* installing *source* package ‘oce’ ... ** package ‘oce’ successfully unpacked and MD5 sums checked ** libs clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c adv_vector_time.c -o adv_vector_time.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c bin_average.c -o bin_average.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c binmap.c -o binmap.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c biosonics.c -o biosonics.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c bisect.c -o bisect.o bisect.c:58:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int npass = floor(5.0 + log2(0.0 + nx)); // for safety, add 5; should never get close ~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c bitwise.c -o bitwise.o bitwise.c:54:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32] pres[i] = pseq[i] + cumulative; ~ ~~~~~~~~^~~~~~~~~~~~ bitwise.c:142:56: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+20]) | ((unsigned short)pbuf[i+21] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitwise.c:171:51: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+20]) | ((unsigned short)pbuf[i+21] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitwise.c:221:41: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion] check_value = (((short)keyp[0]) << 8) | (short)keyp[1]; ~ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ bitwise.c:237:40: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion] checksum = (((short)bufp[n-1]) << 8) | (short)bufp[n-2]; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ bitwise.c:277:50: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] seq_this = (((unsigned short)bufp[i + 3]) << 8) | (unsigned short)bufp[i + 2]; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitwise.c:308:50: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] seq_this = (((unsigned short)bufp[i + 3]) << 8) | (unsigned short)bufp[i + 2]; ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitwise.c:385:32: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion] short lsequence2 = lsequence / 2; ~~~~~~~~~~ ~~~~~~~~~~^~~ bitwise.c:387:49: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion] short check_value = (((short)pkey[0]) << 8) | (short)pkey[1]; ~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ bitwise.c:403:61: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion] short check_sum = (((short)pbuf[i+lsequence-1]) << 8) | (short)pbuf[i+lsequence-2]; ~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c fillgap.c -o fillgap.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c geod.c -o geod.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c get_bit.c -o get_bit.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c gradient.c -o gradient.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c interp_barnes.c -o interp_barnes.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c latlon_trim.c -o latlon_trim.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c ldc_rdi.c -o ldc_rdi.o ldc_rdi.c:70:70: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+bytes_to_check+0]) | ((unsigned short)pbuf[i+bytes_to_check+1] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ldc_rdi.c:100:63: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+bytes_to_check]) | ((unsigned short)pbuf[i+bytes_to_check+1] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. gfortran-4.2 -mtune=native -fPIC -g -O2 -c magdec.f -o magdec.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c matrix_smooth.c -o matrix_smooth.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c misc.c -o misc.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c oce_approx.c -o oce_approx.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c oce_convolve.c -o oce_convolve.o oce_convolve.c:34:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion] int endflag = floor(0.5 + (*endp)); ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c oce_filter.c -o oce_filter.o gfortran-4.2 -mtune=native -fPIC -g -O2 -c ocecp.f -o ocecp.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c sfm_enu.c -o sfm_enu.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c sontek_adp.c -o sontek_adp.o sontek_adp.c:117:66: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+chunk_length]) | ((unsigned short)pbuf[i+chunk_length+1] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sontek_adp.c:148:61: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion] desired_check_sum = ((unsigned short)pbuf[i+chunk_length]) | ((unsigned short)pbuf[i+chunk_length+1] << 8); ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c stutter_time.c -o stutter_time.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c sw.c -o sw.o sw.c:317:53: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign] while (fabs(g = strho_f(*x = (x1 + x2) / 2.0, teos=teos)) > ftol || fabs (x1 - x2) > xresolution) { ~~~~^~~~~ 1 warning generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c teos.c -o teos.o teos.c:69:12: warning: initializing 'double (*)(double, double)' with an expression of type 'void *' converts between void pointer and function pointer [-Wpedantic] double (*f2)(double, double) = dlsym(teos_handle, *name); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ teos.c:104:12: warning: initializing 'double (*)(double, double, double)' with an expression of type 'void *' converts between void pointer and function pointer [-Wpedantic] double (*f3)(double, double, double) = dlsym(teos_handle, *name); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ teos.c:139:12: warning: initializing 'double (*)(double, double, double, double)' with an expression of type 'void *' converts between void pointer and function pointer [-Wpedantic] double (*f4)(double, double, double, double) = dlsym(teos_handle, *name); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c topo_interpolate.c -o topo_interpolate.o clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c trap.c -o trap.o trap.c:62:13: warning: variable 'resp' is uninitialized when used here [-Wuninitialized] resp[0] = 0.0; // prevent compiler warning ^~~~ trap.c:28:17: note: initialize the variable 'resp' to silence this warning double *resp; ^ = NULL 1 warning generated. clang -mtune=native -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oce.so adv_vector_time.o bin_average.o binmap.o biosonics.o bisect.o bitwise.o fillgap.o geod.o get_bit.o gradient.o interp_barnes.o latlon_trim.o ldc_rdi.o magdec.o matrix_smooth.o misc.o oce_approx.o oce_convolve.o oce_filter.o ocecp.o sfm_enu.o sontek_adp.o stutter_time.o sw.o teos.o topo_interpolate.o trap.o -L/usr/lib/gcc/i686-apple-darwin11/4.2.1/x86_64 -L/usr/lib/gcc/i686-apple-darwin11/4.2.1 -L/usr/lib -lgfortran -L/Users/ripley/R/R-clang/lib -lR -dylib_file libRblas.dylib:/Users/ripley/R/R-clang/lib/libRblas.dylib -Wl,-framework -Wl,CoreFoundation installing to /Users/ripley/R/packages/tests-clang/oce.Rcheck/oce/libs ** R ** data ** demo ** inst ** preparing package for lazy loading Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘oce’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ‘oce.Rnw’ ** testing if installed package can be loaded * DONE (oce)