=> Building biology/plink build started at Mon Sep 18 18:49:38 PDT 2017 port directory: /usr/ports/biology/plink building for: DragonFly pkgbox64.dragonflybsd.org 4.9-DEVELOPMENT DragonFly v4.9.0.503.g33553-DEVELOPMENT #21: Fri Aug 4 16:51:32 PDT 2017 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../07//usr/ports/biology/plink/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400908 Jail OSVERSION: 400801 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release48-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=plink-1.07_7 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool MASTERNAME=Release48-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/plink XDG_CONFIG_HOME=/wrkdirs/biology/plink HOME=/wrkdirs/biology/plink TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/biology/plink XDG_CONFIG_HOME=/wrkdirs/biology/plink HOME=/wrkdirs/biology/plink TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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-- OSREL=4.8 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/plink" EXAMPLESDIR="share/examples/plink" DATADIR="share/plink" WWWDIR="www/plink" ETCDIR="etc/plink" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plink DOCSDIR=/usr/local/share/doc/plink EXAMPLESDIR=/usr/local/share/examples/plink WWWDIR=/usr/local/www/plink ETCDIR=/usr/local/etc/plink --End SUB_LIST-- ---Begin make.conf--- NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> plink-1.07_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> plink-1.07_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plink-1.07_7 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plink-1.07_7 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plink-1.07_7 for building => SHA256 Checksum OK for plink-1.07-src.zip. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plink-1.07_7 for building ===> Extracting for plink-1.07_7 => SHA256 Checksum OK for plink-1.07-src.zip. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for plink-1.07_7 ===> Applying ports patches for plink-1.07_7 =========================================================================== =================================================== ===> plink-1.07_7 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.4.0_3.txz Installing gcc5-5.4.0_3... `-- Installing binutils-2.28,1... | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.2.6... | | `-- Extracting indexinfo-0.2.6: .... done | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done `-- Extracting binutils-2.28,1: .......... done `-- Installing gmp-6.1.2... `-- Extracting gmp-6.1.2: .......... done `-- Installing mpc-1.0.3... | `-- Installing mpfr-3.1.5_1... | `-- Extracting mpfr-3.1.5_1: .......... done `-- Extracting mpc-1.0.3: ...... done Extracting gcc5-5.4.0_3: .......... done Message from gcc5-5.4.0_3: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> plink-1.07_7 depends on executable: gfortran5 - found ===> Returning to build of plink-1.07_7 ===> plink-1.07_7 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... Extracting gmake-4.2.1_1: .......... done ===> plink-1.07_7 depends on executable: gmake - found ===> Returning to build of plink-1.07_7 ===> plink-1.07_7 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== ===> plink-1.07_7 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.5.0_3.txz Installing lapack-3.5.0_3... `-- Installing blas-3.5.0_3... `-- Extracting blas-3.5.0_3: ....... done Extracting lapack-3.5.0_3: .......... done ===> plink-1.07_7 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of plink-1.07_7 =========================================================================== =================================================== ===> Configuring for plink-1.07_7 =========================================================================== =================================================== ===> Building for plink-1.07_7 gmake[1]: Entering directory '/wrkdirs/biology/plink/plink-1.07-src' c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c plink.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c options.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c input.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c binput.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tinput.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genome.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c helper.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c stats.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c filters.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c locus.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multi.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c crandom.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cluster.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mds.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c output.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c informative.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c assoc.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c epi.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c prephap.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c phase.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c trio.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tdt.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sharing.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genepi.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sets.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c perm.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mh.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genedrop.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gxe.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c merge.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hotel.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multiple.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploCC.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploTDT.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c poo.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c webcheck.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qfam.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linear.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c bmerge.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c parse.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mishap.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c legacy.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c homozyg.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c segment.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c model.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c logistic.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c glm.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dcdflib.cpp dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c elf.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dfam.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c fisher.cpp fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:501:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] prterr(20, "This should never occur."); ^ c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linput.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sockets.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c proxy.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c pdriver.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploQTL.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplohelper.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplowindow.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genogroup.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nonfounderphasing.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c clumpld.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genoerr.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c em.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c impute.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaem.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c profile.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nlist.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c whap.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c simul.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gvar.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnv.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c step.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c greport.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c flip.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qualscores.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnvqt.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cfamily.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c setscreen.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c idhelp.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tag.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hapglm.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup2.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c blox.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zed.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dosage.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c annot.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaanal.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c r.cpp In file included from r.cpp:29:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c Rconnection.cpp In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:11: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^ c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zfstream.cpp c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lapackf.cpp lapackf.cpp: In function 'bool svd_lapack(int, vector_t&, vector_t&, matrix_t&)': lapackf.cpp:58:104: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &optim_lwork, &lwork, &iwork[0], &info); ^ lapackf.cpp:63:100: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &work[0], &lwork, &iwork[0], &info); ^ lapackf.cpp: In function 'bool eigen_lapack(int, vector_t&, vector_t&, matrix_t&)': lapackf.cpp:132:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] &info ); ^ lapackf.cpp:132:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] lapackf.cpp:132:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] lapackf.cpp:158:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] &info ); ^ lapackf.cpp:158:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] lapackf.cpp:158:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] c++ -pipe -O2 -fno-strict-aliasing -I. -DUNIX -Dfopen64=fopen -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o lapackf.o -lcrypt -lz -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -llapack -lblas gmake[1]: Leaving directory '/wrkdirs/biology/plink/plink-1.07-src' =========================================================================== =================================================== ===> plink-1.07_7 depends on executable: gfortran5 - found =========================================================================== =================================================== ===> Staging for plink-1.07_7 ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/biology/plink/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/plink/plink-1.07-src/plink /wrkdirs/biology/plink/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for plink-1.07_7 file sizes/checksums [4]: . done packing files [4]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for plink-1.07_7 build of biology/plink ended at Mon Sep 18 18:55:10 PDT 2017 build time: 00:05:32