############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.76.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyio.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyio.buildbin-libdir affyio_1.76.0.tar.gz' >>>>>>> * installing *source* package ‘affyio’ ... ** using staged installation checking for gcc... clang -arch x86_64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -arch x86_64 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c fread_functions.c -o fread_functions.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_abatch.c -o read_abatch.o read_abatch.c:656:207: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^~~ %lu read_abatch.c:656:212: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^ %zu read_abatch.c:665:177: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:665:182: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:764:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^~~ %lu read_abatch.c:764:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^ %zu read_abatch.c:774:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:774:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:785:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:785:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:795:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:795:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:805:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:805:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:870:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^~~ %lu read_abatch.c:870:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); ~~ ^ %zu read_abatch.c:879:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:879:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:890:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:890:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:901:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:901:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:913:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:913:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:924:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:924:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1567:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1567:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1578:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1578:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1589:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1589:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1665:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1665:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1701:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1701:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1769:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1769:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1780:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1780:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1791:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1791:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1801:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1801:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu read_abatch.c:1811:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~ %lu read_abatch.c:1811:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); ~~ ^~~~ %zu 54 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c:849:42: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat] error("Unable to open the file %s",filename); ~~ ^~~~~~~~ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_cdffile2.c -o read_cdffile2.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_celfile_generic.c -o read_celfile_generic.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_clf.c -o read_clf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_generic.c -o read_generic.o read_generic.c:1293:42: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] Rprintf("Its a float value is %f\n",temp32); ~~ ^~~~~~ %d read_generic.c:1293:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized] Rprintf("Its a float value is %f\n",temp32); ^~~~~~ read_generic.c:1283:13: note: initialize the variable 'temp32' to silence this warning int temp32; ^ = 0 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_pgf.c -o read_pgf.o read_pgf.c:363:12: warning: unused function 'token_ends_with' [-Wunused-function] static int token_ends_with(char *token, char *ends_in){ ^ 1 warning generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/affyio.buildbin-libdir/00LOCK-affyio/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyio) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR affyio.buildbin-libdir/affyio/libs/affyio.so >>>>>>> >>>>>>> Paths before fix: affyio.buildbin-libdir/affyio/libs/affyio.so: affyio.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so" >>>>>>> Paths after fix: affyio.buildbin-libdir/affyio/libs/affyio.so: affyio.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)