Date: Thu, 20 Aug 2020 08:52:46 GMT From: pkg-fallout@FreeBSD.org To: jrm@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][biology/paml] Failed for paml-4.9j in build Message-ID: <202008200852.07K8qkBv056985@beefy17.nyi.freebsd.org>
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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: jrm@FreeBSD.org Last committer: jrm@FreeBSD.org Ident: $FreeBSD: head/biology/paml/Makefile 518150 2019-11-22 15:32:40Z jrm $ Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p545479_s364329/logs/paml-4.9j.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p545479_s364329 Log: =>> Building biology/paml build started at Thu Aug 20 08:52:31 UTC 2020 port directory: /usr/ports/biology/paml package name: paml-4.9j building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 i386 maintained by: jrm@FreeBSD.org Makefile ident: $FreeBSD: head/biology/paml/Makefile 518150 2019-11-22 15:32:40Z jrm $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300109 Job Id: 05 !!! Jail is newer than host. (Jail: 1300109, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1300109 UNAME_v=FreeBSD 13.0-CURRENT 1300109 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-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 paml-4.9j: 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-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/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 -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="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml --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 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300109 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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> paml-4.9j depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-i386-default-job-05] Installing pkg-1.14.7... [head-i386-default-job-05] Extracting pkg-1.14.7: .......... done ===> paml-4.9j depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.9j =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9j for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9j for building => SHA256 Checksum OK for paml4.9j.tgz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9j for building ===> Extracting for paml-4.9j => SHA256 Checksum OK for paml4.9j.tgz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for paml-4.9j ===> Converting DOS text files to UNIX text files =========================================================================== =======================<phase: build-depends >============================ ===> paml-4.9j depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [head-i386-default-job-05] Installing gmake-4.3_2... [head-i386-default-job-05] `-- Installing gettext-runtime-0.21... [head-i386-default-job-05] | `-- Installing indexinfo-0.3.1... [head-i386-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done [head-i386-default-job-05] `-- Extracting gettext-runtime-0.21: .......... done [head-i386-default-job-05] Extracting gmake-4.3_2: .......... done ===> paml-4.9j depends on package: gmake>=4.3 - found ===> Returning to build of paml-4.9j =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for paml-4.9j =========================================================================== =======================<phase: build >============================ ===> Building for paml-4.9j gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/paml/work/paml4.9j/src' cc -O3 -o baseml baseml.c tools.c -lm In file included from baseml.c:131: ./treesub.c:86:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] zt = (char*)malloc(com.ls*lpatt * sizeof(char)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./treesub.c:105:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:105:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:143:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:143:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:256:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] zt = (char*)malloc(npatt0*lpatt * sizeof(char)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./treesub.c:280:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:280:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:313:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:313:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:1310:30: warning: incompatible pointer types passing 'char *[7000]' to parameter of type 'unsigned char **' [-Wincompatible-pointer-types] printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); ^~~~~~~~~~ ./paml.h:150:63: note: passing argument to parameter 'spnames' here void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); ^ In file included from baseml.c:131: ./treesub.c:1404:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] zt = (char*)malloc(com.ls*lpatt * sizeof(char)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./treesub.c:1427:27: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:1427:41: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:1476:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~ /usr/include/string.h:82:25: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:1476:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt); ^~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:82:39: note: passing argument to parameter here int strcmp(const char *, const char *) __pure; ^ In file included from baseml.c:131: ./treesub.c:4650:37: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign] for (i = 0; i < ns0; i++) z0[i] = com.z[i]; ^ ~~~~~~~~ ./treesub.c:4775:24: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign] FOR(i, ns0) { z0[i] = com.z[i]; spname0[i] = com.spname[i]; } ^ ~~~~~~~~ ./treesub.c:4790:19: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] com.z[i] = z0[order[i]]; ^ ~~~~~~~~~~~~ ./treesub.c:5897:23: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign] print1seq(fout, zanc + j*com.npatt, lst, com.pose); ^~~~~~~~~~~~~~~~~~ ./treesub.c:1861:41: note: passing argument to parameter 'z' here int print1seq(FILE*fout, unsigned char *z, int ls, int pose[]) ^ ./treesub.c:8695:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pch = strchr(nodes[i].annotation, '#')) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./treesub.c:8695:15: note: place parentheses around the assignment to silence this warning if (pch = strchr(nodes[i].annotation, '#')) ^ ( ) ./treesub.c:8695:15: note: use '==' to turn this assignment into an equality comparison if (pch = strchr(nodes[i].annotation, '#')) ^ == ./treesub.c:8843:30: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign] data.z[locus][i] = com.z[i]; ^ ~~~~~~~~ ./treesub.c:9087:42: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] for (i = 0; i < com.ns; i++) com.z[i] = data.z[locus][i]; ^ ~~~~~~~~~~~~~~~~ 23 warnings generated. ld: error: duplicate symbol: OutTreeOptions >>> defined at baseml.c >>> /tmp/baseml-cb2243.o:(OutTreeOptions) >>> defined at tools.c >>> /tmp/tools-352a72.o:(.bss+0xAFCD90) ld: error: duplicate symbol: SeqTypes >>> defined at baseml.c >>> /tmp/baseml-cb2243.o:(SeqTypes) >>> defined at tools.c >>> /tmp/tools-352a72.o:(.bss+0xAFCD8C) cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [Makefile:12: baseml] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml4.9j/src' *** Error code 2 Stop. make: stopped in /usr/ports/biology/paml
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