From nobody Thu Apr 20 19:44:46 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Q2SmG65pBz46VrK for ; Thu, 20 Apr 2023 19:44:46 +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 4Q2SmG4ZYHz3kg7; Thu, 20 Apr 2023 19:44:46 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1682019886; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=wnRZ3zaFMb2bahDEcaWRM2MpHkhOHzR9KhM/JveGaH8=; b=RMFg9oiNvAmtQq2PkR2kJkGMPUFBjz0DRypJMj/Zg5SFFB5Up2v+7hfQMMJ5+JIJeB1FVZ YOAgWZXP4ppI/d9zw0o8FBLV/yqaLjQ9lZ7x1PmiXTE/onGkpEPvZUSvIsBXv5puKfOL4l mUz6eIlOxoVJEVu2spCg3oblH1mg6rN0Ig9xAOw7AZFeb2vTs32Z5DZrimnSErVE0Pl8Wq J0BN6crUC7yD5CKKBkLlSeEyZiTKaaS9dwIaYTe7iPZ/WANkoaG7Jqiab15YRRuLnWXk8E lv0b7qLrQt+GCuBUSek9z++VwBOUNSVZUPVuMy3jyYW4gSlZQnhx5d0IrplJwQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1682019886; a=rsa-sha256; cv=none; b=m+gZAr00EuQb2zSamkUc34YB/HPmOlQKt5b24qmBvv/9ldqSaL5N2y++gSmHMD7sTSNYUw DgnQKirL7symJ3LdopONEnjLl+EEZGqgYwEsar0Fy4sbKULuXKMo1uPVNbwGLWEt3HnkFS LSsWZm9sz7OFYH3hF66X7tkWYmyxcETW+Ee2H4BQNMMYCS3trfWXdV/IaSMSGiKJAKQsOJ M0y5ybeaXIu6CqV0SNFlsOa8w7CP22d19usnay9jnpmEnvanfSa+AYwbG7id75NVwKBvn4 nGBj0IMm3H83A/9D4spxMcNQGLt8mw1JpqSj78bso3Iy6V/C8KQSZan1CGWXfg== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) (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 4Q2SmG3YDZzrQR; Thu, 20 Apr 2023 19:44:46 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (localhost [127.0.0.1]) by beefy18.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 33KJikOA090097; Thu, 20 Apr 2023 19:44:46 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 33KJikhb090089; Thu, 20 Apr 2023 19:44:46 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 20 Apr 2023 19:44:46 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202304201944.33KJikhb090089@beefy18.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - main-amd64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_7 in build Cc: pkg-fallout@FreeBSD.org X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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 Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/pc43292c24918_sf369f10dd8/logs/ncbi-toolkit-2017.01.06_7.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pc43292c24918_sf369f10dd8 Log: =>> Building biology/ncbi-toolkit build started at Thu Apr 20 19:42:25 UTC 2023 port directory: /usr/ports/biology/ncbi-toolkit package name: ncbi-toolkit-2017.01.06_7 building for: FreeBSD main-amd64-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400086 amd64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400086 Job Id: 09 !!! Jail is newer than host. (Jail: 1400086, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400086 UNAME_v=FreeBSD 14.0-CURRENT 1400086 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=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-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_7: 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 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 -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_PRO GRAM="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 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/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_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_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400086 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES 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) 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-- =================================================== =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-amd64-default-job-09] Installing pkg-1.19.1_1... [main-amd64-default-job-09] Extracting pkg-1.19.1_1: .......... done ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2017.01.06_7 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building ===> Extracting for ncbi-toolkit-2017.01.06_7 => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for ncbi-toolkit-2017.01.06_7 ===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_7 from /usr/ports/biology/ncbi-toolkit/files =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.7.2,1.pkg [main-amd64-default-job-09] Installing libX11-1.7.2,1... [main-amd64-default-job-09] `-- Installing libxcb-1.15_1... [main-amd64-default-job-09] | `-- Installing libXau-1.0.9... sprintf (cip->description, fmt); ^~~ sqnutil3.c:33201:35: note: treat the string as an argument to avoid this sprintf (cip->description, fmt); ^ "%s", sqnutil3.c:34051:38: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] if (StringHasNoText (name)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 4 warnings generated. 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 sqnutil4.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] sqnutil4.c:7308:53: warning: expression which evaluates to zero treated as a null pointer constant of type 'DeflineFeatureRequestListPtr' (aka 'struct deflinefeaturerequestlist *') [-Wnon-literal-null-conversion] expected_product_name = GetProductName (cds, bsp, FALSE); ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sqnutil4.c:10750:37: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] if (new_fcp == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sqnutil4.c:10752:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] if (vnp == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sqnutil4.c:27751:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] if (sdp == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sqnutil4.c:27753:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion] if (pdp == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ sqnutil4.c:28869:17: warning: result of comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while (*val <= 256 && *val >= -1 && isspace (*val)) { ~~~~ ^ ~~~ sqnutil4.c:28931:34: warning: result of comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while (last > val && *last <= 256 && *last >= -1 && isspace (*last)) { ~~~~~ ^ ~~~ 7 warnings generated. 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 subutil.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] subutil.c:774:41: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion] if (delta_seq_entry == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ subutil.c:775:48: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion] if (IS_Bioseq_set(delta_seq_entry)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ subutil.c:776:56: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion] if (delta_seq_entry->data.ptrvalue == NULL) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ subutil.c:782:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ subutil.c:3639:32: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] if (AA_for_tRNA != '\0') ^~~~ (void *)0 subutil.c:4050:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqGraphPtr' (aka 'struct seqgraph *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 6 warnings generated. 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 edutil.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] edutil.c:2062:48: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if ((oldbsp == NULL) || (from < 0)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ edutil.c:2203:50: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion] if ((sourceid == NULL) || (from < 0)) return FALSE; ^~~~~ ./include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 2 warnings generated. 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 asn2ff1.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] 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 asn2ff2.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] asn2ff2.c:1358:8: warning: type specifier missing, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] static ChoicePID(SeqIdPtr sid) ~~~~~~ ^ int 1 warning generated. 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 asn2ff3.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] asn2ff3.c:2717:28: warning: format specifies type 'char *' but the argument has type 'Nlm_VoidPtr' (aka 'void *') [-Wformat] sprintf(val, "GeneID:%s", vnp->data.ptrvalue); ~~ ^~~~~~~~~~~~~~~~~~ 1 warning generated. 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 asn2ff4.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] asn2ff4.c:1126:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] }else{ ^ asn2ff4.c:1347:8: warning: type specifier missing, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) ~~~~~~ ^ int asn2ff4.c:2069:26: warning: comparison of array 'gbp->accession' equal to a null pointer is always false [-Wtautological-pointer-compare] if (gbp == NULL || gbp->accession == NULL) ~~~~~^~~~~~~~~ ~~~~ asn2ff4.c:2660:12: warning: address of array 'gbp->locus' will always evaluate to 'true' [-Wpointer-bool-conversion] if (gbp->locus) { ~~ ~~~~~^~~~~ asn2ff4.c:2664:12: warning: address of array 'gbp->accession' will always evaluate to 'true' [-Wpointer-bool-conversion] if (gbp->accession) { ~~ ~~~~~^~~~~~~~~ 5 warnings generated. 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 asn2ff5.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] asn2ff5.c:1683:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ asn2ff5.c:2128:10: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion] temp = '\0'; ^~~~ asn2ff5.c:2124:12: warning: expression result unused [-Wunused-value] temp++; *ptr_in++; ^~~~~~~~~ 3 warnings generated. 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 asn2ff6.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] 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 asn2gnb1.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] 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 asn2gnb2.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] asn2gnb2.c:1742:18: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (accp != '\0' && prevp != '\0') { ^~~~ (void *)0 asn2gnb2.c:1742:37: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (accp != '\0' && prevp != '\0') { ^~~~ (void *)0 asn2gnb2.c:1767:41: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue; ^~~~ (void *)0 asn2gnb2.c:3409:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] string = PrintDate (spb->created); ^ asn2gnb2.c:3409:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion] string = PrintDate (spb->created); ^ ~~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb2.c:3417:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] string = PrintDate (spb->sequpd); ^ asn2gnb2.c:3417:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion] string = PrintDate (spb->sequpd); ^ ~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb2.c:3424:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] string = PrintDate (spb->annotupd); ^ asn2gnb2.c:3424:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion] string = PrintDate (spb->annotupd); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings and 3 errors generated. *** Error code 1 Stop. make[1]: stopped 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 in /usr/ports/biology/ncbi-toolkit