Date: Sun, 17 Jan 2021 02:08:55 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 121arm64-quarterly][biology/bowtie2] Failed for bowtie2-2.4.2 in build Message-ID: <202101170208.10H28tNj035627@ampere1.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: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: branches/2021Q1/biology/bowtie2/Makefile 554390 2020-11-07 13:47:41Z jwb $ Log URL: http://ampere1.nyi.freebsd.org/data/121arm64-quarterly/561759/logs/bowtie2-2.4.2.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=561759 Log: =>> Building biology/bowtie2 build started at Sun Jan 17 02:08:05 UTC 2021 port directory: /usr/ports/biology/bowtie2 package name: bowtie2-2.4.2 building for: FreeBSD 121arm64-quarterly-job-07 12.1-RELEASE FreeBSD 12.1-RELEASE arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2021Q1/biology/bowtie2/Makefile 554390 2020-11-07 13:47:41Z jwb $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300134 Jail OSVERSION: 1201000 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE UNAME_r=12.1-RELEASE 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=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/121arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=121arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/121arm64-quarterly/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 bowtie2-2.4.2: 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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -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-- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=12.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie2 DOCSDIR=/usr/local/share/doc/bowtie2 EXAMPLESDIR=/usr/local/share/examples/bowtie2 WWWDIR=/usr/local/www/bowtie2 ETCDIR=/usr/local/etc/bowtie2 --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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.1-RELEASE OSREL=12.1 OSVERSION=1201000 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-- =======================<phase: check-sanity >============================ ===> License GPLv3+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bowtie2-2.4.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.1.txz [121arm64-quarterly-job-07] Installing pkg-1.16.1... [121arm64-quarterly-job-07] Extracting pkg-1.16.1: .......... done ===> bowtie2-2.4.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie2-2.4.2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.4.2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.4.2 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.2_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.4.2 for building ===> Extracting for bowtie2-2.4.2 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.2_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bowtie2-2.4.2 ===> Applying FreeBSD patches for bowtie2-2.4.2 from /usr/ports/biology/bowtie2/files =========================================================================== =======================<phase: build-depends >============================ ===> bowtie2-2.4.2 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [121arm64-quarterly-job-07] Installing gmake-4.3_2... [121arm64-quarterly-job-07] `-- Installing gettext-runtime-0.21... [121arm64-quarterly-job-07] | `-- Installing indexinfo-0.3.1... [121arm64-quarterly-job-07] | `-- Extracting indexinfo-0.3.1: .... done [121arm64-quarterly-job-07] `-- Extracting gettext-runtime-0.21: .......... done [121arm64-quarterly-job-07] Extracting gmake-4.3_2: .......... done ===> bowtie2-2.4.2 depends on package: gmake>=4.3 - found ===> Returning to build of bowtie2-2.4.2 ===> bowtie2-2.4.2 depends on file: /usr/local/bin/python3.7 - not found ===> Installing existing package /packages/All/python37-3.7.9_1.txz [121arm64-quarterly-job-07] Installing python37-3.7.9_1... [121arm64-quarterly-job-07] `-- Installing libffi-3.3_1... [121arm64-quarterly-job-07] `-- Extracting libffi-3.3_1: .......... done [121arm64-quarterly-job-07] `-- Installing readline-8.0.4... [121arm64-quarterly-job-07] `-- Extracting readline-8.0.4: .......... done <snip> third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 9 warnings and 2 errors generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:59: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 9 warnings and 2 errors generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:59: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 9 warnings and 2 errors generated. gmake[1]: *** [Makefile:346: bowtie2-build-s] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: *** [Makefile:354: bowtie2-build-l] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.4.2' ===> 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/bowtie2
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