=>> Building biology/sra-tools build started at Sun Mar 31 14:06:12 BST 2024 port directory: /usr/ports/biology/sra-tools package name: sra-tools-3.0.6 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2171 Aug 12 2023 /usr/ports/biology/sra-tools/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 0f2f80ca38 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 05 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for sra-tools-3.0.6: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/sra-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/sra-tools/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/sra-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/sra-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/sra-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/sra-tools/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/sra-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/sra-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig DONTSTRIP=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/sra-tools/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-pipe -g -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-pipe -g -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -m 555" BSD_INSTALL_LIB="install -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTEXAMPLES="" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" CMAKE_BUILD_TYPE="debug" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/sra-tools" EXAMPLESDIR="share/examples/sra-tools" DATADIR="share/sra-tools" WWWDIR="www/sra-tools" ETCDIR="etc/sra-tools" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/sra-tools DOCSDIR=/usr/local/share/doc/sra-tools EXAMPLESDIR=/usr/local/share/examples/sra-tools WWWDIR=/usr/local/www/sra-tools ETCDIR=/usr/local/etc/sra-tools --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> sra-tools-3.0.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> sra-tools-3.0.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of sra-tools-3.0.6 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by sra-tools-3.0.6 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by sra-tools-3.0.6 for building => SHA256 Checksum OK for ncbi-sra-tools-3.0.6_GH0.tar.gz. => SHA256 Checksum OK for ncbi-ncbi-vdb-3.0.6_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by sra-tools-3.0.6 for building ===> Extracting for sra-tools-3.0.6 => SHA256 Checksum OK for ncbi-sra-tools-3.0.6_GH0.tar.gz. => SHA256 Checksum OK for ncbi-ncbi-vdb-3.0.6_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for sra-tools-3.0.6 ===> Applying FreeBSD patches for sra-tools-3.0.6 from /usr/ports/biology/sra-tools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> sra-tools-3.0.6 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.26_1.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.26_1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.26_1: .......... done ===> sra-tools-3.0.6 depends on executable: bash - found ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on file: /usr/local/openjdk18/bin/java - not found ===> Installing existing package /packages/All/openjdk18-18.0.2+9.1_2.pkg [pkg-builder.dan.net.uk] Installing openjdk18-18.0.2+9.1_2... [pkg-builder.dan.net.uk] `-- Installing alsa-lib-1.2.10_1... [pkg-builder.dan.net.uk] `-- Extracting alsa-lib-1.2.10_1: .......... done [pkg-builder.dan.net.uk] `-- Installing fontconfig-2.15.0_2,1... [pkg-builder.dan.net.uk] | `-- Installing expat-2.6.1... 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[pkg-builder.dan.net.uk] | `-- Extracting libXrender-0.9.10_2: ....... done [pkg-builder.dan.net.uk] `-- Extracting libXrandr-1.5.2_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | `-- Installing libICE-1.1.0_2,1... [pkg-builder.dan.net.uk] | `-- Extracting libICE-1.1.0_2,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libSM-1.2.3_1,1... [pkg-builder.dan.net.uk] | `-- Extracting libSM-1.2.3_1,1: ........ done [pkg-builder.dan.net.uk] `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXtst-1.2.3_3... [pkg-builder.dan.net.uk] `-- Extracting libXtst-1.2.3_3: .......... done [pkg-builder.dan.net.uk] `-- Installing png-1.6.43... [pkg-builder.dan.net.uk] `-- Extracting png-1.6.43: .......... done [pkg-builder.dan.net.uk] `-- Installing xorg-fonts-truetype-7.7_1... [pkg-builder.dan.net.uk] | `-- Installing dejavu-2.37_3... [pkg-builder.dan.net.uk] | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | `-- Installing encodings-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting encodings-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] Extracting openjdk18-18.0.2+9.1_2: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.2: -- 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/index.html, if documentation was installed). ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===== Message from dejavu-2.37_3: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===== Message from openjdk18-18.0.2+9.1_2: -- This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ===> sra-tools-3.0.6 depends on file: /usr/local/openjdk18/bin/java - found ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on executable: bison - not found ===> Installing existing package /packages/All/bison-3.8.2_1,1.pkg [pkg-builder.dan.net.uk] Installing bison-3.8.2_1,1... [pkg-builder.dan.net.uk] `-- Installing libtextstyle-0.22.3... [pkg-builder.dan.net.uk] `-- Extracting libtextstyle-0.22.3: .......... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] Extracting bison-3.8.2_1,1: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> sra-tools-3.0.6 depends on executable: bison - found ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> sra-tools-3.0.6 depends on file: /usr/local/bin/cmake - found ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===> sra-tools-3.0.6 depends on executable: ninja - found ===> Returning to build of sra-tools-3.0.6 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> sra-tools-3.0.6 depends on shared library: libxml2.so - not found ===> Installing existing package /packages/All/libxml2-2.11.7.pkg [pkg-builder.dan.net.uk] Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] Extracting libxml2-2.11.7: .......... done ===> sra-tools-3.0.6 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.12.2_2,1.pkg [pkg-builder.dan.net.uk] Installing hdf5-1.12.2_2,1... [pkg-builder.dan.net.uk] Extracting hdf5-1.12.2_2,1: .......... done ===> sra-tools-3.0.6 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on shared library: libepoll-shim.so - not found ===> Installing existing package /packages/All/libepoll-shim-0.0.20230411.pkg [pkg-builder.dan.net.uk] Installing libepoll-shim-0.0.20230411... [pkg-builder.dan.net.uk] Extracting libepoll-shim-0.0.20230411: .......... done ===> sra-tools-3.0.6 depends on shared library: libepoll-shim.so - found (/usr/local/lib/libepoll-shim.so) ===> Returning to build of sra-tools-3.0.6 ===> sra-tools-3.0.6 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for sra-tools-3.0.6 /usr/bin/sed -i.bak -e 's|/usr/local/etc/ncbi|/usr/local/etc/ncbi|g' /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/libs/kfg/config.c /usr/bin/sed -i.bak -e 's|/usr/local/bin|/usr/local/bin|g' /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/tools/external/driver-tool/file-path.posix.cpp cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build && cmake .. && make -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at build/env.cmake:32 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:78 (include) VERSION=3.0.6 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /usr/local/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Found Python3: /usr/local/bin/python3.9 (found version "3.9.18") found components: Interpreter -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) RUN_SANITIZER_TESTS: OFF Using local mbedtls headers from interfaces/ext/mbedtls Building local copy ext/mbedtls... -- Looking for gnu/libc-version.h -- Looking for gnu/libc-version.h - not found No mbedtls libs found installed in the system, using local copy... -- Configuring done (2.9s) -- Generating done (0.3s) -- Build files have been written to: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testenv.cpp.o [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testcase.cpp.o [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testrunner.cpp.o [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/unix/systestenv.cpp.o [ 0%] Linking CXX static library ../../lib/libktst.a [ 0%] Built target ktst [ 0%] Building C object libs/align/CMakeFiles/ncbi-bam.dir/bam.c.o [ 0%] Linking C static library ../../ilib/libncbi-bam.a [ 0%] Built target ncbi-bam [ 0%] Building C object libs/align/CMakeFiles/align-writer.dir/dna-reverse-cmpl.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/reader-cmn.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/reference-cmn.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/reader-refseq.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/reader-wgs.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/refseq-mgr.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-cmn.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-refseq.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-alignment.c.o [ 1%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-sequence.c.o [ 2%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-ref.c.o [ 2%] Building C object libs/align/CMakeFiles/align-writer.dir/writer-reference.c.o /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/libs/align/writer-reference.c:1635:14: warning: variable 'wopt' set but not used [-Wunused-but-set-variable] uint32_t wopt = 0; ^ 1 warning generated. [ 2%] Linking C static library ../../ilib/libalign-writer.a [ 2%] Built target align-writer [ 2%] Building C object libs/align/CMakeFiles/align-access.dir/align-access.c.o [ 2%] Linking C static library ../../ilib/libalign-access.a [ 2%] Built target align-access [ 2%] Building C object libs/align/CMakeFiles/sam-extract.dir/zz_samextract-grammar.c.o [ 2%] Building C object libs/align/CMakeFiles/sam-extract.dir/zz_samextract-lex.c.o [ 2%] Building CXX object libs/align/CMakeFiles/sam-extract.dir/samextract-lib.cpp.o In file included from /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/libs/align/samextract-lib.cpp:44: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/kproc/thread.hpp:48:24: warning: mangled name of 'Make' will change in C++17 due to non-throwing exception specification in function signature [-Wc++17-compat-mangling] static inline rc_t Make ( KThread **t, ^ 1 warning generated. [ 2%] Building CXX object libs/align/CMakeFiles/sam-extract.dir/samextract-bam.cpp.o In file included from /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/libs/align/samextract-bam.cpp:41: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/kproc/thread.hpp:48:24: warning: mangled name of 'Make' will change in C++17 due to non-throwing exception specification in function signature [-Wc++17-compat-mangling] static inline rc_t Make ( KThread **t, ^ 1 warning generated. 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/libs/inc -Wall -pipe -g -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -pipe -g -fstack-protector-strong -fno-strict-aliasing -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/EBI_ReferenceSequence.c [ 2% 12/407] /ccache/libexec/ccache/cc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/libs/inc -Wall -pipe -g -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -pipe -g -fstack-protector-strong -fno-strict-aliasing -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o -MF ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o.d -o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/SRA_Statistics.c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/SRA_Statistics.c:272:72: warning: implicit conversion from 'long long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] if ( *end == 0 && errno == 0 && dbl >= LLONG_MIN && dbl <= LLONG_MAX ) ~~ ^~~~~~~~~ /usr/include/sys/limits.h:69:19: note: expanded from macro 'LLONG_MAX' #define LLONG_MAX __LLONG_MAX /* max for a long long */ ^~~~~~~~~~~ /usr/include/x86/_limits.h:74:21: note: expanded from macro '__LLONG_MAX' #define __LLONG_MAX 0x7fffffffffffffffLL /* max value for a long long */ ^~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/SRA_Statistics.c:318:81: warning: implicit conversion from 'long long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] if ( node -> value . real < LLONG_MIN || node -> value . real > LLONG_MAX ) ~ ^~~~~~~~~ /usr/include/sys/limits.h:69:19: note: expanded from macro 'LLONG_MAX' #define LLONG_MAX __LLONG_MAX /* max for a long long */ ^~~~~~~~~~~ /usr/include/x86/_limits.h:74:21: note: expanded from macro '__LLONG_MAX' #define __LLONG_MAX 0x7fffffffffffffffLL /* max value for a long long */ ^~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/SRA_Statistics.c:366:64: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] if ( *end == 0 && errno == 0 && dbl >= 0 && dbl <= ULLONG_MAX ) ~~ ^~~~~~~~~~ /usr/include/sys/limits.h:68:20: note: expanded from macro 'ULLONG_MAX' #define ULLONG_MAX __ULLONG_MAX /* max for an unsigned long long */ ^~~~~~~~~~~~ /usr/include/x86/_limits.h:73:22: note: expanded from macro '__ULLONG_MAX' #define __ULLONG_MAX 0xffffffffffffffffULL ^~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs/SRA_Statistics.c:412:73: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] if ( node -> value . real < 0 || node -> value . real > ULLONG_MAX ) ~ ^~~~~~~~~~ /usr/include/sys/limits.h:68:20: note: expanded from macro 'ULLONG_MAX' #define ULLONG_MAX __ULLONG_MAX /* max for an unsigned long long */ ^~~~~~~~~~~~ /usr/include/x86/_limits.h:73:22: note: expanded from macro '__ULLONG_MAX' #define __ULLONG_MAX 0xffffffffffffffffULL ^~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ncbi/ngs-jni -Wall -pipe -g -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -pipe -g -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -MF ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o.d -o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp [ 29% 121/407] : && /usr/local/bin/cmake -E rm -f ilib/libngs-bind-java.a && /usr/bin/llvm-ar qc ilib/libngs-bind-java.a ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o 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ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o && /usr/bin/llvm-ranlib lib/libncbi-ngs.a && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib && rm -f libncbi-ngs.a.3.0.6 && mv libncbi-ngs.a libncbi-ngs.a.3.0.6 && ln -f -s libncbi-ngs.a.3.0.6 libncbi-ngs.a.3 && ln -f -s libncbi-ngs.a.3 libncbi-ngs.a && ln -f -s libncbi-ngs.a libncbi-ngs-static.a [ 35% 144/407] : && /ccache/libexec/ccache/c++ -fPIC -Wall -pipe -g -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -pipe -g -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -shared -Wl,-soname,libncbi-ngs.so -o lib/libncbi-ngs.so ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build/lib /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build/lib/libkapp.a ilib/libtk-version.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib && rm -f libncbi-ngs.so.3.0.6 && mv libncbi-ngs.so libncbi-ngs.so.3.0.6 && ln -f -s libncbi-ngs.so.3.0.6 libncbi-ngs.so.3 && ln -f -s libncbi-ngs.so.3 libncbi-ngs.so [ 35% 145/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClearClassFiles.cmake && /usr/local/bin/javac -classpath :/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java:/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir @/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java ngs/itf/Refcount.java:57: warning: [removal] finalize() in Object has been deprecated and marked for removal protected void finalize () ^ Note: gov/nih/nlm/ncbi/ngs/LibVersionChecker.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. 1 warning [ 35% 146/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClassFilelist.cmake [ 36% 147/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/local/bin/jar -cf /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-java.jar @java_class_filelist && /usr/local/bin/cmake -D_JAVA_TARGET_DIR=/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/local/share/cmake/Modules/UseJava/Symlinks.cmake [ 36% 148/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && /usr/local/bin/javadoc -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs Loading source files for package gov.nih.nlm.ncbi.ngs... Loading source files for package ngs... Constructing Javadoc information... Creating destination directory: "/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/" Building index for all the packages and classes... Standard Doclet version 18.0.2+9-1 Building tree for all the packages and classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:38: warning: no initial description * @return What went wrong ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: use of default constructor, which does not provide a comment public class LibDependencies { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: use of default constructor, which does not provide a comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Package.java:37: warning: no initial description * @return package version as a 1..3 part string ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Package.java:33: warning: use of default constructor, which does not provide a comment public class Package ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Pileup.java:58: warning: no initial description * @return base at current Reference position ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadCollection.java:88: warning: no initial description * @param spec the name of a contained read group ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadCollection.java:121: warning: no initial description * @param spec the name of a contained Reference ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index.html... Building index for all classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index-all.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... 52 warnings [ 36% 149/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/local/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-doc.jar\ . [ 36% 150/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && bash -c /usr/local/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java [ 37% 151/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/examples && /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClearClassFiles.cmake && /usr/local/bin/javac -classpath :/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/examples:/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib:/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-java.jar -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples [ 37% 152/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/examples && /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClassFilelist.cmake [ 37% 153/407] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/local/bin/jar -cf /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-examples.jar @java_class_filelist && /usr/local/bin/cmake -D_JAVA_TARGET_DIR=/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/local/share/cmake/Modules/UseJava/Symlinks.cmake [ 37% 154/407] /ccache/libexec/ccache/cc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/libs/inc -I/usr/local/include/libxml2 -Wall -pipe -g -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -pipe -g -fstack-protector-strong -fno-strict-aliasing -std=c11 -fPIC -MD -MT 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/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/tools/external/driver-tool && sh generate-args-info.sh /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin [ 40% 2/5] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && /usr/local/bin/javadoc -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs Loading source files for package gov.nih.nlm.ncbi.ngs... Loading source files for package ngs... Constructing Javadoc information... Building index for all the packages and classes... Standard Doclet version 18.0.2+9-1 Building tree for all the packages and classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:38: warning: no initial description * @return What went wrong ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: use of default constructor, which does not provide a comment public class LibDependencies { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: use of default constructor, which does not provide a comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Package.java:37: warning: no initial description * @return package version as a 1..3 part string ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Package.java:33: warning: use of default constructor, which does not provide a comment public class Package ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Pileup.java:58: warning: no initial description * @return base at current Reference position ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadCollection.java:88: warning: no initial description * @param spec the name of a contained read group ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadCollection.java:121: warning: no initial description * @param spec the name of a contained Reference ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index.html... Building index for all classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index-all.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... 52 warnings [ 60% 4/5] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/local/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-doc.jar\ . [ 80% 4/5] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.0.6/ngs/ngs-java && bash -c /usr/local/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java [ 80% 5/5] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build && /usr/local/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a.3.0.6 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ncbi-vdb/NGS.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/FragTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/AlignTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/AlignSliceTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/PileupTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/RefTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/DumpReferenceFASTA.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/expected.txt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/Makefile -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/README.txt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a.3.0.6 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so.3.0.6 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a.3.0.6 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.so.3.0.6 -- Installing: 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/wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/win/stdbool.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/win/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/PileupEventIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Fragment.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReadGroupIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/FragmentItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReadCollectionItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReferenceSequenceItf.hpp -- Installing: 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/wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3.0.6 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info true /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/*.3.0.6 /bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools /bin/mkdir -p /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools /bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools/* /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools /bin/rmdir /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools /bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/java /bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/python ====> Compressing man pages (compress-man) ===> Installing ldconfig configuration file =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-31T13:06:12+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=0f2f80ca38' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for sra-tools-3.0.6 ===> Building sra-tools-3.0.6 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-3.6.1.min.js:No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/sra-tools =>> Cleaning up wrkdir ===> Cleaning for sra-tools-3.0.6 build of biology/sra-tools | sra-tools-3.0.6 ended at Sun Mar 31 14:55:03 BST 2024 build time: 00:48:52 !!! build failure encountered !!!