From nobody Mon Mar 13 22:09:57 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 4Pb9nK4pMwz3yH0H for ; Mon, 13 Mar 2023 22:09:57 +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 4Pb9nK29vGz3KkK for ; Mon, 13 Mar 2023 22:09:57 +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=1678745397; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=+NB8T4dvGA5rY2n7vtBXZNDIvV1EMQ70XeQ0+zi7U5A=; b=xrf3a7it+qBCq2t9CK65gFWMpDxFYRDGwX6BMHO9t6QKtuMJJ9369bC3ReqmtVII8IyoNZ orrzMJW0BZsxrc+o/h9CR4vq9bR1V+ChJU0O69qm7AOA/RV4MFirG/L9w9PpuAJYZ6S4Lq gP1iTlRfN6OkFdlOQ6cFI4n1AXxouzeN7Gyn5eTis1rLFiwgz9B6g9QSu6BHFD3RNd4BD9 XjLDfyF0Dz5gM8vpWaNvyRTxxzYJXAE/SruWOG+uhxtFYJ3KvLFatcLoB+UmbAUe0ld3KA aLCOXGxO12MfL7XeE6pV/NGyJgKUZTF5Lje85c5OhJa2pxNZp/36Pv+bzJFUpg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1678745397; a=rsa-sha256; cv=none; b=nCjHJlk/kbSwZ7iuR7tOlhtJ/UqkcPQ6RgcLlX5nA2RvmcsjfRPqMSVxVZ52SO1S0QY91u p/rjhO5djcRHY1KF3iknPQ7W5bqM7u/P4EmTns4V1uMtblFMsJD5GbTZ09Tn9ChCZiYMEU adPnvakNdhw1ICcKcK0meNUwDu8LujNsCVOHgLZRQnpE8Vm8AOx2uHHLdaiJVu0Lao38zR UZcMcHHAQdzhGZUpGIqrkJMYW8dXPdMc2sA2QfBFOeIc2eN6sNGMh3ZjixVA4eQaIB5qRQ L8AYxDRKhT2j2pIsL6i+jJD1qhbd5HuLwsJOAncM3nu83z5kVGSpNrow1h3OLg== 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 4Pb9nK1FfVz19Sg for ; Mon, 13 Mar 2023 22:09:57 +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 32DM9vJM021954 for ; Mon, 13 Mar 2023 22:09:57 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 32DM9v3c021953; Mon, 13 Mar 2023 22:09:57 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Mon, 13 Mar 2023 22:09:57 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202303132209.32DM9v3c021953@beefy18.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-amd64-default][biology/wise] Failed for wise-2.4.1_1 in build 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: ports@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p6a11326d040c_s44b31d37ad/logs/wise-2.4.1_1.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p6a11326d040c_s44b31d37ad Log: =>> Building biology/wise build started at Mon Mar 13 22:09:33 UTC 2023 port directory: /usr/ports/biology/wise package name: wise-2.4.1_1 building for: FreeBSD main-amd64-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400082 amd64 maintained by: ports@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400082 Job Id: 01 !!! Jail is newer than host. (Jail: 1400082, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400082 UNAME_v=FreeBSD 14.0-CURRENT 1400082 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 wise-2.4.1_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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="" PORTEXAMPLES="" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/wise" EXAMPLESDIR="share/examples/wise" DATADIR="share/wise" WWWDIR="www/wise" ETCDIR="etc/wise" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wise DOCSDIR=/usr/local/share/doc/wise EXAMPLESDIR=/usr/local/share/examples/wise WWWDIR=/usr/local/www/wise ETCDIR=/usr/local/etc/wise --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=1400082 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-- =================================================== ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-amd64-default-job-01] Installing pkg-1.19.1_1... [main-amd64-default-job-01] Extracting pkg-1.19.1_1: .......... done ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gaplib.c -o gaplib.o --- mott_api.o --- mott_api.c:64:3: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] free(freq0); ^ mott_api.c:64:3: note: include the header or explicitly provide a declaration for 'free' mott_api.c:179:16: warning: call to undeclared library function 'calloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^ mott_api.c:179:16: note: include the header or explicitly provide a declaration for 'calloc' mott_api.c:207:12: warning: call to undeclared library function 'toupper' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] freq[toupper(seq[n])]++; ^ mott_api.c:207:12: note: include the header or explicitly provide a declaration for 'toupper' 3 warnings generated. --- wise2_mott_bridge.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c --- libmott.a --- ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: warning: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi (cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisesocket.a ) --- functionserver.o --- --- functionclient.o --- --- functionserver.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionserver.c --- functionclient.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionclient.c functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types] connect(out->socket, &server, sizeof(server)); ^~~~~~~ /usr/include/sys/socket.h:686:41: note: passing argument to parameter here int connect(int, const struct sockaddr *, socklen_t); ^ 1 warning generated. --- anonobj.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ anonobj.c --- transferinterface.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transferinterface.c --- directsocketwrite.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ directsocketwrite.c --- libwisesocket.a --- ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: warning: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) --- kmer_assembly.o --- --- kmer_index_interface.o --- --- kmer_assembly.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c --- kmer_index_interface.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c --- kmer_assembly.o --- kmer_assembly.dy:296:44: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly.dy:302:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly.dy:309:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ~~~ ^~~ kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ~^ --- kmer_direct.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c --- kmer_hash.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy:318:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); ~~~~~~ ^~~~~~~~~~~~~ %016llx kmer_hash.dy:319:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); ~~~~~~ ^~~~~~~~~~~~~ %016llx --- kmer_assembly.o --- 5 warnings generated. --- kmer_count.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c --- kmer_hash.o --- 2 warnings generated. --- kmer_glib_index.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c --- singleseqspace.o --- --- dnamapping.o --- --- singleseqspace.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c --- dnamapping.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c --- largeseqreader.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c --- kmer_assembly_untangler.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c --- kmer_assembly_contig.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c --- kmer_assembly_untangler.o --- kmer_assembly_untangler.dy:52:65: warning: cast to smaller integer type 'int' from 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wpointer-to-int-cast] fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); ^~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:120:80: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:141:71: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:141:99: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:157:73: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:159:69: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:444:89: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); ~~~ ^~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long[10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^~~~~~~~~~~~~~~~~ ./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ kmer_assembly_untangler.dy:746:149: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:746:182: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld --- kmer_assembly_error.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy:93:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_error.dy:105:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat] fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); ~~ ^~~~~~~~~~~~ --- kmer_assembly_untangler.o --- 10 warnings generated. --- assembly.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly.c --- kmer_assembly_error.o --- 3 warnings generated. --- assembly_stream_interface.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c --- assembly_stream_fasta.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c --- assembly_sanger_project.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c --- assembly_stream_cons.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c --- compressed_protein_index.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy:223:10: error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion] return NULL; ^~~~ /usr/include/sys/_null.h:34:14: note: expanded from macro 'NULL' #define NULL ((void *)0) ^~~~~~~~~~~ 1 error generated. *** [compressed_protein_index.o] Error code 1 make[2]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/dnaindex 1 error make[2]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/dnaindex *** [realall] Error code 2 make[1]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src 1 error make[1]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/wise