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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p992875ed070f_s58811b0ae09/logs/ncbi-toolkit-2017.01.06_9.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p992875ed070f_s58811b0ae09 Log: =>> Building biology/ncbi-toolkit build started at Wed May 13 07:46:15 UTC 2026 port directory: /usr/ports/biology/ncbi-toolkit package name: ncbi-toolkit-2017.01.06_9 building for: FreeBSD main-arm64-default-job-12 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 2813 Oct 6 2024 /usr/ports/biology/ncbi-toolkit/Makefile Ports top last git commit: 992875ed070f349edc2d61d5b59b10f6f5814cb1 Ports top unclean checkout: no Port dir last git commit: 4485bd8221c2c5630b87826d37da850b3361b782 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1600014 Jail OSVERSION: 1600018 Job Id: 12 !!! Jail is newer than host. (Jail: 1600018, Host: 1600014) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 UNAME_r=16.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-arm64-default/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for ncbi-toolkit-2017.01.06_9: 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 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- MOTIFLIB="-L/usr/local/lib -lXm" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-poin ter-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG " 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=16.0 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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) 8192 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 pipebuf (-y) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [main-arm64-default-job-12] Installing pkg-2.7.5... [main-arm64-default-job-12] Extracting pkg-2.7.5: .......... done ===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2017.01.06_9 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building ===> Extracting for ncbi-toolkit-2017.01.06_9 => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for ncbi-toolkit-2017.01.06_9 ===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_9 from /usr/ports/biology/ncbi-toolkit/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ncbi-toolkit-2017.01.06_9 depends on package: gettext-runtime>=0.26 - not found ===> Installing existing package /packages/All/gettext-runtime-1.0.pkg [main-arm64-default-job-12] Installing gettext-runtime-1.0... [main-arm64-default-job-12] `-- Installing indexinfo-0.3.1_1... [main-arm64-default-job-12] `-- Extracting indexinfo-0.3.1_1: .... done [main-arm64-default-job-12] Extracting gettext-runtime-1.0: .......... done ===> ncbi-toolkit-2017.01.06_9 depends on package: gettext-runtime>=0.26 - found ===> Returning to build of ncbi-toolkit-2017.01.06_9 ===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.8.13_1,1.pkg [main-arm64-default-job-12] Installing libX11-1.8.13_1,1... [main-arm64-default-job-12] `-- Installing libxcb-1.17.0... [main-arm64-default-job-12] | `-- Installing libXau-1.0.12... [main-arm64-default-job-12] | `-- Extracting libXau-1.0.12: .......... done [main-arm64-default-job-12] | `-- Installing libXdmcp-1.1.5... [main-arm64-default-job-12] | | `-- Installing xorgproto-2025.1... <snip> toporg.c:4796:12: note: add parentheses after the '!' to evaluate the comparison first 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^ | ( ) toporg.c:4796:12: note: add parentheses around left hand side expression to silence this warning 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^ | ( ) 1 warning generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pobutil.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] pobutil.c:2380:44: warning: 'size' argument to memset is '0'; did you mean to transpose the last two arguments? [-Wmemset-transposed-args] 2380 | MemSet((Pointer) (&tmp), sizeof(ValNode), 0); | ^ pobutil.c:2380:44: note: parenthesize the third argument to silence pobutil.c:2381:42: warning: 'size' argument to memset is '0'; did you mean to transpose the last two arguments? [-Wmemset-transposed-args] 2381 | MemSet((Pointer) (&si), sizeof(SeqInt), 0); | ^ pobutil.c:2381:42: note: parenthesize the third argument to silence 2 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF stsutil.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggadj.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggest.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggslp.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] blast.c:3179:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 3179 | if (virtual_oidlist = rdfp_chain->oidlist) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blast.c:3179:29: note: place parentheses around the assignment to silence this warning 3179 | if (virtual_oidlist = rdfp_chain->oidlist) { | ^ | ( ) blast.c:3179:29: note: use '==' to turn this assignment into an equality comparison 3179 | if (virtual_oidlist = rdfp_chain->oidlist) { | ^ | == blast.c:3210:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast.c:3210:29: note: place parentheses around the assignment to silence this warning 3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { | ^ | ( ) blast.c:3210:29: note: use '==' to turn this assignment into an equality comparison 3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { | ^ | == blast.c:10121:25: warning: add explicit braces to avoid dangling else [-Wdangling-else] 10121 | else if( del_index < new_index ) | ^ 3 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastutl.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] blastutl.c:7554:12: warning: expression result unused [-Wunused-value] 7554 | stop_timer("after repeat filtering"); | ^~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:10282:12: warning: expression result unused [-Wunused-value] 10282 | stop_timer("after BlastGappedScoreInternal"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastool.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastconcat.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF splutil.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gapxdrop.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] gapxdrop.c:866:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] 866 | else if ((t/10)%3 == 2) k = 3; | ^ gapxdrop.c:869:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] 869 | else if ((t/30) == 2) k = 3; | ^ 2 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg0.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] bandalg0.c:277:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] 277 | } else { | ^ 1 warning generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg1.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] bandalg1.c:210:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] 210 | else data->CD[leftd - 1].DD = e; | ^ 1 warning generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg2.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg3.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg4.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] bandalg4.c:828:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] 828 | else if ((t/10)%3 == 2) k = 3; | ^ bandalg4.c:831:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] 831 | else if ((t/30) == 2) k = 3; | ^ 2 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg5.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] bandalg5.c:294:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] 294 | else if ((t/10)%3 == 2) k = 3; | ^ bandalg5.c:297:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] 297 | else if ((t/30) == 2) k = 3; | ^ 2 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalgn.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastkar.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] blastkar.c:4936:10: warning: implicit conversion from 'double' to 'Nlm_Int2' (aka 'short') changes value from 0.5 to 0 [-Wliteral-conversion] 4936 | return 0.5; | ~~~~~~ ^~~ 1 warning generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF actutils.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] actutils.c:3026:84: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] 3026 | slp = SeqLocCopyRegion (sip, sfp->location, bsp, 0, bsp->length - 1, strand, FALSE); | ^~~~~ ../include/ncbistd.h:247:15: note: expanded from macro 'FALSE' 247 | #define FALSE ((Nlm_Boolean)0) | ^~~~~~~~~~~~~~~~ actutils.c:3035:88: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] 3035 | slp = SeqLocCopyRegion (sip, cbp->loc, bsp, 0, bsp->length - 1, strand, FALSE); | ^~~~~ ../include/ncbistd.h:247:15: note: expanded from macro 'FALSE' 247 | #define FALSE ((Nlm_Boolean)0) | ^~~~~~~~~~~~~~~~ actutils.c:3047:94: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion] 3047 | slp = SeqLocCopyRegion (sip, trp->anticodon, bsp, 0, bsp->length - 1, strand, FALSE); | ^~~~~ ../include/ncbistd.h:247:15: note: expanded from macro 'FALSE' 247 | #define FALSE ((Nlm_Boolean)0) | ^~~~~~~~~~~~~~~~ 3 warnings generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF posit.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] lookup.c:1198:56: warning: for loop has empty body [-Wempty-body] 1198 | index>0; index=mb_lt->next_pos[index], pcount++); | ^ lookup.c:1198:56: note: put the semicolon on a separate line to silence this warning 1 warning generated. cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF readdb.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] readdb.c:2506:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] 2506 | else | ^ readdb.c:2734:33: warning: 'memset' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] 2734 | memset(blast_dir, 0, sizeof(blast_dir)); | ~~~~~~~~~ ^~~~~~~~~ readdb.c:2734:33: note: did you mean to provide an explicit length? 2734 | memset(blast_dir, 0, sizeof(blast_dir)); | ^~~~~~~~~ readdb.c:3167:37: warning: format specifies type 'long long *' but the argument has type 'Nlm_Int8 *' (aka 'long *') [-Wformat] 3167 | sscanf(ptr, "%lld", &(rdbap->len)); | ~~~~ ^~~~~~~~~~~~~ | %ld readdb.c:4896:45: error: chained comparison 'X <= Y <= Z' does not behave the same as a mathematical expression [-Wparentheses] 4896 | if (rdfp_var->start <= oid <= rdfp_var->stop) | ^ readdb.c:6366:34: warning: 'memset' call operates on objects of type 'char' while the size is based on a different type 'Nlm_CharPtr' (aka 'char *') [-Wsizeof-pointer-memaccess] 6366 | MemSet(defline, '\0', sizeof(defline)); | ~~~~~~~ ^~~~~~~ readdb.c:6366:34: note: did you mean to provide an explicit length? 6366 | MemSet(defline, '\0', sizeof(defline)); | ^~~~~~~ readdb.c:9804:26: warning: address of array 'srp->div' will always evaluate to 'true' [-Wpointer-bool-conversion] 9804 | srp->div ? srp->div : "N/A", (long) SequenceLen, | ~~~~~^~~ ~ readdb.c:9853:45: warning: address of array 'pc->div' will always evaluate to 'true' [-Wpointer-bool-conversion] 9853 | (long) direc.owner, pc->div ? pc->div : "N/A", | ~~~~^~~ ~ readdb.c:12404:26: warning: format specifies type 'int' but the argument has type 'Nlm_Int8' (aka 'long') [-Wformat] 12404 | fprintf(fp, "%d\n", gi->data.intvalue); | ~~ ^~~~~~~~~~~~~~~~~ | %ld 7 warnings and 1 error generated. *** Error code 1 Stop. make[1]: stopped making "all" in /wrkdirs/usr/ports/biology/ncbi-toolkit/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. make: stopped making "build" in /usr/ports/biology/ncbi-toolkit
