OceanGenomics / mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates
BSD 3-Clause "New" or "Revised" License
31 stars 7 forks source link

Compiling error on MacOS #21

Closed jianshu93 closed 2 years ago

jianshu93 commented 2 years ago

Hi team,

The following error on MacOS:

The following warnings were emitted during compilation:

warning: curl/lib/connect.c: In function 'singleipconnect': warning: curl/lib/connect.c:1279:10: warning: implicit declaration of function 'builtin_available'; did you mean '__builtin_scalbl'? [-Wimplicit-function-declaration] warning: 1279 | if(builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) { warning: | ^~~~~~~ warning: | __builtin_scalbl warning: curl/lib/connect.c:1279:30: error: 'macOS' undeclared (first use in this function) warning: 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) { warning: | ^~~~~ warning: curl/lib/connect.c:1279:30: note: each undeclared identifier is reported only once for each function it appears in warning: curl/lib/connect.c:1279:35: error: expected ')' before numeric constant warning: 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, *)) { warning: | ~ ^~ warning: | )

error: failed to run custom build command for curl-sys v0.4.52+curl-7.81.0

Caused by: process didn't exit successfully: /Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-9b4192310196e29f/build-script-build (exit status: 1) --- stdout cargo:rerun-if-changed=curl cargo:rustc-link-lib=clang_rt.osx cargo:rustc-link-search=/opt/homebrew/Cellar/llvm/13.0.1/lib/clang/13.0.1/lib/darwin cargo:root=/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out cargo:include=/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/include cargo:static=1 cargo:rustc-cfg=libcurl_vendored cargo:rustc-cfg=link_libz /Library/Developer/CommandLineTools unable to determine Xcode version, assuming >= 9 TARGET = Some("aarch64-apple-darwin") OPT_LEVEL = Some("3") HOST = Some("aarch64-apple-darwin") CC_aarch64-apple-darwin = None CC_aarch64_apple_darwin = None HOST_CC = None CC = None CFLAGS_aarch64-apple-darwin = None CFLAGS_aarch64_apple_darwin = None HOST_CFLAGS = None CFLAGS = None CRATE_CC_NO_DEFAULTS = None DEBUG = Some("false") CARGO_CFG_TARGET_FEATURE = Some("aes,crc,dit,dotprod,dpb,dpb2,fcma,fhm,flagm,fp,fp16,frintts,jsconv,lor,lse,neon,pan,pauth,pmuv3,ras,rcpc,rcpc2,rdm,sb,sha2,sha3,ssbs,v8.1a,v8.2a,v8.3a,v8.4a,vh") running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/conncache.o" "-c" "curl/lib/conncache.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/asyn-thread.o" "-c" "curl/lib/asyn-thread.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/content_encoding.o" "-c" "curl/lib/content_encoding.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/bufref.o" "-c" "curl/lib/bufref.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/altsvc.o" "-c" "curl/lib/altsvc.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/base64.o" "-c" "curl/lib/base64.c" running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/connect.o" "-c" "curl/lib/connect.c" cargo:warning=curl/lib/connect.c: In function 'singleipconnect': cargo:warning=curl/lib/connect.c:1279:10: warning: implicit declaration of function 'builtin_available'; did you mean '__builtin_scalbl'? [-Wimplicit-function-declaration] cargo:warning= 1279 | if(builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) { cargo:warning= | ^~~~~~~ cargo:warning= | __builtin_scalbl cargo:warning=curl/lib/connect.c:1279:30: error: 'macOS' undeclared (first use in this function) cargo:warning= 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) { cargo:warning= | ^~~~~ cargo:warning=curl/lib/connect.c:1279:30: note: each undeclared identifier is reported only once for each function it appears in cargo:warning=curl/lib/connect.c:1279:35: error: expected ')' before numeric constant cargo:warning= 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) { cargo:warning= | ~ ^~ cargo:warning= | ) exit status: 1 running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/cookie.o" "-c" "curl/lib/cookie.c" exit status: 0 exit status: 0 exit status: 0 exit status: 0 exit status: 0 exit status: 0 exit status: 0

--- stderr fatal: not a git repository (or any of the parent directories): .git

error occurred: Command "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS=\"unknown\"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-DAPPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/connect.o" "-c" "curl/lib/connect.c" with args "cc" did not execute successfully (status code exit status: 1).

warning: build failed, waiting for other jobs to finish... error: build failed

Any idea

Thanks,

Jianshu

rob-p commented 2 years ago

Hi @jianshu93,

Thanks for the bug report. I think this is related to pulling in of curl, which is an optional dependency of rust-htslib, and building that on some OS X systems. The current source builds cleanly on our OS X systems — can you tell us what version of OS X you are on, and what version of OS X developer tools you have installed on the machine where you are trying to build this?

Regardless, I've pushed a modified Cargo.toml that removes curl from the set of included features. Can you try to pull from the repo and build again and let us know if this works for you?

Thanks, Rob

rob-p commented 2 years ago

Hi @jianshu93 — I'll also note you should now be able to install mudskipper directly through cargo, as well as using bioconda.

--Rob

haghshenas commented 2 years ago

Hi @jianshu93 Did you get a chance to try the latest code on github, or try to install from cargo or bioconda?