From owner-freebsd-pkg-fallout@freebsd.org Tue Aug 25 16:26:14 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 170243B0812 for ; Tue, 25 Aug 2020 16:26:14 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 4BbZ9y0663z4dmg for ; Tue, 25 Aug 2020 16:26:14 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 01C0E3B0810; Tue, 25 Aug 2020 16:26:14 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 018323B04B3 for ; Tue, 25 Aug 2020 16:26:14 +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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4BbZ9x6dvlz4dWY; Tue, 25 Aug 2020 16:26:13 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f2]) (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 C82672CBFF; Tue, 25 Aug 2020 16:26:13 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy17.nyi.freebsd.org (localhost [127.0.0.1]) by beefy17.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 07PGQDLS032127; Tue, 25 Aug 2020 16:26:13 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy17.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 07PGQD5F032126; Tue, 25 Aug 2020 16:26:13 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 25 Aug 2020 16:26:13 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202008251626.07PGQD5F032126@beefy17.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - head-i386-default][biology/cufflinks] Failed for cufflinks-2.2.1.89_1 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 25 Aug 2020 16:26:14 -0000 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 Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $ Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p546132_s364744/logs/cufflinks-2.2.1.89_1.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p546132_s364744 Log: =>> Building biology/cufflinks build started at Tue Aug 25 16:21:50 UTC 2020 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.89_1 building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 i386 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300111 Job Id: 05 !!! Jail is newer than host. (Jail: 1300111, 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=1300111 UNAME_v=FreeBSD 13.0-CURRENT 1300111 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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/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 -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " 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-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --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-rc2-0-g414f32a9e86) 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-rc2-0-g414f32a9e86) 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-rc2-0-g414f32a9e86) 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=1300111 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 BSL accepted by the user =========================================================================== =================================================== ===> cufflinks-2.2.1.89_1 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 ===> cufflinks-2.2.1.89_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.89_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building =========================================================================== =================================================== ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building ===> Extracting for cufflinks-2.2.1.89_1 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for cufflinks-2.2.1.89_1 ===> Applying distribution patches for cufflinks-2.2.1.89_1 ===> Applying FreeBSD patches for cufflinks-2.2.1.89_1 from /usr/ports/biology/cufflinks/files =========================================================================== =================================================== ===> cufflinks-2.2.1.89_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.7.txz [head-i386-default-job-05] Installing eigen-3.3.7... In file included from /usr/local/include/boost/math/special_functions/erf.hpp:15: In file included from /usr/local/include/boost/math/special_functions/gamma.hpp:24: In file included from /usr/local/include/boost/math/constants/constants.hpp:13: In file included from /usr/local/include/boost/math/tools/convert_from_string.hpp:15: In file included from /usr/local/include/boost/lexical_cast.hpp:30: In file included from /usr/local/include/boost/range/iterator_range_core.hpp:38: In file included from /usr/local/include/boost/range/functions.hpp:20: In file included from /usr/local/include/boost/range/size.hpp:25: In file included from /usr/local/include/boost/utility.hpp:21: /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1541:60: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here boost::shared_ptr disperser = boost::shared_ptr(new PoissonDispersionModel("")); ^ In file included from gtf_to_sam.cpp:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ gtf_to_sam.cpp:142:86: warning: format specifies type 'int' but the argument has type 'RefID' (aka 'unsigned long long') [-Wformat] fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id()); ~~ ^~~~~~~~~~~~~~ %llu In file included from gtf_to_sam.cpp:23: In file included from ./bundles.h:16: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine::seed' requested here { lcf.seed(cnv(x0)); } ^ 3 warnings generated. mv -f .deps/gtf_to_sam.Tpo .deps/gtf_to_sam.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT compress_gtf.o -MD -MP -MF .deps/compress_gtf.Tpo -c -o compress_gtf.o compress_gtf.cpp In file included from compress_gtf.cpp:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from compress_gtf.cpp:24: In file included from ./bundles.h:16: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine::seed' requested here { lcf.seed(cnv(x0)); } ^ In file included from compress_gtf.cpp:29: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 14 warnings generated. mv -f .deps/cuffdiff.Tpo .deps/cuffdiff.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gffread.o -MD -MP -MF .deps/gffread.Tpo -c -o gffread.o gffread.cpp mv -f .deps/gffread.Tpo .deps/gffread.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffquant.o -MD -MP -MF .deps/cuffquant.Tpo -c -o cuffquant.o cuffquant.cpp 3 warnings generated. mv -f .deps/compress_gtf.Tpo .deps/compress_gtf.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffnorm.o -MD -MP -MF .deps/cuffnorm.Tpo -c -o cuffnorm.o cuffnorm.cpp In file included from cuffquant.cpp:19: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cuffnorm.cpp:18: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cuffquant.cpp:24: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cuffnorm.cpp:23: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cuffquant.cpp:37: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cuffquant.cpp:742:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ cuffquant.cpp:760:25: warning: unused variable 'ab_group' [-Wunused-variable] const AbundanceGroup& ab_group = abundances[i]->transcripts; ^ In file included from cuffnorm.cpp:38: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cuffquant.cpp:1513:34: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(buf, "q%lu", i); ~~~ ^ %u cuffquant.cpp:1536:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] srand48(random_seed); ^ cuffquant.cpp:1531:5: note: previous statement is here if (random_seed == -1) ^ In file included from cuffnorm.cpp:38: ./differential.h:215:5: warning: field 'sample_labels' will be initialized after field 'headers_written' [-Wreorder-ctor] sample_labels(sls), ^ ./differential.h:614:56: warning: more '%' conversions than data arguments [-Wformat] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ~~^ In file included from cuffnorm.cpp:41: ./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined] #define MAX(a,b) (((a)>(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:311:9: note: previous definition is here #define MAX(a,b) (((a)>(b))?(a):(b)) ^ In file included from cuffnorm.cpp:41: ./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined] #define MIN(a,b) (((a)<(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:310:9: note: previous definition is here #define MIN(a,b) (((a)<(b))?(a):(b)) ^ In file included from cuffquant.cpp:20: In file included from ./bundles.h:16: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine::seed' requested here { lcf.seed(cnv(x0)); } ^ cuffnorm.cpp:1186:38: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(buf, "q%lu", i); ~~~ ^ %u cuffnorm.cpp:1210:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] srand48(random_seed); ^ cuffnorm.cpp:1205:5: note: previous statement is here if (random_seed == -1) ^ In file included from cuffnorm.cpp:19: In file included from ./bundles.h:16: In file included from /usr/local/include/boost/random.hpp:36: In file included from /usr/local/include/boost/random/additive_combine.hpp:27: /usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if(_x <= 0 && _x != 0) { ~~~~~~~~^~~~~~~~~~ /usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine::seed' requested here { lcf.seed(cnv(x0)); } ^ 10 warnings generated. mv -f .deps/cuffnorm.Tpo .deps/cuffnorm.Po rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o ranlib libcufflinks.a rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ranlib libgc.a c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz ld: error: duplicate symbol: curwin >>> defined at startlf.c:236 (locfit/startlf.c:236) >>> startlf.o:(curwin) in archive libcufflinks.a >>> defined at c_plot.c:12 (locfit/c_plot.c:12) >>> c_plot.o:(.bss+0x0) in archive libcufflinks.a c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:804: cufflinks] Error 1 gmake[3]: *** Waiting for unfinished jobs.... 8 warnings generated. mv -f .deps/cuffquant.Tpo .deps/cuffquant.Po gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[2]: *** [Makefile:402: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[1]: *** [Makefile:343: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' ===> 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/cufflinks