From nobody Mon Jun 26 12:51:58 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 4QqSR24zjMz4jtWY for ; Mon, 26 Jun 2023 12:51:58 +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 4QqSR21yMQz4L3T for ; Mon, 26 Jun 2023 12:51:58 +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=1687783918; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=NPpoYKXRPfZa3n1Q73qlNKiisgNL7QT/kk0mXViX0hE=; b=uTIX4KoKLTmGbN8MjzptKMUePHcu4FwVwhqBuaryK3u8RvANgVTmqJEIVdAXmWjbzQEBvW 4dBLEEp7gU8LrTHKMRNtJciW3uWi3I0iiZZF7bPWyoaMBsBZh852rwMq+mcU5X6FQjuBpT uB7FAPSwZa09XT9cHN1n8yIxdLgbZI2cZQBs3cAaDzPj1zy1pwxp/ehp+nipKrLf5Skisn y/QMXiAjIRvn6w0j5cp9hrGRI1jODVXbeQtoXsec4e+wp7lM2SsgQHm1JBpj8qf4hva8Eg qJyAhBY1yrWCIA4tjafQGQH76XYEr1PQaV+DoaiRTicmxjJTEun4y3TuuRsUFw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1687783918; a=rsa-sha256; cv=none; b=Du4rHle/8a58AcB+PTn6UOoQ0CqCCrgnnZrNOK3aMt1eFHI5u2+LrJTVqsOpsdrugLxrWW 5yRwGzRAemi5XIeDd6mEMK37SBGutPGPzmnIyojA4PzlGLc7my3xfbmvrHGmv45h24fdN9 A9QM1zn6j8mpZyarjeuTJAFJttC/8S8k/xTu0UEB5xjb2s9l1vvNSb8j/JhyA9xOlygme/ RSS1iw1jRsCsiMEi6eScNq+IDSifRUL2zYRfxuWGejU3o+aek5EFZscZ4j+MXQLVaT8Cuf vRDxd92lJxOwWw6MARiyb+gS/0+fvk0nnzm23DD0qSNs/jkrwK/Ptf8h6v4MxA== Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:20]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QqSR21396z19jt for ; Mon, 26 Jun 2023 12:51:58 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 23c2 by beefy17.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy17.nyi.freebsd.org); Mon, 26 Jun 2023 12:51:58 +0000 To: jwb@FreeBSD.org Subject: [package - main-i386-default][biology/haplohseq] Failed for haplohseq-0.1.2_8 in build Cc: pkg-fallout@FreeBSD.org Date: Mon, 26 Jun 2023 12:51:58 +0000 Message-Id: <649989ee.23c2.2dee7e21@beefy17.nyi.freebsd.org> From: 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: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p4785b313b958_se8efee297c/logs/haplohseq-0.1.2_8.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p4785b313b958_se8efee297c Log: =>> Building biology/haplohseq build started at Mon Jun 26 12:51:45 UTC 2023 port directory: /usr/ports/biology/haplohseq package name: haplohseq-0.1.2_8 building for: FreeBSD main-i386-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 i386 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400091 Job Id: 09 !!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=i386 UNAME_m=i386 OSVERSION=1400091 UNAME_v=FreeBSD 14.0-CURRENT 1400091 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-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-i386-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 haplohseq-0.1.2_8: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/haplohseq/work/.cache HOME=/wrkdirs/usr/ports/biology/haplohseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/haplohseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/haplohseq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- STRIP=-s XDG_DATA_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/haplohseq/work/.cache HOME=/wrkdirs/usr/ports/biology/haplohseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/haplohseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/haplohseq/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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/haplohseq" EXAMPLESDIR="share/examples/haplohseq" DATADIR="share/haplohseq" WWWDIR="www/haplohseq" ETCDIR="etc/haplohseq" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/haplohseq DOCSDIR=/usr/local/share/doc/haplohseq EXAMPLESDIR=/usr/local/share/examples/haplohseq WWWDIR=/usr/local/www/haplohseq ETCDIR=/usr/local/etc/haplohseq --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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: i386-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" "-m" "elf_i386_fbsd" "-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 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400091 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) 524288 stack size (kbytes, -s) 65536 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-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> haplohseq-0.1.2_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-i386-default-job-09] Installing pkg-1.19.1_1... [main-i386-default-job-09] Extracting pkg-1.19.1_1: .......... done ===> haplohseq-0.1.2_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of haplohseq-0.1.2_8 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by haplohseq-0.1.2_8 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by haplohseq-0.1.2_8 for building => SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by haplohseq-0.1.2_8 for building ===> Extracting for haplohseq-0.1.2_8 => SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for haplohseq-0.1.2_8 ===> Applying FreeBSD patches for haplohseq-0.1.2_8 from /usr/ports/biology/haplohseq/files =========================================================================== =================================================== ===> haplohseq-0.1.2_8 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-i386-default-job-09] Installing gmake-4.3_2... [main-i386-default-job-09] `-- Installing gettext-runtime-0.21.1... [main-i386-default-job-09] | `-- Installing indexinfo-0.3.1... [main-i386-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done [main-i386-default-job-09] `-- Extracting gettext-runtime-0.21.1: .......... done [main-i386-default-job-09] Extracting gmake-4.3_2: .......... done ===> haplohseq-0.1.2_8 depends on package: gmake>=4.3 - found ===> Returning to build of haplohseq-0.1.2_8 ===> haplohseq-0.1.2_8 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.17.pkg [main-i386-default-job-09] Installing python39-3.9.17... [main-i386-default-job-09] `-- Installing libffi-3.4.4... [main-i386-default-job-09] `-- Extracting libffi-3.4.4: .......... done [main-i386-default-job-09] `-- Installing mpdecimal-2.5.1... [main-i386-default-job-09] `-- Extracting mpdecimal-2.5.1: .......... done [main-i386-default-job-09] `-- Installing readline-8.2.1... [main-i386-default-job-09] `-- Extracting readline-8.2.1: .......... done [main-i386-default-job-09] Extracting python39-3.9.17: .......... done ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> haplohseq-0.1.2_8 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of haplohseq-0.1.2_8 =========================================================================== =================================================== ===> haplohseq-0.1.2_8 depends on shared library: libboost_system.so - not found ===> Installing existing package /packages/All/boost-libs-1.82.0_1.pkg [main-i386-default-job-09] Installing boost-libs-1.82.0_1... [main-i386-default-job-09] `-- Installing icu-73.2,1... [main-i386-default-job-09] `-- Extracting icu-73.2,1: .......... done [main-i386-default-job-09] Extracting boost-libs-1.82.0_1: .......... done ===== Message from boost-libs-1.82.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> haplohseq-0.1.2_8 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Returning to build of haplohseq-0.1.2_8 =========================================================================== =================================================== ===> Configuring for haplohseq-0.1.2_8 =========================================================================== =================================================== ===> Building for haplohseq-0.1.2_8 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/haplohseq/work/haplohseq-0.1.2' mkdir -p build build/bin build/obj mkdir -p build/test cp -r src/test/resources build/test c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp src/util/StringUtil.cpp:51:76: error: no member named 'ptr_fun' in namespace 'std' s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun(std::isspace)))); ~~~~~^ src/util/StringUtil.cpp:51:87: error: expected '(' for function-style cast or type construction s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun(std::isspace)))); ~~~^ src/util/StringUtil.cpp:51:92: error: expected '(' for function-style cast or type construction s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun(std::isspace)))); ~~~^ src/util/StringUtil.cpp:57:67: error: no member named 'ptr_fun' in namespace 'std' s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun(std::isspace))).base(), s.end()); ~~~~~^ src/util/StringUtil.cpp:57:78: error: expected '(' for function-style cast or type construction s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun(std::isspace))).base(), s.end()); ~~~^ src/util/StringUtil.cpp:57:83: error: expected '(' for function-style cast or type construction s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun(std::isspace))).base(), s.end()); ~~~^ 6 errors generated. gmake[1]: *** [makefile:51: build/obj/StringUtil.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/haplohseq/work/haplohseq-0.1.2' ===> 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/haplohseq