------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/freetype2-2.10.2.txz ===== Message from freetype2-2.10.2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/expat-2.2.8.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/libidn-1.35.txz Installing /packages/All/png-1.6.37.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/jbig2dec-0.18.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/jpeg-turbo-2.0.4.txz Installing /packages/All/tiff-4.1.0.txz Installing /packages/All/libdaemon-0.14_1.txz Installing /packages/All/libICE-1.0.10,1.txz Installing /packages/All/libSM-1.2.3,1.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.13.1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/dbus-1.12.20.txz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/pcre-8.44.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.56.3_9,1.txz No schema files found: doing nothing. Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.18.1_1.txz Installing /packages/All/gobject-introspection-1.56.1_1,1.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.7_3.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/nettle-3.6.txz Installing /packages/All/libtasn1-4.16.0.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- 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. 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 Installing /packages/All/bash-5.0.18_3.txz Installing /packages/All/bash-completion-2.11,2.txz ===== Message from bash-completion-2.11,2: -- To enable the bash completion library, add the following to your .bashrc file: [[ $PS1 && -f /usr/local/share/bash-completion/bash_completion.sh ]] && \ source /usr/local/share/bash-completion/bash_completion.sh See /usr/local/share/doc/bash-completion/README.md for more information. Installing /packages/All/p11-kit-0.23.21.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_3.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_3: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.15.txz Installing /packages/All/cups-2.3.3_1.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/poppler-data-0.4.9_5.txz Installing /packages/All/ghostscript9-agpl-base-9.52_8.txz ===== Message from ghostscript9-agpl-base-9.52_8: -- This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. 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/perl5-5.32.0.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz Installing /packages/All/libsysinfo-0.0.3_2.txz SUCCEEDED 00:00:42 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vsearch-2.15.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vsearch-2.15.0 for building => SHA256 Checksum OK for torognes-vsearch-v2.15.0_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vsearch-2.15.0 for building ===> Extracting for vsearch-2.15.0 => SHA256 Checksum OK for torognes-vsearch-v2.15.0_GH0.tar.gz. Extracted Memory Use: 1.48M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for vsearch-2.15.0 ===> Applying ports patches for vsearch-2.15.0 from /xports/biology/vsearch/files ===> Applying dragonfly patches for vsearch-2.15.0 from /xports/biology/vsearch/dragonfly SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on package: ghostscript9-agpl-base>=9.16_2 - found ===> vsearch-2.15.0 depends on package: gmake>=4.3 - found ===> vsearch-2.15.0 depends on package: autoconf>=2.69 - found ===> vsearch-2.15.0 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> vsearch-2.15.0 depends on package: ghostscript9-agpl-base>=9.16_2 - found ===> vsearch-2.15.0 depends on package: gmake>=4.3 - found ===> vsearch-2.15.0 depends on package: autoconf>=2.69 - found ===> vsearch-2.15.0 depends on package: automake>=1.16.1 - found ===> vsearch-2.15.0 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) ===> Configuring for vsearch-2.15.0 configure.ac:101: installing './compile' configure.ac:6: installing './config.guess' configure.ac:6: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' src/Makefile.am: installing './depcomp' configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 checking target system type... x86_64-portbld-dragonfly5.9 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 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 whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for ranlib... ranlib checking for pthread_create in -lpthread... yes checking for dlopen in -ldl... yes checking for GetProcessMemoryInfo in -lpsapi... no checking how to run the C++ preprocessor... c++ -E 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 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 getopt.h... (cached) yes checking for fcntl.h... (cached) yes checking for float.h... (cached) yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for ctype.h... (cached) yes checking for locale.h... (cached) yes checking for limits.h... (cached) yes checking for string.h... (cached) yes checking for sys/time.h... (cached) yes checking for dlfcn.h... (cached) yes checking for inline... inline checking for size_t... (cached) yes checking for uint32_t... (cached) yes checking for int64_t... (cached) yes checking for uint64_t... (cached) yes checking for uint8_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working strtod... (cached) yes checking for working alloca.h... yes checking for alloca... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for memmove... (cached) yes checking for memcpy... (cached) yes checking for posix_memalign... yes checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for memchr... (cached) yes checking for memset... (cached) yes checking for pow... yes checking for regcomp... yes checking for strcasecmp... (cached) yes checking for strchr... (cached) yes checking for strcspn... (cached) yes checking for sysinfo... no checking for library containing pthread_create... none required checking for ps2pdf... yes checking for pthread.h... (cached) yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for zlib.h... (cached) yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no 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 that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands SUCCEEDED 00:00:14 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for vsearch-2.15.0 gmake[1]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' gmake all-recursive gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' Making all in src gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/src' depbase=`echo align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT align.o -MD -MP -MF $depbase.Tpo -c -o align.o align.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo align_simd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT align_simd.o -MD -MP -MF $depbase.Tpo -c -o align_simd.o align_simd.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo allpairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT allpairs.o -MD -MP -MF $depbase.Tpo -c -o allpairs.o allpairs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo arch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT arch.o -MD -MP -MF $depbase.Tpo -c -o arch.o arch.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo attributes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT attributes.o -MD -MP -MF $depbase.Tpo -c -o attributes.o attributes.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo bitmap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT bitmap.o -MD -MP -MF $depbase.Tpo -c -o bitmap.o bitmap.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo chimera.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT chimera.o -MD -MP -MF $depbase.Tpo -c -o chimera.o chimera.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cluster.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cluster.o -MD -MP -MF $depbase.Tpo -c -o cluster.o cluster.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cut.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cut.o -MD -MP -MF $depbase.Tpo -c -o cut.o cut.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo db.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT db.o -MD -MP -MF $depbase.Tpo -c -o db.o db.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dbhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dbhash.o -MD -MP -MF $depbase.Tpo -c -o dbhash.o dbhash.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dbindex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dbindex.o -MD -MP -MF $depbase.Tpo -c -o dbindex.o dbindex.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo derep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT derep.o -MD -MP -MF $depbase.Tpo -c -o derep.o derep.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dynlibs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dynlibs.o -MD -MP -MF $depbase.Tpo -c -o dynlibs.o dynlibs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo eestats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT eestats.o -MD -MP -MF $depbase.Tpo -c -o eestats.o eestats.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fasta.o -MD -MP -MF $depbase.Tpo -c -o fasta.o fasta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastq.o -MD -MP -MF $depbase.Tpo -c -o fastq.o fastq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastqjoin.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastqjoin.o -MD -MP -MF $depbase.Tpo -c -o fastqjoin.o fastqjoin.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastqops.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastqops.o -MD -MP -MF $depbase.Tpo -c -o fastqops.o fastqops.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastx.o -MD -MP -MF $depbase.Tpo -c -o fastx.o fastx.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT filter.o -MD -MP -MF $depbase.Tpo -c -o filter.o filter.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo getseq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT getseq.o -MD -MP -MF $depbase.Tpo -c -o getseq.o getseq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo kmerhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT kmerhash.o -MD -MP -MF $depbase.Tpo -c -o kmerhash.o kmerhash.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo linmemalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT linmemalign.o -MD -MP -MF $depbase.Tpo -c -o linmemalign.o linmemalign.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo maps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT maps.o -MD -MP -MF $depbase.Tpo -c -o maps.o maps.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo mask.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mask.o -MD -MP -MF $depbase.Tpo -c -o mask.o mask.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo mergepairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mergepairs.o -MD -MP -MF $depbase.Tpo -c -o mergepairs.o mergepairs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo minheap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minheap.o -MD -MP -MF $depbase.Tpo -c -o minheap.o minheap.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo msa.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT msa.o -MD -MP -MF $depbase.Tpo -c -o msa.o msa.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo otutable.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT otutable.o -MD -MP -MF $depbase.Tpo -c -o otutable.o otutable.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rerep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rerep.o -MD -MP -MF $depbase.Tpo -c -o rerep.o rerep.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo results.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT results.o -MD -MP -MF $depbase.Tpo -c -o results.o results.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo search.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT search.o -MD -MP -MF $depbase.Tpo -c -o search.o search.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo searchcore.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT searchcore.o -MD -MP -MF $depbase.Tpo -c -o searchcore.o searchcore.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo searchexact.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT searchexact.o -MD -MP -MF $depbase.Tpo -c -o searchexact.o searchexact.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sffconvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sffconvert.o -MD -MP -MF $depbase.Tpo -c -o sffconvert.o sffconvert.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sha1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT sha1.o -MD -MP -MF $depbase.Tpo -c -o sha1.o sha1.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo showalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT showalign.o -MD -MP -MF $depbase.Tpo -c -o showalign.o showalign.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo shuffle.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT shuffle.o -MD -MP -MF $depbase.Tpo -c -o shuffle.o shuffle.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sintax.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sintax.o -MD -MP -MF $depbase.Tpo -c -o sintax.o sintax.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbylength.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbylength.o -MD -MP -MF $depbase.Tpo -c -o sortbylength.o sortbylength.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbysize.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbysize.o -MD -MP -MF $depbase.Tpo -c -o sortbysize.o sortbysize.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo subsample.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT subsample.o -MD -MP -MF $depbase.Tpo -c -o subsample.o subsample.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo udb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT udb.o -MD -MP -MF $depbase.Tpo -c -o udb.o udb.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo unique.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT unique.o -MD -MP -MF $depbase.Tpo -c -o unique.o unique.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo userfields.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT userfields.o -MD -MP -MF $depbase.Tpo -c -o userfields.o userfields.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo util.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT util.o -MD -MP -MF $depbase.Tpo -c -o util.o util.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vsearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT vsearch.o -MD -MP -MF $depbase.Tpo -c -o vsearch.o vsearch.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -Wno-sign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcityhash_a-city.o -MD -MP -MF .deps/libcityhash_a-city.Tpo -c -o libcityhash_a-city.o `test -f 'city.cc' || echo './'`city.cc c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -mssse3 -DSSSE3 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcpu_ssse3_a-cpu.o -MD -MP -MF .deps/libcpu_ssse3_a-cpu.Tpo -c -o libcpu_ssse3_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc mv -f .deps/libcityhash_a-city.Tpo .deps/libcityhash_a-city.Po c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -msse2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcpu_sse2_a-cpu.o -MD -MP -MF .deps/libcpu_sse2_a-cpu.Tpo -c -o libcpu_sse2_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc rm -f libcityhash.a ar cru libcityhash.a libcityhash_a-city.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcityhash.a mv -f .deps/libcpu_ssse3_a-cpu.Tpo .deps/libcpu_ssse3_a-cpu.Po rm -f libcpu_ssse3.a ar cru libcpu_ssse3.a libcpu_ssse3_a-cpu.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcpu_ssse3.a mv -f .deps/libcpu_sse2_a-cpu.Tpo .deps/libcpu_sse2_a-cpu.Po rm -f libcpu_sse2.a ar cru libcpu_sse2.a libcpu_sse2_a-cpu.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcpu_sse2.a c++ -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o ../bin/vsearch align.o align_simd.o allpairs.o arch.o attributes.o bitmap.o chimera.o cluster.o cut.o db.o dbhash.o dbindex.o derep.o dynlibs.o eestats.o fasta.o fastq.o fastqjoin.o fastqops.o fastx.o filter.o getseq.o kmerhash.o linmemalign.o maps.o mask.o md5.o mergepairs.o minheap.o msa.o otutable.o rerep.o results.o search.o searchcore.o searchexact.o sffconvert.o sha1.o showalign.o shuffle.o sintax.o sortbylength.o sortbysize.o subsample.o udb.o unique.o userfields.o util.o vsearch.o libcityhash.a libcpu_ssse3.a libcpu_sse2.a -ldl -lpthread -L/usr/local/lib gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/src' Making all in man gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/man' sed -e 's/\\-/-/g' vsearch.1 | \ if [ $(uname) == "Darwin" ] ; then \ iconv -f UTF-8 -t ISO-8859-1 ; \ else \ cat ; \ fi | \ groff -W space -t -m mandoc -T ps -P -pa4 | ps2pdf - vsearch_manual.pdf /bin/sh: groff: not found cat: stdout: Broken pipe sed: stdout: Broken pipe gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/man' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[1]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' SUCCEEDED 00:00:27 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for vsearch-2.15.0 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' Making install in src gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/src' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/src' /bin/mkdir -p '/construction/biology/vsearch/stage/usr/local/bin' install -s -m 555 ../bin/vsearch '/construction/biology/vsearch/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/src' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/src' Making install in man gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/man' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0/man' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/vsearch/stage/usr/local/share/doc/vsearch' install -m 0644 vsearch_manual.pdf '/construction/biology/vsearch/stage/usr/local/share/doc/vsearch' /bin/mkdir -p '/construction/biology/vsearch/stage/usr/local/man/man1' install -m 0644 vsearch.1 '/construction/biology/vsearch/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/man' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0/man' gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' gmake[1]: Leaving directory '/construction/biology/vsearch/vsearch-2.15.0' ====> 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 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for vsearch-2.15.0 file sizes/checksums [3]: 0% file sizes/checksums [3]: 100% packing files [3]: 0% packing files [3]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:01:25