################################################################################################################################################################## Running command:###### rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.80.0.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_1.80.0.tar.gz'>>>>>>> * installing *source* package ‘affyio’ ...** this is package ‘affyio’ version ‘1.80.0’** using staged installationchecking for gcc... clang -arch x86_64checking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C compiler... yeschecking whether clang -arch x86_64 accepts -g... yeschecking for clang -arch x86_64 option to accept ISO C89... none neededchecking how to run the C preprocessor... clang -arch x86_64 -Echecking for grep that handles long lines and -e... /usr/bin/grepchecking for egrep... /usr/bin/grep -Echecking for ANSI C header files... rm: conftest.dSYM: is a directoryrm: conftest.dSYM: is a directoryyeschecking for sys/types.h... yeschecking for sys/stat.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for memory.h... yeschecking for strings.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for unistd.h... yeschecking for main in -lz... yeschecking zlib.h usability... yeschecking zlib.h presence... yeschecking for zlib.h... yeschecking if zlib version >= 1.1.3... yeschecking for pthread_create in -lpthread... yeschecking if we can use pthreads... yeschecking if PTHREAD_STACK_MIN is defined... yesconfigure: Enabling threading for affyioconfigure: creating ./config.statusconfig.status: creating src/Makevars** libsusing C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’using SDK: ‘MacOSX11.3.1.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.oclang -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.oclang -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.oread_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); ~~ ^~~ %luread_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); ~~ ^ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zuread_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); ~~ ^~~ %luread_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); ~~ ^~~~ %zu54 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.oread_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.oclang -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.oclang -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.oclang -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.oclang -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.oread_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); ~~ ^~~~~~ %dread_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; ^ = 02 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.oclang -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.oread_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 Rinstalling to /Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)