=> Bootstrap dependency digest>=20211023: found digest-20220214 WARNING: [license.mk] Every package should define a LICENSE. ===> Building for ncbi-bin-20120620 cd /Users/pbulk/build/wip/ncbi-bin/work/ncbi/.. && /usr/bin/env PREFIX=/opt/pkg USETOOLS=no GOTMPDIR=/Users/pbulk/build MOTIFLIB=-L/opt/pkg/lib\ \ -L/opt/pkg/lib\ -lXm\ -lXft MOTIFBASE=/opt/pkg PTHREAD_CFLAGS=\ -D_REENTRANT PTHREAD_LDFLAGS= PTHREAD_LIBS=-lpthread PTHREADBASE= MACOSX_DEPLOYMENT_TARGET=11.3 CC=clang CFLAGS=-pipe\ -Os\ -I/opt/pkg/include\ -I/opt/pkg/include/freetype2 CPPFLAGS=-DPNG_NO_ASSEMBLER_CODE\ -I/opt/pkg/include\ -I/opt/pkg/include/freetype2 CXX=clang++ CXXFLAGS=-pipe\ -Os\ -I/opt/pkg/include\ -I/opt/pkg/include/freetype2 COMPILER_RPATH_FLAG=-L F77=f77 FC=f77 FFLAGS=-O LANG=C LC_ALL=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/opt/pkg/lib\ -L/opt/pkg/lib LINKER_RPATH_FLAG=-L PATH=/Users/pbulk/build/wip/ncbi-bin/work/.cwrapper/bin:/Users/pbulk/build/wip/ncbi-bin/work/.buildlink/bin:/Users/pbulk/build/wip/ncbi-bin/work/.tools/bin:/opt/pkg/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/pkg/bin:/opt/pkg/bin PREFIX=/opt/pkg MAKELEVEL=0 CONFIG_SITE= PKG_SYSCONFDIR=/opt/pkg/etc CXXCPP=clang\ -E HOME=/Users/pbulk/build/wip/ncbi-bin/work/.home CWRAPPERS_CONFIG_DIR=/Users/pbulk/build/wip/ncbi-bin/work/.cwrapper/config CPP=clang\ -E LOCALBASE=/opt/pkg X11BASE=/opt/pkg PKGMANDIR=share/man PKGINFODIR=info PKGGNUDIR=gnu/ MAKECONF=/dev/null OBJECT_FMT=Mach-O USETOOLS=no BSD_INSTALL_PROGRAM=/usr/bin/install\ -c\ \ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_SCRIPT=/usr/bin/install\ -c\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_LIB=/usr/bin/install\ -c\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ staff\ -m\ 644 BSD_INSTALL_MAN=/usr/bin/install\ -c\ -o\ pbulk\ -g\ staff\ -m\ 644 BSD_INSTALL=/usr/bin/install BSD_INSTALL_PROGRAM_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_LIB_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_DATA_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_MAN_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 755 BSD_INSTALL_GAME=/usr/bin/install\ -c\ \ -o\ pbulk\ -g\ staff\ -m\ 2555 BSD_INSTALL_GAME_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ staff\ -m\ 664 BSD_INSTALL_GAME_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ staff\ -m\ 775 INSTALL_INFO= MAKEINFO=/Users/pbulk/build/wip/ncbi-bin/work/.tools/bin/makeinfo FLEX= BISON= ITSTOOL=/Users/pbulk/build/wip/ncbi-bin/work/.tools/bin/itstool GDBUS_CODEGEN=/Users/pbulk/build/wip/ncbi-bin/work/.tools/bin/gdbus-codegen PKG_CONFIG=/Users/pbulk/build/wip/ncbi-bin/work/.tools/bin/pkg-config PKG_CONFIG_LIBDIR=/Users/pbulk/build/wip/ncbi-bin/work/.buildlink/lib/pkgconfig:/Users/pbulk/build/wip/ncbi-bin/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/Users/pbulk/build/wip/ncbi-bin/work/.pkg-config.log PKG_CONFIG_PATH= CWRAPPERS_CONFIG_DIR=/Users/pbulk/build/wip/ncbi-bin/work/.cwrapper/config ncbi/make/makedis.csh platform is darwin Darwin pkgsrc-mac-0.local 22.2.0 Darwin Kernel Version 22.2.0: Fri Nov 11 02:03:51 PST 2022; root:xnu-8792.61.2~4/RELEASE_ARM64_T6000 arm64 Disabling assert(). BLAST version is 2.2.26 make CFLAGS1="-DNDEBUG -O2 -c " LDFLAGS1="-framework CoreServices -O2" OTHERLIBS="-lc" SHELL="/bin/sh" LCL="dwn" RAN="ranlib" AR="ar" CC="cc -pipe" LIB30=libncbicn3d.a LIB28=libvibgif.a LIB4=libvibrant.a LIB20=libncbidesk.a LIB45=libddvlib.a VIBFLAG="-DWIN_MAC -I/Developer/Headers/FlatCarbon" VIBLIBS="-framework Carbon" all chmod -R ug+rw,o+r . ../include ./ln-if-absent ../corelib/tsprintf.h ../include ./ln-if-absent ../corelib/gifgen.h ../include ./ln-if-absent ../corelib/ncbi*.h ../include ./ln-if-absent ../corelib/tree*.h ../include ./ln-if-absent ../corelib/regex.h ../include ./ln-if-absent ../corelib/matrix.h ../include ./ln-if-absent ../corelib/binary.h ../include ./ln-if-absent ../corelib/morefile/*.h ../include ./ln-if-absent ../corelib/morefile/*.c . ./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include ./ln-if-absent ../corelib/ncbilcl.dwn ../include/ncbilcl.h ./ln-if-absent ../corelib/*.c . ./ln-if-absent ../corelib/core*.h . ./ln-if-absent ../asnlib/*.h . rm -f ../include/asn.h mv asn.h ../include ./ln-if-absent ../asnlib/*.c . ./ln-if-absent ../connect/*.c . ./ln-if-absent ../connect/ncbi_ansi_ext.h . ./ln-if-absent ../connect/ncbi_assert.h . ./ln-if-absent ../connect/ncbi_priv.h . ./ln-if-absent ../connect/ncbi_comm.h . ./ln-if-absent ../connect/ncbi_config.h . ./ln-if-absent ../connect/ncbi_connssl.h . ./ln-if-absent ../connect/ncbi_lbsm.h . *** Error code 1 (ignored) ./ln-if-absent ../connect/ncbi_lbsm_ipc.h . *** Error code 1 (ignored) ./ln-if-absent ../connect/ncbi_host_infop.h . ./ln-if-absent ../connect/ncbi_server_infop.h . ./ln-if-absent ../connect/ncbi_servicep.h . ./ln-if-absent ../connect/ncbi_socketp.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/ncbi_local.h . ./ln-if-absent ../connect/ncbi_lb.h . ./ln-if-absent ../connect/ncbi_version.h . ./ln-if-absent ../connect/ncbi_base64.h . ./ln-if-absent ../connect/urlquery.h ../include mkdir ../include/connect chmod ug+rw,o+r ../include/connect cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect ./ln-if-absent ../util/tables/*.c . mkdir -p ../include/util/tables cp -fp ../util/tables/*.h ../include/util/tables ./ln-if-absent ../util/creaders/*.c . mkdir -p ../include/util/creaders cp -fp ../util/creaders/*.h ../include/util/creaders ./ln-if-absent ../ctools/*.c . ./ln-if-absent ../ctools/*.h . mkdir ../include/ctools chmod ug+rw,o+r ../include/ctools cp -fp ../ctools/*.h ../include/ctools ./ln-if-absent ../object/*.c . ./ln-if-absent ../object/*.h ../include ./ln-if-absent ../access/*.c . ./ln-if-absent ../access/*.h ../include ./ln-if-absent ../asnstat/*.h ../include ./ln-if-absent ../api/*.h ../include ./ln-if-absent ../api/*.c . ./ln-if-absent ../api/*.inc . ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../cdromlib/*.c . ./ln-if-absent ../vibrant/*.h ../include ./ln-if-absent ../vibrant/*.c . ./ln-if-absent ../desktop/*.h ../include ./ln-if-absent ../desktop/*.c . ./ln-if-absent ../biostruc/*.h ../include ./ln-if-absent ../biostruc/*.c . ./ln-if-absent ../biostruc/cdd/*.h ../include ./ln-if-absent ../biostruc/cdd/*.c . ./ln-if-absent ../biostruc/cn3d/*.h ../include ./ln-if-absent ../biostruc/cn3d/*.c . ./ln-if-absent ../tools/*.h ../include ./ln-if-absent ../tools/*.c . ./ln-if-absent ../cn3d/*.h ../include ./ln-if-absent ../cn3d/*.c . ./ln-if-absent ../gif/*.c . ./ln-if-absent ../gif/*.h ../include ./ln-if-absent ../ddv/*.h ../include ./ln-if-absent ../ddv/*.c . ./ln-if-absent ../regexp/*.c . ./ln-if-absent ../regexp/*.h ../include ./ln-if-absent ../internal/compr/*.c . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/compr/*.h ../include set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/libindx/*.c . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/libindx/*.h ../include set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/libpars/*.c . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/libpars/*.h ../include set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ideogram/*.c . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ideogram/*.dat . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ideogram/ideochr*.h ../include set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ideogram/ideoorgs.h . *** Error code 1 (ignored) ./ln-if-absent ../internal/ccap/*.c . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ccap/*.dat . set: No match. *** Error code 1 (ignored) ./ln-if-absent ../internal/ccap/*.h ../include set: No match. *** Error code 1 (ignored) ./ln-if-absent ncbidraw.c ncbidrwg.c ./ln-if-absent ncbithr.c ncbithrs.c ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id2arch/*.h ../include mkdir -p ../include/algo/blast/core ./ln-if-absent ../algo/blast/core/*.c . ./ln-if-absent ../algo/blast/core/*.h . ./ln-if-absent ../algo/blast/core/*.inl . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/composition_adjustment ./ln-if-absent ../algo/blast/composition_adjustment/*.c . ./ln-if-absent ../algo/blast/composition_adjustment/*.h ../include cp -fp ../algo/blast/composition_adjustment/*.h ../include/algo/blast/composition_adjustment mkdir -p ../include/algo/blast/api ./ln-if-absent ../algo/blast/api/*.c . cp -fp ../algo/blast/api/*.h ../include/algo/blast/api chmod -R ug+rw,o+r . cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbithr.c cp -p ncbithr.o ../lib cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbimain.c ncbimain.c:81:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main(int argc, char *argv[]) ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbibs.c cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon wwwutils.c cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbierr.c ncbierr.c:955:31: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(path,file,sizeof(path)); ^~~~~~~~~~~~ ncbierr.c:955:31: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(path,file,sizeof(path)); ^~~~~~~~~~~~ sizeof(path) - strlen(path) - 1 ncbierr.c:1380:13: warning: comparison of array 'info->logfile' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (info->logfile != NULL && *info->logfile == '\0') ~~~~~~^~~~~~~ ~~~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbienv.c ncbienv.c:2025:11: warning: 'FSPathMakeRef' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] err = FSPathMakeRef ((unsigned char *) aPath, &contentsFRef, &isDirectory); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Files.h:4115:18: note: 'FSPathMakeRef' has been explicitly marked deprecated here extern OSStatus FSPathMakeRef(const UInt8 *path, FSRef *ref, Boolean *isDirectory) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbienv.c:2471:10: warning: 'Gestalt' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Gestalt.h:123:1: note: 'Gestalt' has been explicitly marked deprecated here Gestalt( ^ ncbienv.c:2471:19: warning: 'gestaltSystemVersion' is deprecated: first deprecated in macOS 10.8 - Use NSProcessInfo's operatingSystemVersion property instead. [-Wdeprecated-declarations] if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Gestalt.h:2081:1: note: '' has been explicitly marked deprecated here enum { ^ ncbienv.c:2490:10: warning: 'Gestalt' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Gestalt.h:123:1: note: 'Gestalt' has been explicitly marked deprecated here Gestalt( ^ ncbienv.c:2490:19: warning: 'gestaltSystemVersion' is deprecated: first deprecated in macOS 10.8 - Use NSProcessInfo's operatingSystemVersion property instead. [-Wdeprecated-declarations] if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Gestalt.h:2081:1: note: '' has been explicitly marked deprecated here enum { ^ 5 warnings generated. cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbifile.c ncbifile.c:1207:16: warning: 'tempnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tempnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] filename = tempnam("/tmp", "ncbi."); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/usr/include/stdio.h:302:1: note: 'tempnam' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tempnam(3), it is highly recommended that you use mkstemp(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/usr/include/sys/cdefs.h:200:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbiprop.c cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbimath.c cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbimem.c ncbimem.c:554:24: warning: 'NewHandle' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] hnd = (Nlm_Handle) NewHandle (size); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:451:1: note: 'NewHandle' has been explicitly marked deprecated here NewHandle(Size byteCount) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:626:5: warning: 'SetHandleSize' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] SetHandleSize ((Handle)hnd, (Size)size); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:1321:1: note: 'SetHandleSize' has been explicitly marked deprecated here SetHandleSize( ^ ncbimem.c:628:9: warning: 'MemError' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] if (MemError() != noErr) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:330:1: note: 'MemError' has been explicitly marked deprecated here MemError(void) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:666:9: warning: 'DisposeHandle' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] DisposeHandle ((Handle) hnd); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:1278:1: note: 'DisposeHandle' has been explicitly marked deprecated here DisposeHandle(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:707:5: warning: 'HLock' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] HLock ((Handle) hnd); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:725:1: note: 'HLock' has been explicitly marked deprecated here HLock(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:742:9: warning: 'HUnlock' is deprecated: first deprecated in macOS 10.8 [-Wdeprecated-declarations] HUnlock ((Handle) hnd); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:791:1: note: 'HUnlock' has been explicitly marked deprecated here HUnlock(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ 6 warnings generated. cc -pipe -DNDEBUG -O2 -c -I../include -DWIN_MAC -I/Developer/Headers/FlatCarbon ncbimisc.c ncbimisc.c:1269:22: error: non-void function 'MergeStringArray' should return a value [-Wreturn-type] if (rsult == NULL) return; ^ ncbimisc.c:2250:27: warning: 'memset' call operates on objects of type 'struct md5context_' while the size is based on a different type 'Nlm_MD5ContextPtr' (aka 'struct md5context_ *') [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ~~~ ^~~ ncbimisc.c:2250:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^~~ 1 warning and 1 error generated. *** Error code 1 Stop. make: stopped in /Users/pbulk/build/wip/ncbi-bin/work/ncbi/build Fatal error building NCBI core libraries. Please be sure that you have X11 and Motif libraries installed. The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful. *** Error code 1 Stop. bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/wip/ncbi-bin *** Error code 1 Stop. bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/wip/ncbi-bin