From owner-freebsd-pkg-fallout@freebsd.org Sat Apr 17 23:29:40 2021 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 1E8D85E691F for ; Sat, 17 Apr 2021 23:29:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 4FN8S40Jsqz3ht3 for ; Sat, 17 Apr 2021 23:29:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 0AB855E6436; Sat, 17 Apr 2021 23:29:40 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 0A6F45E65EA for ; Sat, 17 Apr 2021 23:29:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FN8S36rK7z3hkZ for ; Sat, 17 Apr 2021 23:29:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id DE13A20E70 for ; Sat, 17 Apr 2021 23:29:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (localhost [127.0.0.1]) by ampere2.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 13HNTdxt015681 for ; Sat, 17 Apr 2021 23:29:39 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere2.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 13HNTd4f015680; Sat, 17 Apr 2021 23:29:39 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 17 Apr 2021 23:29:39 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202104172329.13HNTd4f015680@ampere2.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-arm64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_6 in stage X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 17 Apr 2021 23:29:40 -0000 You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: @FreeBSD.org Ident: Makefile ident: Log URL: http://ampere2.nyi.freebsd.org/data/main-arm64-default/p9d5f4ef1a469_s86046cf55f/logs/ncbi-toolkit-2017.01.06_6.log Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p9d5f4ef1a469_s86046cf55f Log: =>> Building biology/ncbi-toolkit build started at Sat Apr 17 23:12:12 UTC 2021 port directory: /usr/ports/biology/ncbi-toolkit package name: ncbi-toolkit-2017.01.06_6 building for: FreeBSD main-arm64-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400008 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300139 Jail OSVERSION: 1400008 Job Id: 13 !!! Jail is newer than host. (Jail: 1400008, Host: 1300139) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1400008 UNAME_v=FreeBSD 14.0-CURRENT 1400008 UNAME_r=14.0-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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-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_6: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --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" 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="cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -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=14.0 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 #### /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 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400008 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 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-- =================================================== =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [main-arm64-default-job-13] Installing pkg-1.16.3... [main-arm64-default-job-13] Extracting pkg-1.16.3: .......... done ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2017.01.06_6 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_6 for building =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_6 for building => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_6 for building ===> Extracting for ncbi-toolkit-2017.01.06_6 => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for ncbi-toolkit-2017.01.06_6 ===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_6 from /usr/ports/biology/ncbi-toolkit/files =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.6.12,1.txz [main-arm64-default-job-13] Installing libX11-1.6.12,1... [main-arm64-default-job-13] `-- Installing libxcb-1.14_1... [main-arm64-default-job-13] | `-- Installing libXau-1.0.9... [main-arm64-default-job-13] | `-- Extracting libXau-1.0.9: .......... done [main-arm64-default-job-13] | `-- Installing libXdmcp-1.1.3... [main-arm64-default-job-13] | | `-- Installing xorgproto-2020.1... [main-arm64-default-job-13] | | `-- Extracting xorgproto-2020.1: .......... done [main-arm64-default-job-13] | `-- Extracting libXdmcp-1.1.3: ......... done sequin1.c:20931:13: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch] switch (wiz->virus_class) { ^ sequin1.c:21036:13: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch] switch (wiz->cultured_kingdom) { ^ sequin1.c:21347:11: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ sequin1.c:21394:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:21552:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:21632:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding] -Use the <93>Import Source Table<94> button to import a tab-delimited table\n\ ^~~~ ~~~~ sequin1.c:22401:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch] switch (wiz->wizard_type) { ^ 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) { ^ 26 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. 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. 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) { ^ sequin8.c:17767:33: warning: self-comparison always evaluates to false [-Wtautological-compare] } else if (fcontext2.itemID < fcontext2.itemID) { ^ 4 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 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 -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm : sbtedit 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 -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -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] 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 -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -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. 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 -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm 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 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. 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 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 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 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 -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm : entrez2 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* ********************************************************* =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xau.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xft.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xrender.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found =========================================================================== =================================================== ===> Staging for ncbi-toolkit-2017.01.06_6 ===> 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 *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-toolkit