpython3.2mu -o build/lib.linux-x86_64-3.2/numpy/lib/_compiled_base.cpython-32mu.so building 'numpy.numarray._capi' extension compiling C sources C compiler: gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -g -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -fPIC creating build/temp.linux-x86_64-3.2/numpy/numarray compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-3.2/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.2mu -Ibuild/src.linux-x86_64-3.2/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.2/numpy/core/src/umath -c' gcc: numpy/numarray/_capi.c numpy/numarray/_capi.c: In function ‘deferred_libnumarray_init’: numpy/numarray/_capi.c:31:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_callCUFuncCore’: numpy/numarray/_capi.c:579:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_new_cfunc’: numpy/numarray/_capi.c:1018:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_OutputArray’: numpy/numarray/_capi.c:1104:5: warning: passing argument 2 of ‘(int (*)(struct PyArrayObject *, struct PyArrayObject *))*(PyArray_API + 2296u)’ from incompatible pointer type [enabled by default] numpy/numarray/_capi.c:1104:5: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ numpy/numarray/_capi.c: In function ‘NA_callStrideConvCFuncCore’: numpy/numarray/_capi.c:2644:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_IeeeMask32’: numpy/numarray/_capi.c:3073:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_IeeeMask64’: numpy/numarray/_capi.c:3117:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.2 -lpython3.2mu -o build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `NA_checkFPErrors': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3019: undefined reference to `fetestexcept' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3026: undefined reference to `feclearexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `int_overflow_error': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:263: undefined reference to `feraiseexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_atanh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:233: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_asinh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `log' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:190: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_pow': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:207: undefined reference to `pow' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log10': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:198: undefined reference to `log10' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_round': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `ceil' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `floor' collect2: ld returned 1 exit status build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `NA_checkFPErrors': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3019: undefined reference to `fetestexcept' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3026: undefined reference to `feclearexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `int_overflow_error': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:263: undefined reference to `feraiseexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_atanh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:233: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_asinh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `log' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:190: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_pow': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:207: undefined reference to `pow' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log10': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:198: undefined reference to `log10' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_round': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `ceil' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `floor' collect2: ld returned 1 exit status error: Command "gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.2 -lpython3.2mu -o build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so" failed with exit status 1 Output of "strace python3 setup.py build" stat("build/lib.linux-x86_64-3.2/numpy/core/umath_tests.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=54991, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/core/umath_tests.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=54991, ...}) = 0 stat("build/src.linux-x86_64-3.2/numpy/core/src/umath/umath_tests.c", {st_mode=S_IFREG|0644, st_size=14253, ...}) = 0 stat("build/src.linux-x86_64-3.2/numpy/core/src/umath/umath_tests.c", {st_mode=S_IFREG|0644, st_size=14253, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/core/multiarray_tests.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=56661, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/core/multiarray_tests.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=56661, ...}) = 0 stat("build/src.linux-x86_64-3.2/numpy/core/src/multiarray/multiarray_tests.c", {st_mode=S_IFREG|0644, st_size=14087, ...}) = 0 stat("build/src.linux-x86_64-3.2/numpy/core/src/multiarray/multiarray_tests.c", {st_mode=S_IFREG|0644, st_size=14087, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/lib/_compiled_base.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=100309, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/lib/_compiled_base.cpython-32mu.so", {st_mode=S_IFREG|0755, st_size=100309, ...}) = 0 stat("numpy/lib/src/_compiled_base.c", {st_mode=S_IFREG|0644, st_size=50102, ...}) = 0 stat("numpy/lib/src/_compiled_base.c", {st_mode=S_IFREG|0644, st_size=50102, ...}) = 0 stat("build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so", 0x7fff78c15920) = -1 ENOENT (No such file or directory) write(1, "\33[39mbuilding 'numpy.numarray._c"..., 51building 'numpy.numarray._capi' extension ) = 51 write(1, "\33[39mcompiling C sources\33[0m\n", 29compiling C sources ) = 29 write(1, "\33[39mC compiler: gcc -pthread -D"..., 408C compiler: gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -g -O2 -g -frecord-gcc-switches -Wstrict-aliasing=2 -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -fPIC ) = 408 write(1, "\n", 1 ) = 1 stat("build/temp.linux-x86_64-3.2/numpy/numarray", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0 write(1, "\33[39mcompile options: '-Inumpy/c"..., 415compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-3.2/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.2mu -Ibuild/src.linux-x86_64-3.2/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.2/numpy/core/src/umath -c' ) = 415 write(1, "\33[39mgcc: numpy/numarray/_capi.c"..., 37gcc: numpy/numarray/_capi.c ) = 37 getcwd("/usr/local/src/numpy-1.7.1/build/py3k", 1026) = 38 getcwd("/usr/local/src/numpy-1.7.1/build/py3k", 1026) = 38 open("/tmp/tmpicyzqn/npoyom", O_RDWR|O_CREAT|O_EXCL|O_NOFOLLOW, 0600) = 3 fcntl(3, F_GETFD) = 0 fcntl(3, F_SETFD, FD_CLOEXEC) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c13e48) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c13bf8) = -1 ENOTTY (Inappropriate ioctl for device) lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 close(3) = 0 open("/tmp/tmpicyzqn/w8jsoc", O_RDWR|O_CREAT|O_EXCL|O_NOFOLLOW, 0600) = 3 fcntl(3, F_GETFD) = 0 fcntl(3, F_SETFD, FD_CLOEXEC) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c13e48) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c13bf8) = -1 ENOTTY (Inappropriate ioctl for device) lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 close(3) = 0 rt_sigaction(SIGINT, {SIG_IGN, [], SA_RESTORER, 0x7f6f35d55250}, {0x7f6f363dfe70, [], SA_RESTORER, 0x7f6f35d55250}, 8) = 0 rt_sigaction(SIGQUIT, {SIG_IGN, [], SA_RESTORER, 0x7f6f35d55250}, {SIG_DFL, [], SA_RESTORER, 0x7f6f35d55250}, 8) = 0 rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0 clone(child_stack=0, flags=CLONE_PARENT_SETTID|SIGCHLD, parent_tidptr=0x7fff78c1475c) = 24562 wait4(24562, numpy/numarray/_capi.c: In function ‘deferred_libnumarray_init’: numpy/numarray/_capi.c:31:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_callCUFuncCore’: numpy/numarray/_capi.c:579:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_new_cfunc’: numpy/numarray/_capi.c:1018:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_OutputArray’: numpy/numarray/_capi.c:1104:5: warning: passing argument 2 of ‘(int (*)(struct PyArrayObject *, struct PyArrayObject *))*(PyArray_API + 2296u)’ from incompatible pointer type [enabled by default] numpy/numarray/_capi.c:1104:5: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ numpy/numarray/_capi.c: In function ‘NA_callStrideConvCFuncCore’: numpy/numarray/_capi.c:2644:5: warning: dereferencing type-punned pointer might break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_IeeeMask32’: numpy/numarray/_capi.c:3073:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] numpy/numarray/_capi.c: In function ‘NA_IeeeMask64’: numpy/numarray/_capi.c:3117:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 24562 rt_sigaction(SIGINT, {0x7f6f363dfe70, [], SA_RESTORER, 0x7f6f35d55250}, NULL, 8) = 0 rt_sigaction(SIGQUIT, {SIG_DFL, [], SA_RESTORER, 0x7f6f35d55250}, NULL, 8) = 0 rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0 --- {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=24562, si_status=0, si_utime=0, si_stime=0} (Child exited) --- open("/tmp/tmpicyzqn/w8jsoc", O_RDONLY) = 3 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c141c8) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 read(3, "0\n", 8192) = 2 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2 read(3, "", 8192) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2 read(3, "", 8192) = 0 close(3) = 0 unlink("/tmp/tmpicyzqn/w8jsoc") = 0 open("/tmp/tmpicyzqn/npoyom", O_RDONLY) = 3 fstat(3, {st_mode=S_IFREG|0600, st_size=1514, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c141c8) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=1514, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=1514, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 read(3, "numpy/numarray/_capi.c: In funct"..., 8192) = 1514 fstat(3, {st_mode=S_IFREG|0600, st_size=1514, ...}) = 0 lseek(3, 0, SEEK_CUR) = 1514 read(3, "", 8192) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=1514, ...}) = 0 lseek(3, 0, SEEK_CUR) = 1514 read(3, "", 8192) = 0 close(3) = 0 unlink("/tmp/tmpicyzqn/npoyom") = 0 stat("build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so", 0x7fff78c15290) = -1 ENOENT (No such file or directory) stat("build/lib.linux-x86_64-3.2/numpy/numarray", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0 write(1, "\33[39mgcc -pthread -shared -Wl,--"..., 299gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.2 -lpython3.2mu -o build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so ) = 299 getcwd("/usr/local/src/numpy-1.7.1/build/py3k", 1026) = 38 getcwd("/usr/local/src/numpy-1.7.1/build/py3k", 1026) = 38 open("/tmp/tmpicyzqn/pur_c5", O_RDWR|O_CREAT|O_EXCL|O_NOFOLLOW, 0600) = 3 fcntl(3, F_GETFD) = 0 fcntl(3, F_SETFD, FD_CLOEXEC) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c14468) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c14218) = -1 ENOTTY (Inappropriate ioctl for device) lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 close(3) = 0 open("/tmp/tmpicyzqn/vscch3", O_RDWR|O_CREAT|O_EXCL|O_NOFOLLOW, 0600) = 3 fcntl(3, F_GETFD) = 0 fcntl(3, F_SETFD, FD_CLOEXEC) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c14468) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c14218) = -1 ENOTTY (Inappropriate ioctl for device) lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 close(3) = 0 rt_sigaction(SIGINT, {SIG_IGN, [], SA_RESTORER, 0x7f6f35d55250}, {0x7f6f363dfe70, [], SA_RESTORER, 0x7f6f35d55250}, 8) = 0 rt_sigaction(SIGQUIT, {SIG_IGN, [], SA_RESTORER, 0x7f6f35d55250}, {SIG_DFL, [], SA_RESTORER, 0x7f6f35d55250}, 8) = 0 rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0 clone(child_stack=0, flags=CLONE_PARENT_SETTID|SIGCHLD, parent_tidptr=0x7fff78c14d7c) = 24570 wait4(24570, build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `NA_checkFPErrors': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3019: undefined reference to `fetestexcept' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3026: undefined reference to `feclearexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `int_overflow_error': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:263: undefined reference to `feraiseexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_atanh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:233: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_asinh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `log' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:190: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_pow': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:207: undefined reference to `pow' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log10': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:198: undefined reference to `log10' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_round': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `ceil' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `floor' collect2: ld returned 1 exit status [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 24570 rt_sigaction(SIGINT, {0x7f6f363dfe70, [], SA_RESTORER, 0x7f6f35d55250}, NULL, 8) = 0 rt_sigaction(SIGQUIT, {SIG_DFL, [], SA_RESTORER, 0x7f6f35d55250}, NULL, 8) = 0 rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0 --- {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=24570, si_status=0, si_utime=0, si_stime=0} (Child exited) --- open("/tmp/tmpicyzqn/vscch3", O_RDONLY) = 3 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c147e8) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 read(3, "1\n", 8192) = 2 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2 read(3, "", 8192) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2 read(3, "", 8192) = 0 close(3) = 0 unlink("/tmp/tmpicyzqn/vscch3") = 0 open("/tmp/tmpicyzqn/pur_c5", O_RDONLY) = 3 fstat(3, {st_mode=S_IFREG|0600, st_size=2091, ...}) = 0 ioctl(3, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fff78c147e8) = -1 ENOTTY (Inappropriate ioctl for device) fstat(3, {st_mode=S_IFREG|0600, st_size=2091, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 lseek(3, 0, SEEK_CUR) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2091, ...}) = 0 lseek(3, 0, SEEK_CUR) = 0 read(3, "build/temp.linux-x86_64-3.2/nump"..., 8192) = 2091 fstat(3, {st_mode=S_IFREG|0600, st_size=2091, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2091 read(3, "", 8192) = 0 fstat(3, {st_mode=S_IFREG|0600, st_size=2091, ...}) = 0 lseek(3, 0, SEEK_CUR) = 2091 read(3, "", 8192) = 0 close(3) = 0 unlink("/tmp/tmpicyzqn/pur_c5") = 0 write(1, "build/temp.linux-x86_64-3.2/nump"..., 2090build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `NA_checkFPErrors': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3019: undefined reference to `fetestexcept' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:3026: undefined reference to `feclearexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `int_overflow_error': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:263: undefined reference to `feraiseexcept' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_atanh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:233: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_asinh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `log' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:228: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `sqrt' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:190: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_acosh': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:213: undefined reference to `log' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_pow': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:207: undefined reference to `pow' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_log10': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:198: undefined reference to `log10' build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o: In function `num_round': /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `ceil' /usr/local/src/numpy-1.7.1/build/py3k/numpy/numarray/_capi.c:239: undefined reference to `floor' collect2: ld returned 1 exit status) = 2090 write(1, "\n", 1 ) = 1 chdir("/usr/local/src/numpy-1.7.1") = 0 write(2, "error: Command \"gcc -pthread -sh"..., 333error: Command "gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags build/temp.linux-x86_64-3.2/numpy/numarray/_capi.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.2 -lpython3.2mu -o build/lib.linux-x86_64-3.2/numpy/numarray/_capi.cpython-32mu.so" failed with exit status 1 ) = 333 lstat("/tmp/tmpicyzqn", {st_mode=S_IFDIR|0700, st_size=4096, ...}) = 0 open("/tmp/tmpicyzqn", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3 getdents(3, /* 2 entries */, 32768) = 48 getdents(3, /* 0 entries */, 32768) = 0 close(3) = 0 rmdir("/tmp/tmpicyzqn") = 0 rt_sigaction(SIGINT, {SIG_DFL, [], SA_RESTORER, 0x7f6f360bc960}, {0x7f6f363dfe70, [], SA_RESTORER, 0x7f6f35d55250}, 8) = 0 exit_group(1)

1 0

ANN: New WinPython with Python 2.7.4 and 3.3.1 (32/64bit)
by Pierre Raybaut 03 May '13

03 May '13

Hi all, I am pleased to announce that four new versions of WinPython have been released yesterday with Python 2.7.4 and 3.3.1, 32 and 64 bits. Many packages have been added or upgraded (see the automatically-generated changelogs). Special thanks to Christoph Gohlke for building most of the binary packages bundled in WinPython. WinPython is a free open-source portable distribution of Python for Windows, designed for scientists. It is a full-featured (see http://code.google.com/p/winpython/wiki/PackageIndex) Python-based scientific environment: * Designed for scientists (thanks to the integrated libraries NumPy, SciPy, Matplotlib, guiqwt, etc.: * Regular *scientific users*: interactive data processing and visualization using Python with Spyder * *Advanced scientific users and software developers*: Python applications development with Spyder, version control with Mercurial and other development tools (like gettext) * *Portable*: preconfigured, it should run out of the box on any machine under Windows (without any installation requirements) and the folder containing WinPython can be moved to any location (local, network or removable drive) * *Flexible*: one can install (or should I write "use" as it's portable) as many WinPython versions as necessary (like isolated and self-consistent environments), even if those versions are running different versions of Python (2.7, 3.3) or different architectures (32bit or 64bit) on the same machine * *Customizable*: using the integrated package manager (wppm, as WinPython Package Manager), it's possible to install, uninstall or upgrade Python packages (see http://code.google.com/p/winpython/wiki/WPPM for more details on supported package formats). *WinPython is not an attempt to replace Python(x,y)*, this is just something different (see http://code.google.com/p/winpython/wiki/Roadmap): more flexible, easier to maintain, movable and less invasive for the OS, but certainly less user-friendly, with less packages/contents and without any integration to Windows explorer [*]. [*] Actually there is an optional integration into Windows explorer, providing the same features as the official Python installer regarding file associations and context menu entry (this option may be activated through the WinPython Control Panel), and adding shortcuts to Windows Start menu. Enjoy!

1 0

GSoC : Performance parity between numpy arrays and Python scalars
by Arink Verma 03 May '13

03 May '13

Hi all! I have written my application[1] for *Performance parity between numpy arrays and Python scalars[2]. *It would be a great help if you view it. Does it look achievable and deliverable according to the project. [1] http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/arinkver… [2] http://projects.scipy.org/scipy/wiki/SummerofCodeIdeas -- Arink Computer Science and Engineering Indian Institute of Technology Ropar www.arinkverma.in

8 20

numPy not imported into Python
by Mark Micklich 02 May '13

02 May '13

Hello -- After installing numPy, I'm getting the following error message when attempting to import numarray: ImportError: No module named numarray I do have numPy installed. I'm running under Lubuntu 12.10 and the Spyder 2.1.10 IDE. I'm fairly new to developing Python on Linux. I assume there is some path issue, but I'm not clear where to start. If numPy is installed, how to I point Spyder to the numPy modules so I can get numarray to work? Thanks, Mark

3 3

nanmean(), nanstd() and other "missing" functions for 1.8
by Benjamin Root 02 May '13

02 May '13

Currently, I am in the process of migrating some co-workers from Matlab and IDL, and the number one complaint I get is that numpy has nansum() but no nanmean() and nanstd(). While we do have an alternative in the form of masked arrays, most of these people are busy enough trying to port their existing code over to python that this sort of stumbling block becomes difficult to explain away. Given how relatively simple these functions are, I can not think of any reason not to include these functions in v1.8. Of course, the documentation for these functions should certainly include mention of masked arrays. There is one other non-trivial function that have been discussed before: np.minmax(). My thinking is that it would return a 2xN array (where N is whatever size of the result that would be returned if just np.min() was used). This would allow one to do "min, max = np.minmax(X)". Are there any other functions that others feel are "missing" from numpy and would like to see for v1.8? Let's discuss them here. Cheers! Ben Root

16 46

GSoC proposal -- Numpy SciPy
by Blake Griffith 01 May '13

01 May '13

Hello, I'm writing a GSoC proposal, mostly concerning SciPy, but it involves a few changes to NumPy. The proposal is titled: Improvements to the sparse package of Scipy: support for bool dtype and better interaction with NumPy and can be found on my GitHub: https://github.com/cowlicks/GSoC-proposal/blob/master/proposal.markdown#num… Basically, I want to change the ufunc class to be aware of SciPy's sparse matrices. So that when a ufunc is passed a sparse matrix as an argument, it will dispatch to a function in the sparse matrix package, which will then decide what to do. I just wanted to ping NumPy to make sure this is reasonable, and I'm not totally off track. Suggestions, feedback and criticism welcome. Thanks!

5 7

Proposal of new function: iteraxis()
by andrew giessel 01 May '13

01 May '13

Hello all- A while back I emailed the list about function for the numpy namespace, iteraxis(), which allows you to generalize the default iteration behavior of numpy arrays over any axis. I've implemented this function more cleanly and the pull request is here: https://github.com/numpy/numpy/pull/3262, and includes passing tests and documentation. This is very simple code, which uses np.rollaxis() to bring the desired dimension to the front, and then allows you to loop over slices in this re-structured view of the array. While little more than an alias, I feel this is a very useful function because looping over iterators is a core pattern in python, and makes working with slices of any multidimensional array very pythonic. Adding this function makes this more visible for users, new and old, and I hope members of this list will agree it is worth adding to the namespace. Generalizing this to iterate over multiple axes is something that might be worthwhile, but the specifics of how to implement the axis ordering would take some thought. I'm happy to discuss and tackle this if people are really interested. Hoping for some nice feedback, ag -- Andrew Giessel, PhD Department of Neurobiology, Harvard Medical School 220 Longwood Ave Boston, MA 02115 ph: 617.432.7971 email: andrew_giessel(a)hms.harvard.edu

11 21

clip with None argument changes dtype
by Jonathan Slavin 01 May '13

01 May '13

Hi all, I'm wondering if you think the following behavior in numpy.clip is a bug (it certainly confused me for a while): >>> x = np.arange(5.) >>> xx = x.clip(None,3.) >>> xx array([0.0, 1.0, 2.0, 3.0, 3.0], dtype=object) Since xx now has the dtype of object, doing things like >>> np.exp(xx) AttributeError Traceback (most recent call last) <ipython-input-6-30aa315cc2b1> in <module>() ----> 1 np.exp(xx) Which, if you don't know about the change in the dtype is a very confusing error message. It seems to me that either clip should give an error message when None is given for the a_min argument or, better, should not change the dtype of the input array as it does. This comes up because I want to only clip the maximum. Of course you can clip the minimum by simply omitting the second argument. The asymmetry of this is not good, I think. I suppose that using the maximum function is better in this situation (as I recently found out), though the docs make it seem that one needs to supply two arrays -- even though you don't. Jon -- ______________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ______________________________________________________________

1 0