=> Building biology/plink Started : Sunday, 8 OCT 2017 at 19:52:20 UTC Platform: 4.9-DEVELOPMENT DragonFly v4.9.0.699.g39a93-DEVELOPMENT #22: Tue Sep 19 22:06:52 PDT 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.1-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.1-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- 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=/construction/biology/plink XDG_CONFIG_HOME=/construction/biology/plink HOME=/construction/biology/plink TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/biology/plink XDG_CONFIG_HOME=/construction/biology/plink HOME=/construction/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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/plink/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.1 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500100 OSVERSION=9999999 OSREL=5.1 _OSRELEASE=5.1-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> 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 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plink-1.07_7 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for plink-1.07_7 ===> Applying ports patches for plink-1.07_7 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> plink-1.07_7 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.4.0_4.txz Installing gcc5-5.4.0_4... `-- 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-3.1.6... | `-- Extracting mpfr-3.1.6: .......... done `-- Extracting mpc-1.0.3: ...... done Extracting gcc5-5.4.0_4: .......... done Message from gcc5-5.4.0_4: 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 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> 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 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for plink-1.07_7 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for plink-1.07_7 gmake[1]: Entering directory '/construction/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 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 */ ^ 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 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 '/construction/biology/plink/plink-1.07-src' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> plink-1.07_7 depends on executable: gfortran5 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for plink-1.07_7 ===> Generating temporary packing list /bin/mkdir -p /construction/biology/plink/stage/usr/local/bin install -s -m 555 /construction/biology/plink/plink-1.07-src/plink /construction/biology/plink/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for plink-1.07_7 file sizes/checksums [4]: . done packing files [4]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 8 OCT 2017 at 19:55:13 UTC Duration: 00:02:53