=> Building math/mcsim Started : Friday, 14 FEB 2020 at 17:06:23 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1432.g9cd86-DEVELOPMENT #23: Thu Feb 13 14:43:04 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-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 -------------------------------------------------- ===> The following configuration options are available for mcsim-6.1.0_1: GSL=on: GNU Scientific Library support (recommended) SUNDIALS=off: Sundial's Cvodes integrator ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/math/mcsim XDG_CONFIG_HOME=/construction/math/mcsim HOME=/construction/math/mcsim TMPDIR="/tmp" PATH=/construction/math/mcsim/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/math/mcsim XDG_CONFIG_HOME=/construction/math/mcsim HOME=/construction/math/mcsim TMPDIR="/tmp" PATH=/construction/math/mcsim/.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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " 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/math/mcsim/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- GSL="" NO_GSL="@comment " SUNDIALS="@comment " NO_SUNDIALS="" OSREL=5.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mcsim" EXAMPLESDIR="share/examples/mcsim" DATADIR="share/mcsim" WWWDIR="www/mcsim" ETCDIR="etc/mcsim" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- GSL="" NO_GSL="@comment " SUNDIALS="@comment " NO_SUNDIALS="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mcsim DOCSDIR=/usr/local/share/doc/mcsim EXAMPLESDIR=/usr/local/share/examples/mcsim WWWDIR=/usr/local/www/mcsim ETCDIR=/usr/local/etc/mcsim -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> mcsim-6.1.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0_1.txz Installing pkg-1.12.0_1... Extracting pkg-1.12.0_1: .......... done ===> mcsim-6.1.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mcsim-6.1.0_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mcsim-6.1.0_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mcsim-6.1.0_1 for building => SHA256 Checksum OK for mcsim-6.1.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mcsim-6.1.0_1 for building ===> Extracting for mcsim-6.1.0_1 => SHA256 Checksum OK for mcsim-6.1.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for mcsim-6.1.0_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> mcsim-6.1.0_1 depends on package: indexinfo>=0.3.0 - not found ===> Installing existing package /packages/All/indexinfo-0.3.1.txz Installing indexinfo-0.3.1... Extracting indexinfo-0.3.1: . done ===> mcsim-6.1.0_1 depends on package: indexinfo>=0.3.0 - found ===> Returning to build of mcsim-6.1.0_1 ===> mcsim-6.1.0_1 depends on package: gsl>=2.5 - not found ===> Installing existing package /packages/All/gsl-2.6.txz Installing gsl-2.6... Extracting gsl-2.6: .......... done ===> mcsim-6.1.0_1 depends on package: gsl>=2.5 - found ===> Returning to build of mcsim-6.1.0_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for mcsim-6.1.0_1 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ar... ar checking the archiver (ar) interface... ar checking build system type... x86_64-portbld-dragonfly5.7 checking host system type... x86_64-portbld-dragonfly5.7 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly5.7 file names to x86_64-portbld-dragonfly5.7 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.7 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly5.7 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking dependency style of cc... (cached) gcc3 checking for wish... no checking for gnuplot... no checking for main in -llapack... no checking for main in -lsundials_nvecserial... no checking for main in -lsundials_cvodes... no checking for main in -lgslcblas... no checking for gsl_cdf_gamma_P in -lgsl... no checking for main in -lm... yes checking for main in -lsbml... no checking for ANSI C header files... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for modf... yes checking for pow... yes checking for sqrt... yes checking for strchr... (cached) yes checking for erfc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating mod/Makefile config.status: creating sim/Makefile config.status: creating doc/Makefile config.status: creating sim/makemcsim config.status: creating sim/makemcsimd config.status: creating sim/makemcsims config.status: creating examples/perc/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for mcsim-6.1.0_1 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in mod --- getopt.o --- --- lex.o --- --- lexerr.o --- --- lexfn.o --- --- mod.o --- --- modd.o --- --- modi.o --- --- modiSBML.o --- --- modiSBML2.o --- --- modo.o --- --- strutil.o --- --- getopt.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT getopt.o -MD -MP -MF .deps/getopt.Tpo -c -o getopt.o getopt.c --- lex.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lex.o -MD -MP -MF .deps/lex.Tpo -c -o lex.o lex.c --- lexerr.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexerr.o -MD -MP -MF .deps/lexerr.Tpo -c -o lexerr.o lexerr.c --- lexfn.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexfn.o -MD -MP -MF .deps/lexfn.Tpo -c -o lexfn.o lexfn.c --- mod.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT mod.o -MD -MP -MF .deps/mod.Tpo -c -o mod.o mod.c --- modd.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modd.o -MD -MP -MF .deps/modd.Tpo -c -o modd.o modd.c --- modi.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modi.o -MD -MP -MF .deps/modi.Tpo -c -o modi.o modi.c --- modiSBML.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modiSBML.o -MD -MP -MF .deps/modiSBML.Tpo -c -o modiSBML.o modiSBML.c --- modiSBML2.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modiSBML2.o -MD -MP -MF .deps/modiSBML2.Tpo -c -o modiSBML2.o modiSBML2.c --- modo.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modo.o -MD -MP -MF .deps/modo.Tpo -c -o modo.o modo.c --- strutil.o --- cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT strutil.o -MD -MP -MF .deps/strutil.Tpo -c -o strutil.o strutil.c --- modiSBML2.o --- mv -f .deps/modiSBML2.Tpo .deps/modiSBML2.Po --- strutil.o --- mv -f .deps/strutil.Tpo .deps/strutil.Po --- mod.o --- mv -f .deps/mod.Tpo .deps/mod.Po --- getopt.o --- mv -f .deps/getopt.Tpo .deps/getopt.Po --- lexfn.o --- mv -f .deps/lexfn.Tpo .deps/lexfn.Po --- modi.o --- mv -f .deps/modi.Tpo .deps/modi.Po --- lexerr.o --- mv -f .deps/lexerr.Tpo .deps/lexerr.Po --- modiSBML.o --- mv -f .deps/modiSBML.Tpo .deps/modiSBML.Po --- lex.o --- mv -f .deps/lex.Tpo .deps/lex.Po --- modd.o --- mv -f .deps/modd.Tpo .deps/modd.Po --- modo.o --- modo.c: In function 'Write_R_Model': modo.c:1785:11: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] Rfile = strncpy(Rfile, szFileOut, nbase); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modo.c:1780:11: note: length computed here nbase = strlen(szFileOut); ^~~~~~~~~~~~~~~~~ mv -f .deps/modo.Tpo .deps/modo.Po --- mod --- /bin/sh ../libtool --tag=CC --mode=link cc -O3 -pipe -O2 -fno-strict-aliasing -o mod getopt.o lex.o lexerr.o lexfn.o mod.o modd.o modi.o modiSBML.o modiSBML2.o modo.o strutil.o -lm libtool: link: cc -O3 -pipe -O2 -fno-strict-aliasing -o mod getopt.o lex.o lexerr.o lexfn.o mod.o modd.o modi.o modiSBML.o modiSBML2.o modo.o strutil.o -lm Making all in sim --- delays.lo --- --- getopt.lo --- --- lex.lo --- --- lexerr.lo --- --- lexfn.lo --- --- list.lo --- --- lsodes1.lo --- --- lsodes2.lo --- --- matutil.lo --- --- matutilo.lo --- --- mh.lo --- --- modelu.lo --- --- optdsign.lo --- --- random.lo --- --- sim.lo --- --- delays.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT delays.lo -MD -MP -MF .deps/delays.Tpo -c -o delays.lo delays.c --- getopt.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c --- lexerr.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c -o lexerr.lo lexerr.c --- list.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT list.lo -MD -MP -MF .deps/list.Tpo -c -o list.lo list.c --- lsodes1.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c -o lsodes1.lo lsodes1.c --- lsodes2.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c -o lsodes2.lo lsodes2.c --- matutilo.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c -o matutilo.lo matutilo.c --- modelu.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modelu.lo -MD -MP -MF .deps/modelu.Tpo -c -o modelu.lo modelu.c --- lex.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c -o lex.lo lex.c --- random.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT random.lo -MD -MP -MF .deps/random.Tpo -c -o random.lo random.c --- sim.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c -o sim.lo sim.c --- lexfn.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c -o lexfn.lo lexfn.c --- matutil.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c -o matutil.lo matutil.c --- mh.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c -o mh.lo mh.c --- optdsign.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c -o optdsign.lo optdsign.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c optdsign.c -fPIC -DPIC -o .libs/optdsign.o --- mh.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c mh.c -fPIC -DPIC -o .libs/mh.o --- lex.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c lex.c -fPIC -DPIC -o .libs/lex.o --- lsodes1.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c lsodes1.c -fPIC -DPIC -o .libs/lsodes1.o --- getopt.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -fPIC -DPIC -o .libs/getopt.o --- delays.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT delays.lo -MD -MP -MF .deps/delays.Tpo -c delays.c -fPIC -DPIC -o .libs/delays.o --- matutil.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c matutil.c -fPIC -DPIC -o .libs/matutil.o --- modelu.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modelu.lo -MD -MP -MF .deps/modelu.Tpo -c modelu.c -fPIC -DPIC -o .libs/modelu.o --- sim.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c sim.c -fPIC -DPIC -o .libs/sim.o --- matutilo.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c matutilo.c -fPIC -DPIC -o .libs/matutilo.o --- matutil.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c matutil.c -o matutil.o >/dev/null 2>&1 --- lexfn.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c lexfn.c -fPIC -DPIC -o .libs/lexfn.o --- matutilo.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c matutilo.c -o matutilo.o >/dev/null 2>&1 --- random.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT random.lo -MD -MP -MF .deps/random.Tpo -c random.c -fPIC -DPIC -o .libs/random.o --- delays.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT delays.lo -MD -MP -MF .deps/delays.Tpo -c delays.c -o delays.o >/dev/null 2>&1 --- matutilo.lo --- mv -f .deps/matutilo.Tpo .deps/matutilo.Plo --- simi.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c -o simi.lo simi.c --- lsodes2.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c lsodes2.c -fPIC -DPIC -o .libs/lsodes2.o --- simi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c simi.c -fPIC -DPIC -o .libs/simi.o --- delays.lo --- mv -f .deps/delays.Tpo .deps/delays.Plo --- siminit.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c -o siminit.lo siminit.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c siminit.c -fPIC -DPIC -o .libs/siminit.o --- lexerr.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c lexerr.c -fPIC -DPIC -o .libs/lexerr.o --- list.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT list.lo -MD -MP -MF .deps/list.Tpo -c list.c -fPIC -DPIC -o .libs/list.o --- lexfn.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c lexfn.c -o lexfn.o >/dev/null 2>&1 --- matutil.lo --- mv -f .deps/matutil.Tpo .deps/matutil.Plo --- simmonte.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c -o simmonte.lo simmonte.c --- lexerr.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c lexerr.c -o lexerr.o >/dev/null 2>&1 --- simmonte.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c simmonte.c -fPIC -DPIC -o .libs/simmonte.o --- list.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT list.lo -MD -MP -MF .deps/list.Tpo -c list.c -o list.o >/dev/null 2>&1 mv -f .deps/list.Tpo .deps/list.Plo --- simo.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c -o simo.lo simo.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c simo.c -fPIC -DPIC -o .libs/simo.o --- siminit.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c siminit.c -o siminit.o >/dev/null 2>&1 --- simmonte.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c simmonte.c -o simmonte.o >/dev/null 2>&1 --- simo.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c simo.c -o simo.o >/dev/null 2>&1 --- getopt.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1 --- lexerr.lo --- mv -f .deps/lexerr.Tpo .deps/lexerr.Plo --- strutil.lo --- --- simmonte.lo --- mv -f .deps/simmonte.Tpo .deps/simmonte.Plo --- strutil.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c -o strutil.lo strutil.c --- yourcode.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c -o yourcode.lo yourcode.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c yourcode.c -fPIC -DPIC -o .libs/yourcode.o --- strutil.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c strutil.c -fPIC -DPIC -o .libs/strutil.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c strutil.c -o strutil.o >/dev/null 2>&1 --- simo.lo --- mv -f .deps/simo.Tpo .deps/simo.Plo --- strutil.lo --- mv -f .deps/strutil.Tpo .deps/strutil.Plo --- lexfn.lo --- mv -f .deps/lexfn.Tpo .deps/lexfn.Plo --- yourcode.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c yourcode.c -o yourcode.o >/dev/null 2>&1 --- siminit.lo --- mv -f .deps/siminit.Tpo .deps/siminit.Plo --- getopt.lo --- mv -f .deps/getopt.Tpo .deps/getopt.Plo --- modelu.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT modelu.lo -MD -MP -MF .deps/modelu.Tpo -c modelu.c -o modelu.o >/dev/null 2>&1 --- yourcode.lo --- mv -f .deps/yourcode.Tpo .deps/yourcode.Plo --- optdsign.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c optdsign.c -o optdsign.o >/dev/null 2>&1 --- lex.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c lex.c -o lex.o >/dev/null 2>&1 --- modelu.lo --- mv -f .deps/modelu.Tpo .deps/modelu.Plo --- lsodes2.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c lsodes2.c -o lsodes2.o >/dev/null 2>&1 --- lex.lo --- mv -f .deps/lex.Tpo .deps/lex.Plo --- random.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT random.lo -MD -MP -MF .deps/random.Tpo -c random.c -o random.o >/dev/null 2>&1 --- optdsign.lo --- mv -f .deps/optdsign.Tpo .deps/optdsign.Plo --- sim.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c sim.c -o sim.o >/dev/null 2>&1 --- simi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c simi.c -o simi.o >/dev/null 2>&1 --- sim.lo --- mv -f .deps/sim.Tpo .deps/sim.Plo --- random.lo --- mv -f .deps/random.Tpo .deps/random.Plo --- lsodes1.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c lsodes1.c -o lsodes1.o >/dev/null 2>&1 --- lsodes2.lo --- mv -f .deps/lsodes2.Tpo .deps/lsodes2.Plo --- simi.lo --- mv -f .deps/simi.Tpo .deps/simi.Plo --- mh.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -O3 -pipe -O2 -fno-strict-aliasing -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c mh.c -o mh.o >/dev/null 2>&1 --- lsodes1.lo --- mv -f .deps/lsodes1.Tpo .deps/lsodes1.Plo --- mh.lo --- mv -f .deps/mh.Tpo .deps/mh.Plo --- libmcsim.la --- /bin/sh ../libtool --tag=CC --mode=link cc -O3 -pipe -O2 -fno-strict-aliasing -o libmcsim.la -rpath /usr/local/lib delays.lo getopt.lo lex.lo lexerr.lo lexfn.lo list.lo lsodes1.lo lsodes2.lo matutil.lo matutilo.lo mh.lo modelu.lo optdsign.lo random.lo sim.lo simi.lo siminit.lo simmonte.lo simo.lo strutil.lo yourcode.lo -lm libtool: link: cc -shared -fPIC -DPIC .libs/delays.o .libs/getopt.o .libs/lex.o .libs/lexerr.o .libs/lexfn.o .libs/list.o .libs/lsodes1.o .libs/lsodes2.o .libs/matutil.o .libs/matutilo.o .libs/mh.o .libs/modelu.o .libs/optdsign.o .libs/random.o .libs/sim.o .libs/simi.o .libs/siminit.o .libs/simmonte.o .libs/simo.o .libs/strutil.o .libs/yourcode.o -lm -O3 -O2 -Wl,-soname -Wl,libmcsim.so.0 -o .libs/libmcsim.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmcsim.so.0" && ln -s "libmcsim.so.0.0.0" "libmcsim.so.0") libtool: link: (cd ".libs" && rm -f "libmcsim.so" && ln -s "libmcsim.so.0.0.0" "libmcsim.so") libtool: link: ar cru .libs/libmcsim.a delays.o getopt.o lex.o lexerr.o lexfn.o list.o lsodes1.o lsodes2.o matutil.o matutilo.o mh.o modelu.o optdsign.o random.o sim.o simi.o siminit.o simmonte.o simo.o strutil.o yourcode.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libmcsim.a libtool: link: ( cd ".libs" && rm -f "libmcsim.la" && ln -s "../libmcsim.la" "libmcsim.la" ) Making all in doc -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> mcsim-6.1.0_1 depends on executable: indexinfo - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for mcsim-6.1.0_1 ===> Generating temporary packing list if test -z 'strip'; then /usr/bin/make INSTALL_PROGRAM="/bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s" install_sh_PROGRAM="/bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s" INSTALL_STRIP_FLAG=-s install; else /usr/bin/make INSTALL_PROGRAM="/bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s" install_sh_PROGRAM="/bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s" INSTALL_STRIP_FLAG=-s "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; fi Making install in mod /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s mod '/construction/math/mcsim/stage/usr/local/bin' libtool: install: /bin/sh /construction/math/mcsim/mcsim-6.1.0/install-sh -c -s mod /construction/math/mcsim/stage/usr/local/bin/mod /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/share/mcsim/mod' install -m 0644 getopt.c getopt.h hungtype.h lex.c lex.h lexerr.c lexerr.h lexfn.c lexfn.h mod.c mod.h modd.c modd.h modi.c modi.h modiSBML.c modiSBML2.c modiSBML.h modo.c modo.h strutil.c strutil.h '/construction/math/mcsim/stage/usr/local/share/mcsim/mod' Making install in sim /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/bin' install -m 555 makemcsim makemcsims makemcsimd '/construction/math/mcsim/stage/usr/local/bin' /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libmcsim.la '/construction/math/mcsim/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libmcsim.so.0.0.0 /construction/math/mcsim/stage/usr/local/lib/libmcsim.so.0.0.0 libtool: install: strip --strip-unneeded /construction/math/mcsim/stage/usr/local/lib/libmcsim.so.0.0.0 libtool: install: (cd /construction/math/mcsim/stage/usr/local/lib && { ln -s -f libmcsim.so.0.0.0 libmcsim.so.0 || { rm -f libmcsim.so.0 && ln -s libmcsim.so.0.0.0 libmcsim.so.0; }; }) libtool: install: (cd /construction/math/mcsim/stage/usr/local/lib && { ln -s -f libmcsim.so.0.0.0 libmcsim.so || { rm -f libmcsim.so && ln -s libmcsim.so.0.0.0 libmcsim.so; }; }) libtool: install: /usr/bin/install -c .libs/libmcsim.lai /construction/math/mcsim/stage/usr/local/lib/libmcsim.la libtool: install: /usr/bin/install -c .libs/libmcsim.a /construction/math/mcsim/stage/usr/local/lib/libmcsim.a libtool: install: strip --strip-debug /construction/math/mcsim/stage/usr/local/lib/libmcsim.a libtool: install: chmod 644 /construction/math/mcsim/stage/usr/local/lib/libmcsim.a libtool: install: ranlib /construction/math/mcsim/stage/usr/local/lib/libmcsim.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/include' install -m 0644 delays.h matutil.h list.h lex.h sim.h lexfn.h hungtype.h modiface.h modelu.h random.h yourcode.h '/construction/math/mcsim/stage/usr/local/include' /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/share/mcsim/sim' install -m 0644 delays.c delays.h getopt.c getopt.h hungtype.h lex.c lex.h lexerr.c lexerr.h lexfn.c lexfn.h list.c list.h lsodes.h lsodes1.c lsodes2.c matutil.c matutil.h matutilo.c matutilo.h mh.c mh.h modelu.c modelu.h modiface.h optdsign.c optdsign.h random.c random.h sim.c sim.h simi.c simi.h siminit.c siminit.h simmonte.c simmonte.h simo.c simo.h strutil.c '/construction/math/mcsim/stage/usr/local/share/mcsim/sim' install -m 0644 strutil.h yourcode.c yourcode.h '/construction/math/mcsim/stage/usr/local/share/mcsim/sim' Making install in doc /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/share/info' install -m 0644 ./mcsim.info '/construction/math/mcsim/stage/usr/local/share/info' /bin/mkdir -p '/construction/math/mcsim/stage/usr/local/include' install -m 0644 config.h '/construction/math/mcsim/stage/usr/local/include' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for mcsim-6.1.0_1 file sizes/checksums [86]: . done packing files [86]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 14 FEB 2020 at 17:07:20 UTC Duration: 00:00:56