------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- 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. Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by scrm-1.7.4 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by scrm-1.7.4 for building => SHA256 Checksum OK for scrm-scrm-v1.7.4_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by scrm-1.7.4 for building ===> Extracting for scrm-1.7.4 => SHA256 Checksum OK for scrm-scrm-v1.7.4_GH0.tar.gz. Extracted Memory Use: 1.77M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for scrm-1.7.4 ===> Applying ports patches for scrm-1.7.4 from /xports/biology/scrm/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on package: gmake>=4.3 - found ===> scrm-1.7.4 depends on package: autoconf>=2.69 - found ===> scrm-1.7.4 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> scrm-1.7.4 depends on package: gmake>=4.3 - found ===> scrm-1.7.4 depends on package: autoconf>=2.69 - found ===> scrm-1.7.4 depends on package: automake>=1.16.1 - found ===> Configuring for scrm-1.7.4 configure.ac:25: installing './compile' configure.ac:16: installing './config.guess' configure.ac:16: installing './config.sub' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' 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 gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether gmake supports nested variables... (cached) yes checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 checking for ranlib... ranlib checking whether gmake supports the include directive... yes (GNU style) 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 c++ accepts -g... yes checking dependency style of c++... gcc3 checking whether c++ supports C++11 features by default... yes checking for gcc... cc 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 TestCase in -lcppunit... no checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline 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 size_t... (cached) yes checking CXXFLAGS for maximum warnings... -Wall checking whether C++ compiler accepts -Wextra... yes checking whether C++ compiler accepts -Wnon-virtual-dtor... yes checking whether C++ compiler accepts -Wcast-align... yes checking whether C++ compiler accepts -Wunused... yes checking whether C++ compiler accepts -Woverloaded-virtual... yes checking whether C++ compiler accepts -pedantic... yes checking whether C++ compiler accepts -Wcatch-value... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for scrm-1.7.4 gmake[1]: Entering directory '/construction/biology/scrm/scrm-1.7.4' c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/summary_statistics/scrm-tmrca.o -MD -MP -MF src/summary_statistics/.deps/scrm-tmrca.Tpo -c -o src/summary_statistics/scrm-tmrca.o `test -f 'src/summary_statistics/tmrca.cc' || echo './'`src/summary_statistics/tmrca.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/summary_statistics/scrm-seg_sites.o -MD -MP -MF src/summary_statistics/.deps/scrm-seg_sites.Tpo -c -o src/summary_statistics/scrm-seg_sites.o `test -f 'src/summary_statistics/seg_sites.cc' || echo './'`src/summary_statistics/seg_sites.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/summary_statistics/scrm-frequency_spectrum.o -MD -MP -MF src/summary_statistics/.deps/scrm-frequency_spectrum.Tpo -c -o src/summary_statistics/scrm-frequency_spectrum.o `test -f 'src/summary_statistics/frequency_spectrum.cc' || echo './'`src/summary_statistics/frequency_spectrum.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/summary_statistics/scrm-newick_tree.o -MD -MP -MF src/summary_statistics/.deps/scrm-newick_tree.Tpo -c -o src/summary_statistics/scrm-newick_tree.o `test -f 'src/summary_statistics/newick_tree.cc' || echo './'`src/summary_statistics/newick_tree.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/summary_statistics/scrm-oriented_forest.o -MD -MP -MF src/summary_statistics/.deps/scrm-oriented_forest.Tpo -c -o src/summary_statistics/scrm-oriented_forest.o `test -f 'src/summary_statistics/oriented_forest.cc' || echo './'`src/summary_statistics/oriented_forest.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/scrm-param.o -MD -MP -MF src/.deps/scrm-param.Tpo -c -o src/scrm-param.o `test -f 'src/param.cc' || echo './'`src/param.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/scrm-forest.o -MD -MP -MF src/.deps/scrm-forest.Tpo -c -o src/scrm-forest.o `test -f 'src/forest.cc' || echo './'`src/forest.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/scrm-node.o -MD -MP -MF src/.deps/scrm-node.Tpo -c -o src/scrm-node.o `test -f 'src/node.cc' || echo './'`src/node.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/scrm-node_container.o -MD -MP -MF src/.deps/scrm-node_container.Tpo -c -o src/scrm-node_container.o `test -f 'src/node_container.cc' || echo './'`src/node_container.cc c++ -DPACKAGE_NAME=\"scrm\" -DPACKAGE_TARNAME=\"scrm\" -DPACKAGE_VERSION=\"1.7.4\" -DPACKAGE_STRING=\"scrm\ 1.7.4\" -DPACKAGE_BUGREPORT=\"https://github.com/paulstaab/scrm/issues\" -DPACKAGE_URL=\"\" -DPACKAGE=\"scrm\" -DVERSION=\"1.7.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -DNDEBUG -Wextra -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -pedantic -Wcatch-value -pipe -O2 -fno-strict-aliasing -Wall -MT src/scrm-time_interval.o -MD -MP -MF src/.deps/scrm-time_interval.Tpo -c -o src/scrm-time_interval.o `test -f 'src/time_interval.cc' || echo './'`src/time_interval.cc In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/tmrca.h:31, from src/summary_statistics/tmrca.cc:22: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1766: src/summary_statistics/scrm-tmrca.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/oriented_forest.h:31, from src/summary_statistics/oriented_forest.cc:22: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1822: src/summary_statistics/scrm-oriented_forest.o] Error 1 In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/seg_sites.h:31, from src/summary_statistics/seg_sites.cc:22: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1780: src/summary_statistics/scrm-seg_sites.o] Error 1 In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/seg_sites.h:31, from src/summary_statistics/frequency_spectrum.h:34, from src/summary_statistics/frequency_spectrum.cc:22: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1794: src/summary_statistics/scrm-frequency_spectrum.o] Error 1 In file included from src/random/random_generator.h:32, from src/contemporaries_container.h:34, from src/forest.h:51, from src/forest.cc:23: src/random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1640: src/scrm-forest.o] Error 1 In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/newick_tree.h:32, from src/summary_statistics/newick_tree.cc:22: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1808: src/summary_statistics/scrm-newick_tree.o] Error 1 In file included from src/random/random_generator.h:32, from src/contemporaries_container.h:34, from src/forest.h:51, from src/time_interval.h:26, from src/time_interval.cc:23: src/random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1682: src/scrm-time_interval.o] Error 1 In file included from src/summary_statistics/../random/random_generator.h:32, from src/summary_statistics/../contemporaries_container.h:34, from src/summary_statistics/../forest.h:51, from src/summary_statistics/tmrca.h:31, from src/param.h:38, from src/param.cc:23: src/summary_statistics/../random/fastfunc.h:31:10: fatal error: malloc.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:1626: src/scrm-param.o] Error 1 mv -f src/.deps/scrm-node.Tpo src/.deps/scrm-node.Po mv -f src/.deps/scrm-node_container.Tpo src/.deps/scrm-node_container.Po gmake[1]: Leaving directory '/construction/biology/scrm/scrm-1.7.4' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/scrm FAILED 00:00:02