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Maintainer: [email protected] Last committer: [email protected] Ident: $FreeBSD: head/biology/ncbi-toolkit/Makefile 481472 2018-10-07 18:29:16Z yuri $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p482948_s339695/logs/ncbi-toolkit-2017.01.06.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p482948_s339695 Log: =>> Building biology/ncbi-toolkit build started at Thu Oct 25 14:13:13 UTC 2018 port directory: /usr/ports/biology/ncbi-toolkit package name: ncbi-toolkit-2017.01.06 building for: FreeBSD head-armv7-default-job-18 13.0-CURRENT FreeBSD 13.0-CURRENT 1300000 arm maintained by: [email protected] Makefile ident: $FreeBSD: head/biology/ncbi-toolkit/Makefile 481472 2018-10-07 18:29:16Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1200085 Jail OSVERSION: 1300000 Job Id: 18 !!! Jail is newer than host. (Jail: 1300000, Host: 1200085) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300000 UNAME_v=FreeBSD 13.0-CURRENT 1300000 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for ncbi-toolkit-2017.01.06: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- MOTIFLIB="-L/usr/local/lib -lXm -lXp" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/ncbi-toolkit" EXAMPLESDIR="share/examples/ncbi-toolkit" DATADIR="share/ncbi-toolkit" WWWDIR="www/ncbi-toolkit" ETCDIR="etc/ncbi-toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-toolkit DOCSDIR=/usr/local/share/doc/ncbi-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-toolkit WWWDIR=/usr/local/www/ncbi-toolkit ETCDIR=/usr/local/etc/ncbi-toolkit --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-armv7-default-job-18] Installing pkg-1.10.5_5... [head-armv7-default-job-18] Extracting pkg-1.10.5_5: .......... done ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2017.01.06 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== <snip> sequin1.c:27538:11: warning: enumeration values 'eWizardType_NormalDialogs', 'eWizardType_Microsatellite', and 'eWizardType_WGS' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:28943:13: warning: 4 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_Microsatellite', 'eWizardType_DLoop'... [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:28976:11: warning: 5 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Microsatellite'... [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:29038:11: warning: 5 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Microsatellite'... [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:32916:58: warning: data argument not used by format string [-Wformat-extra-args] fprintf (lip->fp, "%s (too short)\n", a->id, "Low Quality"); ~~~~~~~~~~~~~~~~~~ ^ sequin1.c:33416:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding] Click <91>Import Nucleotide Alignment<92> to load your nucleotide alignment file.\n\ ^~~~ ~~~~ sequin1.c:33417:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding] Click <91>Custom Alignment Settings<92> if there is trouble reading your alignment file.\n\ ^~~~ ~~~~ sequin1.c:33916:11: warning: 7 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Viruses'... [-Wswitch] switch (frm->wiz->wizard_type) { ^ sequin1.c:34038:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch] switch (frm->wiz->wizard_type) { ^ sequin1.c:34089:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ 28 warnings generated. sequin2.c:7795:56: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (sep == NULL || StringHasNoText (valname)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7796:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (! IS_Bioseq (sep)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7798:68: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (bsp == NULL || bsp->mol != mol || bsp->descr == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:7800:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] if (vnp == NULL || vnp->data.ptrvalue == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:27333:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if (sep == NULL || sep->data.ptrvalue == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin2.c:27348:32: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if (!IS_Bioseq (sep)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 6 warnings generated. sequin3.c:9217:26: warning: '&&' within '||' [-Wlogical-op-parentheses] || must_have_stops && !HasInternalStops (sfp)) ~~ ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ sequin3.c:9217:26: note: place parentheses around the '&&' expression to silence this warning || must_have_stops && !HasInternalStops (sfp)) ^ ( ) 1 warning generated. sequin4.c:4989:52: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sequin_GlobalAlign2Seq(bsp, sbp->bsp, FALSE); ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin4.c:4993:49: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sqn_GlobalAlign2Seq(bsp, sbp->bsp, FALSE); ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin4.c:14072:67: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] salp = Sequin_GlobalAlign2Seq(master_bsp, vnp->data.ptrvalue, FALSE); ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 3 warnings generated. sequin5.c:18184:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sequin5.c:19773:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 2 warnings generated. sequin6.c:11491:12: warning: comparison of array 'hfp->file' equal to a null pointer is always false [-Wtautological-pointer-compare] if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; ~~~~~^~~~ ~~~~ sequin6.c:11766:12: warning: comparison of array 'hfp->file' equal to a null pointer is always false [-Wtautological-pointer-compare] if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; ~~~~~^~~~ ~~~~ 2 warnings generated. sequin7.c:14159:48: warning: '&&' within '||' [-Wlogical-op-parentheses] || best_left == fcontext.left && best_right < fcontext.right) { ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:14159:48: note: place parentheses around the '&&' expression to silence this warning || best_left == fcontext.left && best_right < fcontext.right) { ^ ( ) sequin7.c:15679:46: warning: '&&' within '||' [-Wlogical-op-parentheses] || word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) { ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:15679:46: note: place parentheses around the '&&' expression to silence this warning || word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) { ^ ( ) 2 warnings generated. sequin8.c:10165:39: warning: self-comparison always evaluates to true [-Wtautological-compare] } else if (left2 <= left1 && right2 >= right2) { ^ sequin8.c:10507:69: warning: self-comparison always evaluates to false [-Wtautological-compare] if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { ^ sequin8.c:10513:69: warning: self-comparison always evaluates to false [-Wtautological-compare] if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { ^ 3 warnings generated. sequin9.c:2710:7: warning: comparison of array 'path' equal to a null pointer is always false [-Wtautological-pointer-compare] if (path == NULL || config == NULL || config->data.ptrvalue == NULL) return; ^~~~ ~~~~ 1 warning generated. : Psequin /nxb-bin/usr/bin/cc -o sbtedit -I. -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sbtedit.c -lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -L/usr/local/lib -lXm -lXp -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm : sbtedit /nxb-bin/usr/bin/cc -o Nentrez -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF entrez.c -lncbiid1 -lvibnet -lncbicn3d -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lnetblast -lncbitool -lblastcompadj -lncbiNacc -lnetentr -lnetcli -lncbiacc -lvibrant -lncbicdr -lncbiobj -lncbi -L/usr/local/lib -lXm -lXp -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm /nxb-bin/usr/bin/cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" udvmain.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] /nxb-bin/usr/bin/cc -o udv -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF udvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool -lblastcompadj -lncbiobj -lncbi -L/usr/local/lib -lXm -lXp -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm /nxb-bin/usr/bin/cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ddvmain.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] ddvmain.c:147:13: warning: 'extern' variable has an initializer [-Wextern-initializer] extern Args DDV_myargs[NUMARGS] = { ^ 1 warning generated. /nxb-bin/usr/bin/cc -o ddv -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ddvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool -lblastcompadj -lncbiobj -lncbi -L/usr/local/lib -lXm -lXp -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm /nxb-bin/usr/bin/cc -g -o blastcl3 -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -DBLAST_CS_API blastall.c -lblastapi -lblast -lnetblast -lncbitool -lblastcompadj -lnetcli -lncbiobj -lncbi -lm /nxb-bin/usr/bin/cc -g -o idfetch -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF idfetch.c -lncbiid1 -lnetcli -lncbiobj -lconnssl -lncbi -lm idfetch.c:1422:38: warning: format specifies type 'short' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf( pFormat, "%%s%%0%hdhd", DigitsStart); ~~~ ^~~~~~~~~~~ %d 1 warning generated. /nxb-bin/usr/bin/cc -g -o asn2gb -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2gb.c -lncbiid1 -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi -lm /nxb-bin/usr/bin/cc -o tbl2asn -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF tbl2asn.c -lncbitool -lblastcompadj -lncbiobj -lnetcli -lconnssl -lncbi -lm /nxb-bin/usr/bin/cc -g -o gene2xml -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gene2xml.c -lnetcli -lncbiobj -lncbi -lm /nxb-bin/usr/bin/cc -g -o entrez2 -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF entrez2.c -lncbiid1 -lnetcli -lncbidesk -lblastapi -lblast -lncbimmdb -lncbitool -lblastcompadj -lncbiobj -lvibrant -lncbi -L/usr/local/lib -lXm -lXp -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm : entrez2 /nxb-bin/usr/bin/cc -g -o gbseqget -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gbseqget.c -lncbiid1 -lnetcli -lncbitool -lblastcompadj -lncbiobj -lncbi -lm Put the date stamp to the file ../VERSION ********************************************************* *The new binaries are located in ./ncbi/build/ directory* ********************************************************* =========================================================================== =======================<phase: run-depends >============================ ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xau.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xft.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xrender.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> ncbi-toolkit-2017.01.06 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found =========================================================================== =======================<phase: stage >============================ ===> Staging for ncbi-toolkit-2017.01.06 ===> Generating temporary packing list cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/bin && install -s -m 555 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/bin cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/lib && install -m 0644 *.a /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/lib/ncbi cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/include && install -m 0644 *.h /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/include/ncbi cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/include/connect && install -m 0644 *.h /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/include/ncbi/connect cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/doc/man && install -m 444 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/man/man1 cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/data && install -m 0644 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/share/ncbi-toolkit Abort trap *** Error code 134 Stop. make: stopped in /usr/ports/biology/ncbi-toolkit _______________________________________________ [email protected] mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "[email protected]"
