------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.7_1.txz ===== Message from python37-3.7.7_1: -- 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/ninja-1.10.0,2.txz Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/meson-0.54.2.txz Installing /packages/All/pkgconf-1.6.3,1.txz Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.53.txz ===== Message from ca_root_nss-3.53: -- 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/curl-7.70.0_1.txz Installing /packages/All/htslib-1.9.txz Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. SUCCEEDED 00:00:26 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> pbbam-0.18.0_4 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> pbbam-0.18.0_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by pbbam-0.18.0_4 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> pbbam-0.18.0_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by pbbam-0.18.0_4 for building => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> pbbam-0.18.0_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by pbbam-0.18.0_4 for building ===> Extracting for pbbam-0.18.0_4 => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_GH0.tar.gz. Extracted Memory Use: 16.07M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for pbbam-0.18.0_4 ===> Applying ports patches for pbbam-0.18.0_4 from /xports/biology/pbbam/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> pbbam-0.18.0_4 depends on executable: meson - found ===> pbbam-0.18.0_4 depends on executable: ninja - found ===> pbbam-0.18.0_4 depends on package: pkgconf>=1.3.0_1 - found ===> pbbam-0.18.0_4 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> pbbam-0.18.0_4 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> pbbam-0.18.0_4 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> pbbam-0.18.0_4 depends on executable: meson - found ===> pbbam-0.18.0_4 depends on executable: ninja - found ===> pbbam-0.18.0_4 depends on package: pkgconf>=1.3.0_1 - found ===> pbbam-0.18.0_4 depends on file: /usr/local/bin/python3.7 - found ===> pbbam-0.18.0_4 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> pbbam-0.18.0_4 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Configuring for pbbam-0.18.0_4 The Meson build system Version: 0.54.2 Source dir: /construction/biology/pbbam/pbbam-0.18.0 Build dir: /construction/biology/pbbam/pbbam-0.18.0/_build Build type: native build Project name: PacBioBAM Project version: 0.18.0 Using 'CXX' from environment with value: 'c++' Using 'CXXFLAGS' from environment with value: ' -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' Using 'LDFLAGS' from environment with value: ' ' Using 'CPPFLAGS' from environment with value: '-isystem /usr/local/include' Using 'CXX' from environment with value: 'c++' Using 'CXXFLAGS' from environment with value: ' -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' Using 'LDFLAGS' from environment with value: ' ' Using 'CPPFLAGS' from environment with value: '-isystem /usr/local/include' C++ compiler for the host machine: c++ (gcc 8.3.0 "c++ 8.3 [DragonFly] Release/2019-02-22") C++ linker for the host machine: c++ ld.gold 2.27 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Run-time dependency Boost found: YES 1.72.0 (/usr/local) Using 'PKG_CONFIG' from environment with value: 'pkgconf' Found pkg-config: /usr/local/bin/pkgconf (1.6.3) Run-time dependency zlib found: YES 1.2.11 Did not find CMake 'cmake' Found CMake: NO Run-time dependency htslib found: NO meson.build:63:0: ERROR: Could not generate cargs for htslib: Package liblzma was not found in the pkg-config search path. Perhaps you should add the directory containing `liblzma.pc' to the PKG_CONFIG_PATH environment variable Package 'liblzma', required by 'htslib', not found A full log can be found at /construction/biology/pbbam/pbbam-0.18.0/_build/meson-logs/meson-log.txt ===> Script "configure" failed unexpectedly. Please report the problem to ports@FreeBSD.org [maintainer] and attach the "/construction/biology/pbbam/pbbam-0.18.0/_build/meson-logs/meson-log.txt" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop. make: stopped in /xports/biology/pbbam FAILED 00:00:08