Hi, i am trying to do some analysis using the DEseq2 packages from bioconductor. However, it requires the update of nloptr packages to 1.2.2 and i keep countering the following extremely long error message:
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++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -std=gnu++11 accepts -g... (cached) yes
checking for pkg-config... no
configure: Now testing for NLopt header file.
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 nlopt.h usability... no
checking nlopt.h presence... no
checking for nlopt.h... no
configure: Need to configure and build NLopt
configure: Starting to install library to /private/var/folders/pp/2j6byfkj6vxg6k1p39xk4bcm0000gn/T/RtmpLqDqoN/R.INSTALL4b88331170e0/nloptr/src/nlopt_src
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets (MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... clang
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 accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking for clang option to accept ISO C99... none needed
checking for clang option to accept ISO Standard C... (cached) none needed
checking whether ln -s works... yes
checking whether make sets (MAKE)... (cached) yes
checking build system type... x86_64-apple-darwin19.3.0
checking host system type... x86_64-apple-darwin19.3.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... rm: conftest.dSYM: is a directory
BSD nm
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin19.3.0 file names to x86_64-apple-darwin19.3.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin19.3.0 file names to toolchain format... func_convert_file_noop
checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... dlltool
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... rm: conftest.dSYM: is a directory
no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... rm: conftest.dSYM: is a directory
ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
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checking for lipo... lipo
checking for otool... otool
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checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... clang -E
checking for ANSI C header files... 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 dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin19.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking dependency style of clang++ -std=gnu++11... gcc3
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking for ld used by clang++ -std=gnu++11... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking whether the clang++ -std=gnu++11 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for clang++ -std=gnu++11 option to produce PIC... -fno-common -DPIC
checking if clang++ -std=gnu++11 PIC flag -fno-common -DPIC works... yes
checking if clang++ -std=gnu++11 static flag -static works... no
checking if clang++ -std=gnu++11 supports -c -o file.o... yes
checking if clang++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the clang++ -std=gnu++11 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin19.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking for unistd.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for stdint.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C thread-local keyword... __thread
checking size of unsigned int... 4
checking size of unsigned long... 8
checking for uint32_t... yes
checking for sin in -lm... yes
checking for BSDgettimeofday... no
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checking for qsort_r... yes
checking for getpid... yes
checking for gettid syscall... yes
checking for isnan... yes
checking for isinf... yes
checking for copysign... yes
checking for mkoctfile... no
checking for mex... no
checking for working HUGE_VAL... ok
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating nlopt.pc
config.status: creating api/Makefile
config.status: creating util/Makefile
config.status: creating octave/Makefile
config.status: creating direct/Makefile
config.status: creating cdirect/Makefile
config.status: creating stogo/Makefile
config.status: creating praxis/Makefile
config.status: creating luksan/Makefile
config.status: creating crs/Makefile
config.status: creating mlsl/Makefile
config.status: creating mma/Makefile
config.status: creating cobyla/Makefile
config.status: creating newuoa/Makefile
config.status: creating neldermead/Makefile
config.status: creating auglag/Makefile
config.status: creating bobyqa/Makefile
config.status: creating isres/Makefile
config.status: creating slsqp/Makefile
config.status: creating esch/Makefile
config.status: creating test/Makefile
config.status: creating swig/Makefile
config.status: creating swig/nlopt.scm
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make all-recursive
Making all in util
...........(omit a lot because of word limits, sorry....)
1 warning generated.
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT cobyla.lo -MD -MP -MF .deps/cobyla.Tpo -c cobyla.c -o cobyla.o >/dev/null 2>&1
mv -f .deps/cobyla.Tpo .deps/cobyla.Plo
/bin/sh ../libtool --tag=CC --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o libcobyla.la cobyla.lo -lm
libtool: link: ar cru .libs/libcobyla.a .libs/cobyla.o
libtool: link: ranlib .libs/libcobyla.a
libtool: link: ( cd ".libs" && rm -f "libcobyla.la" && ln -s "../libcobyla.la" "libcobyla.la" )
Making all in newuoa
/bin/sh ../libtool --tag=CC --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT newuoa.lo -MD -MP -MF .deps/newuoa.Tpo -c -o newuoa.lo newuoa.c
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT newuoa.lo -MD -MP -MF .deps/newuoa.Tpo -c newuoa.c -fno-common -DPIC -o .libs/newuoa.o
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
newuoa.c:184:9: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
ret = nlopt_minimize_constrained(NLOPT_LD_MMA, *n, quad_model, &qmd,
^
../api/nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
../api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
newuoa.c:1241:10: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
return nlopt_minimize_constrained(NLOPT_LD_MMA, *n, lag, &ld,
^
../api/nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
../api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
2 warnings generated.
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT newuoa.lo -MD -MP -MF .deps/newuoa.Tpo -c newuoa.c -o newuoa.o >/dev/null 2>&1
mv -f .deps/newuoa.Tpo .deps/newuoa.Plo
/bin/sh ../libtool --tag=CC --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o libnewuoa.la newuoa.lo -lm
libtool: link: ar cru .libs/libnewuoa.a .libs/newuoa.o
libtool: link: ranlib .libs/libnewuoa.a
libtool: link: ( cd ".libs" && rm -f "libnewuoa.la" && ln -s "../libnewuoa.la" "libnewuoa.la" )
Making all in neldermead
/bin/sh ../libtool --tag=CC --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT nldrmd.lo -MD -MP -MF .deps/nldrmd.Tpo -c -o nldrmd.lo nldrmd.c
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT nldrmd.lo -MD -MP -MF .deps/nldrmd.Tpo -c nldrmd.c -fno-common -DPIC -o .libs/nldrmd.o
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT nldrmd.lo -MD -MP -MF .deps/nldrmd.Tpo -c nldrmd.c -o nldrmd.o >/dev/null 2>&1
mv -f .deps/nldrmd.Tpo .deps/nldrmd.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT sbplx.lo -MD -MP -MF .deps/sbplx.Tpo -c -o sbplx.lo sbplx.c
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT sbplx.lo -MD -MP -MF .deps/sbplx.Tpo -c sbplx.c -fno-common -DPIC -o .libs/sbplx.o
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT auglag.lo -MD -MP -MF .deps/auglag.Tpo -c auglag.c -o auglag.o >/dev/null 2>&1
mv -f .deps/auglag.Tpo .deps/auglag.Plo
/bin/sh ../libtool --tag=CC --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o libauglag.la auglag.lo -lm
libtool: link: ar cru .libs/libauglag.a .libs/auglag.o
libtool: link: ranlib .libs/libauglag.a
libtool: link: ( cd ".libs" && rm -f "libauglag.la" && ln -s "../libauglag.la" "libauglag.la" )
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../util -I../api -Wall -g -O2 -MT esch.lo -MD -MP -MF .deps/esch.Tpo -c esch.c -o esch.o >/dev/null 2>&1
mv -f .deps/esch.Tpo .deps/esch.Plo
/bin/sh ../libtool --tag=CC --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o libesch.la esch.lo -lm
libtool: link: ar cru .libs/libesch.a .libs/esch.o
libtool: link: ranlib .libs/libesch.a
libtool: link: ( cd ".libs" && rm -f "libesch.la" && ln -s "../libesch.la" "libesch.la" )
Making all in api
make all-am
/bin/sh ../libtool --tag=CC --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../cdirect -I../direct -I../stogo -I../praxis -I../lbfgs -I../luksan -I../crs -I../mlsl -I../mma -I../cobyla -I../newuoa -I../neldermead -I../auglag -I../bobyqa -I../isres -I../slsqp -I../esch -I../util -Wall -g -O2 -MT general.lo -MD -MP -MF .deps/general.Tpo -c -o general.lo general.c
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../cdirect -I../direct -I../stogo -I../praxis -I../lbfgs -I../luksan -I../crs -I../mlsl -I../mma -I../cobyla -I../newuoa -I../neldermead -I../auglag -I../bobyqa -I../isres -I../slsqp -I../esch -I../util -Wall -g -O2 -MT general.lo -MD -MP -MF .deps/general.Tpo -c general.c -fno-common -DPIC -o .libs/general.o
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
general.c:134:38: warning: 'syscall' is deprecated: first deprecated in macOS 10.12 - syscall(2) is unsupported; please switch to a supported interface. For SYS_kdebug_trace use kdebug_signpost(). [-Wdeprecated-declarations]
nlopt_srand(nlopt_time_seed() + my_gettid() * 314159);
^
general.c:116:23: note: expanded from macro 'my_gettid'
define my_gettid() syscall(SYS_gettid)
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:742:6: note: 'syscall' has been explicitly marked deprecated here
int syscall(int, ...);
^
1 warning generated.
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../cdirect -I../direct -I../stogo -I../praxis -I../lbfgs -I../luksan -I../crs -I../mlsl -I../mma -I../cobyla -I../newuoa -I../neldermead -I../auglag -I../bobyqa -I../isres -I../slsqp -I../esch -I../util -Wall -g -O2 -MT general.lo -MD -MP -MF .deps/general.Tpo -c general.c -o general.o >/dev/null 2>&1
mv -f .deps/general.Tpo .deps/general.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../cdirect -I../direct -I../stogo -I../praxis -I../lbfgs -I../luksan -I../crs -I../mlsl -I../mma -I../cobyla -I../newuoa -I../neldermead -I../auglag -I../bobyqa -I../isres -I../slsqp -I../esch -I../util -Wall -g -O2 -MT options.lo -MD -MP -MF .deps/options.Tpo -c -o options.lo options.c
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../cdirect -I../direct -I../stogo -I../praxis -I../lbfgs -I../luksan -I../crs -I../mlsl -I../mma -I../cobyla -I../newuoa -I../neldermead -I../auglag -I../bobyqa -I../isres -I../slsqp -I../esch -I../util -Wall -g -O2 -MT options.lo -MD -MP -MF .deps/options.Tpo -c options.c -fno-common -DPIC -o .libs/options.o
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from f77api.c:103:
./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:103:
./f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_get_local_search_algorithm(&deriv, &nonderiv, maxeval);
^
./nlopt.h:365:25: note: 'nlopt_get_local_search_algorithm' has been explicitly marked deprecated here
int *maxeval) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:103:
./f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_set_local_search_algorithm(deriv, nonderiv, *maxeval);
^
./nlopt.h:368:24: note: 'nlopt_set_local_search_algorithm' has been explicitly marked deprecated here
int maxeval) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
^
In file included from f77api.c:103:
./f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
nlopt_set_stochastic_population(*pop);
^
./nlopt.h:371:61: note: 'nlopt_set_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(void) nlopt_set_stochastic_population(int pop) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:114:
./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:114:
./f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_get_local_search_algorithm(&deriv, &nonderiv, maxeval);
^
./nlopt.h:365:25: note: 'nlopt_get_local_search_algorithm' has been explicitly marked deprecated here
int *maxeval) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:114:
./f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_set_local_search_algorithm(deriv, nonderiv, *maxeval);
^
./nlopt.h:368:24: note: 'nlopt_set_local_search_algorithm' has been explicitly marked deprecated here
int maxeval) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
In file included from f77api.c:114:
./f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
*pop = nlopt_get_stochastic_population();
^
"/private/var/folders/pp/2j6byfkj6vxg6k1p39xk4bcm0000gn/T/RtmpLqDqoN/R.INSTALL4b88331170e0/nloptr/src/nlopt_src/api/.libs/libapi.a")
libtool: link: (cd .libs/libnlopt_cxx.lax/libutil.a && ar x "/private/var/folders/pp/2j6byfkj6vxg6k1p39xk4bcm0000gn/T/RtmpLqDqoN/R.INSTALL4b88331170e0/nloptr/src/nlopt_src/util/.libs/libutil.a")
libtool: link: ar cru .libs/libnlopt_cxx.a .libs/libnlopt_cxx.lax/libdirect.a/DIRect.o .libs/libnlopt_cxx.lax/libdirect.a/DIRserial.o .libs/libnlopt_cxx.lax/libdirect.a/DIRsubrout.o .libs/libnlopt_cxx.lax/libdirect.a/direct_wrap.o .libs/libnlopt_cxx.lax/libcdirect.a/cdirect.o .libs/libnlopt_cxx.lax/libcdirect.a/hybrid.o .libs/libnlopt_cxx.lax/libstogo.a/global.o .libs/libnlopt_cxx.lax/libstogo.a/linalg.o .libs/libnlopt_cxx.lax/libstogo.a/local.o .libs/libnlopt_cxx.lax/libstogo.a/stogo.o .libs/libnlopt_cxx.lax/libstogo.a/tools.o .libs/libnlopt_cxx.lax/libpraxis.a/praxis.o .libs/libnlopt_cxx.lax/libluksan.a/mssubs.o .libs/libnlopt_cxx.lax/libluksan.a/plip.o .libs/libnlopt_cxx.lax/libluksan.a/plis.o .libs/libnlopt_cxx.lax/libluksan.a/pnet.o .libs/libnlopt_cxx.lax/libluksan.a/pssubs.o .libs/libnlopt_cxx.lax/libcrs.a/crs.o .libs/libnlopt_cxx.lax/libmlsl.a/mlsl.o .libs/libnlopt_cxx.lax/libmma.a/ccsa_quadratic.o .libs/libnlopt_cxx.lax/libmma.a/mma.o .libs/libnlopt_cxx.lax/libcobyla.a/cobyla.o .libs/libnlopt_cxx.lax/libnewuoa.a/newuoa.o .libs/libnlopt_cxx.lax/libneldermead.a/nldrmd.o .libs/libnlopt_cxx.lax/libneldermead.a/sbplx.o .libs/libnlopt_cxx.lax/libauglag.a/auglag.o .libs/libnlopt_cxx.lax/libbobyqa.a/bobyqa.o .libs/libnlopt_cxx.lax/libisres.a/isres.o .libs/libnlopt_cxx.lax/libslsqp.a/slsqp.o .libs/libnlopt_cxx.lax/libesch.a/esch.o .libs/libnlopt_cxx.lax/libapi.a/deprecated.o .libs/libnlopt_cxx.lax/libapi.a/f77api.o .libs/libnlopt_cxx.lax/libapi.a/general.o .libs/libnlopt_cxx.lax/libapi.a/optimize.o .libs/libnlopt_cxx.lax/libapi.a/options.o .libs/libnlopt_cxx.lax/libutil.a/mt19937ar.o .libs/libnlopt_cxx.lax/libutil.a/qsort_r.o .libs/libnlopt_cxx.lax/libutil.a/redblack.o .libs/libnlopt_cxx.lax/libutil.a/rescale.o .libs/libnlopt_cxx.lax/libutil.a/sobolseq.o .libs/libnlopt_cxx.lax/libutil.a/stop.o .libs/libnlopt_cxx.lax/libutil.a/timer.o
libtool: link: ranlib .libs/libnlopt_cxx.a
libtool: link: rm -fr .libs/libnlopt_cxx.lax
libtool: link: ( cd ".libs" && rm -f "libnlopt_cxx.la" && ln -s "../libnlopt_cxx.la" "libnlopt_cxx.la" )
Making all in octave
echo "#define NLOPT_OPTIMIZE_USAGE \" > nlopt_optimize_usage.h
sed 's/"/\"/g' ./nlopt_optimize.m | sed 's,^% ,",;s,^%,",;s,$,\n" \,' >> nlopt_optimize_usage.h
echo "" >> nlopt_optimize_usage.h
make all-am
clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../api -I../util -Wall -g -O2 -MT dummy.o -MD -MP -MF .deps/dummy.Tpo -c -o dummy.o dummy.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
mv -f .deps/dummy.Tpo .deps/dummy.Po
/bin/sh ../libtool --tag=CC --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o dummy dummy.o -lm
libtool: link: clang++ -std=gnu++11 -Wall -g -O2 -o dummy dummy.o -lm
Making all in test
clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../api -I../util -Wall -g -O2 -MT testfuncs.o -MD -MP -MF .deps/testfuncs.Tpo -c -o testfuncs.o testfuncs.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
mv -f .deps/testfuncs.Tpo .deps/testfuncs.Po
clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -I../api -I../util -Wall -g -O2 -MT testopt.o -MD -MP -MF .deps/testopt.Tpo -c -o testopt.o testopt.cpp
testopt.cpp:218:11: warning: 'nlopt_minimize' is deprecated [-Wdeprecated-declarations]
ret = nlopt_minimize(algorithm,
^
../api/nlopt.h:337:35: note: 'nlopt_minimize' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
../api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
define NLOPT_DEPRECATED attribute((deprecated))
^
1 warning generated.
mv -f .deps/testopt.Tpo .deps/testopt.Po
/bin/sh ../libtool --tag=CXX --mode=link clang++ -std=gnu++11 -Wall -g -O2 -o testopt testfuncs.o testopt.o ../libnlopt_cxx.la -lm
libtool: link: clang++ -std=gnu++11 -Wall -g -O2 -o .libs/testopt testfuncs.o testopt.o -Wl,-bind_at_load ../.libs/libnlopt_cxx.dylib -lm
Making install in util
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in direct
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in cdirect
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in stogo
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in praxis
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in luksan
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in crs
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in mlsl
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in mma
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in cobyla
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in newuoa
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in neldermead
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in auglag
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in bobyqa
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in isres
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in slsqp
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in esch
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'.
Making install in api
make install-am
make[3]: Nothing to be done for `install-exec-am'.
.././install-sh -c -d '/private/var/folders/pp/2j6byfkj6vxg6k1p39xk4bcm0000gn/T/RtmpLqDqoN/R.INSTALL4b88331170e0/nloptr/src/nlopt_src/include'
/bin/sh: .././install-sh: Permission denied
make[3]: *** [install-includeHEADERS] Error 1
make[2]: *** [install-am] Error 2
make[1]: *** [install] Error 2
make: *** [install-recursive] Error 1
ERROR: configuration failed for package ‘nloptr’
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nloptr’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nloptr’
The downloaded source packages are in
‘/private/var/folders/pp/2j6byfkj6vxg6k1p39xk4bcm0000gn/T/RtmpOHE4y3/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘nloptr’ had non-zero exit status
Im very sorry for the long error message and i hope u guys can help! Thank you so much!!