=> Building biology/p5-Bio-SCF Started : Wednesday, 18 APR 2018 at 15:56:41 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-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 -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-Bio-SCF XDG_CONFIG_HOME=/construction/biology/p5-Bio-SCF HOME=/construction/biology/p5-Bio-SCF TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-SCF/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- INSTALLDIRS="site" CC="cc" CCFLAGS="-pipe -I/usr/local/include -O2 -fno-strict-aliasing" LD="cc" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib" -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-Bio-SCF XDG_CONFIG_HOME=/construction/biology/p5-Bio-SCF HOME=/construction/biology/p5-Bio-SCF TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-SCF/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -I/usr/local/include -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -I/usr/local/include -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/p5-Bio-SCF/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.1 PERL_VER=5.26 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/5.26 PROFILE="@comment " DOCSDIR="share/doc/Bio-SCF" EXAMPLESDIR="share/examples/Bio-SCF" DATADIR="share/Bio-SCF" WWWDIR="www/Bio-SCF" ETCDIR="etc/Bio-SCF" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Bio-SCF DOCSDIR=/usr/local/share/doc/Bio-SCF EXAMPLESDIR=/usr/local/share/examples/Bio-SCF WWWDIR=/usr/local/www/Bio-SCF ETCDIR=/usr/local/etc/Bio-SCF -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 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=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> p5-Bio-SCF-1.03_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> p5-Bio-SCF-1.03_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-Bio-SCF-1.03_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by p5-Bio-SCF-1.03_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by p5-Bio-SCF-1.03_1 for building => SHA256 Checksum OK for Bio-SCF-1.03.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by p5-Bio-SCF-1.03_1 for building ===> Extracting for p5-Bio-SCF-1.03_1 => SHA256 Checksum OK for Bio-SCF-1.03.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-Bio-SCF-1.03_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-Bio-SCF-1.03_1 depends on file: /usr/local/include/io_lib/scf.h - not found ===> Installing existing package /packages/All/io_lib-1.14.9.txz Installing io_lib-1.14.9... `-- Installing curl-7.59.0... | `-- Installing ca_root_nss-3.36... | `-- Extracting ca_root_nss-3.36: ........ done | `-- Installing krb5-1.16_1... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.6.4... | | `-- Extracting libressl-2.6.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16_1: .......... done | `-- Installing libnghttp2-1.31.0... | `-- Extracting libnghttp2-1.31.0: .......... done `-- Extracting curl-7.59.0: .......... done Extracting io_lib-1.14.9: .......... done Message from ca_root_nss-3.36: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> p5-Bio-SCF-1.03_1 depends on file: /usr/local/include/io_lib/scf.h - found ===> Returning to build of p5-Bio-SCF-1.03_1 ===> p5-Bio-SCF-1.03_1 depends on package: perl5>=5.26<5.27 - not found ===> Installing existing package /packages/All/perl5-5.26.1.txz Installing perl5-5.26.1... Extracting perl5-5.26.1: .......... done Message from perl5-5.26.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> p5-Bio-SCF-1.03_1 depends on package: perl5>=5.26<5.27 - found ===> Returning to build of p5-Bio-SCF-1.03_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-Bio-SCF-1.03_1 Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::SCF Writing MYMETA.yml and MYMETA.json -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-Bio-SCF-1.03_1 --- blib/lib/Bio/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/SCF/.exists --- --- blib/arch/auto/Bio/SCF/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- SCF.c --- "/usr/local/bin/perl5.26.1" "/usr/local/lib/perl5/5.26/ExtUtils/xsubpp" -typemap '/usr/local/lib/perl5/5.26/ExtUtils/typemap' SCF.xs > SCF.xsc --- SCF.bs --- Running Mkbootstrap for SCF () --- pm_to_blib --- --- SCF.bs --- chmod 644 "SCF.bs" --- blib/arch/auto/Bio/SCF/SCF.bs --- "/usr/local/bin/perl5.26.1" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644 --- blibdirs --- --- config --- --- pm_to_blib --- cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm cp SCF.pm blib/lib/Bio/SCF.pm --- SCF.c --- Please specify prototyping behavior for SCF.xs (see perlxs manual) mv SCF.xsc SCF.c --- SCF.o --- cc -c -pipe -I/usr/local/include -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DVERSION=\"1.03\" -DXS_VERSION=\"1.03\" -DPIC -fPIC "-I/usr/local/lib/perl5/5.26/mach/CORE" -DLITTLE_ENDIAN SCF.c In file included from /usr/local/lib/perl5/5.26/mach/CORE/perl.h:5644:0, from SCF.xs:5: SCF.xs: In function 'XS_Bio__SCF_get_scf_pointer': SCF.xs:57:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ret_val = newSViv((int)scf_data); ^ /usr/local/lib/perl5/5.26/mach/CORE/embed.h:413:40: note: in definition of macro 'newSViv' #define newSViv(a) Perl_newSViv(aTHX_ a) ^ SCF.xs: In function 'XS_Bio__SCF_get_scf_fpointer': SCF.xs:80:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ret_val = newSViv((int)scf_data); ^ /usr/local/lib/perl5/5.26/mach/CORE/embed.h:413:40: note: in definition of macro 'newSViv' #define newSViv(a) Perl_newSViv(aTHX_ a) ^ SCF.xs: In function 'XS_Bio__SCF_scf_free': SCF.xs:89:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] scf_deallocate((Scf *)scf_pointer); ^ SCF.xs: In function 'XS_Bio__SCF_get_comments': SCF.xs:95:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_set_comments': SCF.xs:108:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_scf_write': SCF.xs:121:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_scf_fwrite': SCF.xs:137:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_get_from_header': SCF.xs:159:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_get_at': SCF.xs:186:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_set_base_at': SCF.xs:242:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function 'XS_Bio__SCF_set_at': SCF.xs:255:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ --- blib/arch/auto/Bio/SCF/SCF.so --- rm -f blib/arch/auto/Bio/SCF/SCF.so LD_RUN_PATH="/usr/local/lib:/usr/lib" cc -shared -L/usr/local/lib/perl5/5.26/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so -lstaden-read -lz chmod 755 blib/arch/auto/Bio/SCF/SCF.so --- dynamic --- --- linkext --- --- pure_all --- --- manifypods --- Manifying 1 pod document --- all --- -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-Bio-SCF-1.03_1 depends on file: /usr/local/include/io_lib/scf.h - found ===> p5-Bio-SCF-1.03_1 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-Bio-SCF-1.03_1 ===> Generating temporary packing list "/usr/local/bin/perl5.26.1" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644 Manifying 1 pod document Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /construction/biology/p5-Bio-SCF/stage/usr/local/lib/perl5/site_perl/mach/5.26/auto/Bio/SCF/SCF.so Installing /construction/biology/p5-Bio-SCF/stage/usr/local/lib/perl5/site_perl/mach/5.26/Bio/SCF.pm Installing /construction/biology/p5-Bio-SCF/stage/usr/local/lib/perl5/site_perl/mach/5.26/Bio/SCF/Arrays.pm Installing /construction/biology/p5-Bio-SCF/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SCF.3 ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for p5-Bio-SCF-1.03_1 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 15:56:55 UTC Duration: 00:00:14