------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/fastq-trim XDG_CONFIG_HOME=/construction/biology/fastq-trim XDG_CACHE_HOME=/construction/biology/fastq-trim/.cache HOME=/construction/biology/fastq-trim TMPDIR="/tmp" PATH=/construction/biology/fastq-trim/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/fastq-trim/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- VERSION=0.1.2 XDG_DATA_HOME=/construction/biology/fastq-trim XDG_CONFIG_HOME=/construction/biology/fastq-trim XDG_CACHE_HOME=/construction/biology/fastq-trim/.cache HOME=/construction/biology/fastq-trim TMPDIR="/tmp" PATH=/construction/biology/fastq-trim/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/fastq-trim/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/fastq-trim/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fastq-trim" EXAMPLESDIR="share/examples/fastq-trim" DATADIR="share/fastq-trim" WWWDIR="www/fastq-trim" ETCDIR="etc/fastq-trim" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastq-trim DOCSDIR=/usr/local/share/doc/fastq-trim EXAMPLESDIR=/usr/local/share/examples/fastq-trim WWWDIR=/usr/local/www/fastq-trim ETCDIR=/usr/local/etc/fastq-trim SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/libxtend-0.1.8.2.pkg Installing /packages/All/biolibc-0.2.4.3.pkg SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastq-trim-0.1.2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastq-trim-0.1.2 for building => SHA256 Checksum OK for outpaddling-fastq-trim-0.1.2_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastq-trim-0.1.2 for building ===> Extracting for fastq-trim-0.1.2 => SHA256 Checksum OK for outpaddling-fastq-trim-0.1.2_GH0.tar.gz. Extracted Memory Use: 0.46M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for fastq-trim-0.1.2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> fastq-trim-0.1.2 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> fastq-trim-0.1.2 depends on file: /usr/local/bin/ccache - found ===> fastq-trim-0.1.2 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> fastq-trim-0.1.2 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> Configuring for fastq-trim-0.1.2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for fastq-trim-0.1.2 (cd /construction/biology/fastq-trim/fastq-trim-0.1.2 && /usr/bin/make LOCALBASE=/usr/local depend) rm -f Makefile.depend for file in *.c; do cc -isystem ../local/include -isystem /usr/local/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- fastq-trim.o --- --- fastq-trim-class.o --- --- fastq-trim-mutators.o --- cc -c -pipe -O2 -fno-strict-aliasing -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fastq-trim-mutators.c --- fastq-trim.o --- cc -c -pipe -O2 -fno-strict-aliasing -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fastq-trim.c --- fastq-trim-class.o --- cc -c -pipe -O2 -fno-strict-aliasing -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fastq-trim-class.c --- fastq-trim-mutators.o --- fastq-trim-mutators.c:897:83: error: parameter 3 ('new_instream1_element') has incomplete type int fastq_trim_set_instream1_ae(fastq_trim_t *fastq_trim_ptr, size_t c, FILE new_instream1_element) ~~~~~~^~~~~~~~~~~~~~~~~~~~~ fastq-trim-mutators.c: In function 'fastq_trim_set_instream1_ae': fastq-trim-mutators.c:904:27: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream1[c] = new_instream1_element; ^ fastq-trim-mutators.c:904:27: error: dereferencing pointer to incomplete type 'FILE' {aka 'struct __FILE'} fastq-trim-mutators.c: In function 'fastq_trim_set_instream1_cpy': fastq-trim-mutators.c:963:31: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream1[c] = new_instream1[c]; ^ fastq-trim-mutators.c:963:50: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream1[c] = new_instream1[c]; ^ fastq-trim-mutators.c: At top level: fastq-trim-mutators.c:1067:84: error: parameter 3 ('new_outstream1_element') has incomplete type int fastq_trim_set_outstream1_ae(fastq_trim_t *fastq_trim_ptr, size_t c, FILE new_outstream1_element) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ fastq-trim-mutators.c: In function 'fastq_trim_set_outstream1_ae': fastq-trim-mutators.c:1074:28: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream1[c] = new_outstream1_element; ^ fastq-trim-mutators.c: In function 'fastq_trim_set_outstream1_cpy': fastq-trim-mutators.c:1133:32: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream1[c] = new_outstream1[c]; ^ fastq-trim-mutators.c:1133:52: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream1[c] = new_outstream1[c]; ^ fastq-trim-mutators.c: At top level: fastq-trim-mutators.c:1237:83: error: parameter 3 ('new_instream2_element') has incomplete type int fastq_trim_set_instream2_ae(fastq_trim_t *fastq_trim_ptr, size_t c, FILE new_instream2_element) ~~~~~~^~~~~~~~~~~~~~~~~~~~~ fastq-trim-mutators.c: In function 'fastq_trim_set_instream2_ae': fastq-trim-mutators.c:1244:27: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream2[c] = new_instream2_element; ^ fastq-trim-mutators.c: In function 'fastq_trim_set_instream2_cpy': fastq-trim-mutators.c:1303:31: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream2[c] = new_instream2[c]; ^ fastq-trim-mutators.c:1303:50: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->instream2[c] = new_instream2[c]; ^ fastq-trim-mutators.c: At top level: fastq-trim-mutators.c:1407:84: error: parameter 3 ('new_outstream2_element') has incomplete type int fastq_trim_set_outstream2_ae(fastq_trim_t *fastq_trim_ptr, size_t c, FILE new_outstream2_element) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ fastq-trim-mutators.c: In function 'fastq_trim_set_outstream2_ae': fastq-trim-mutators.c:1414:28: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream2[c] = new_outstream2_element; ^ fastq-trim-mutators.c: In function 'fastq_trim_set_outstream2_cpy': fastq-trim-mutators.c:1473:32: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream2[c] = new_outstream2[c]; ^ fastq-trim-mutators.c:1473:52: error: invalid use of undefined type 'struct __FILE' fastq_trim_ptr->outstream2[c] = new_outstream2[c]; ^ *** [fastq-trim-mutators.o] Error code 1 make[1]: stopped in /construction/biology/fastq-trim/fastq-trim-0.1.2 1 error make[1]: stopped in /construction/biology/fastq-trim/fastq-trim-0.1.2 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/fastq-trim FAILED 00:00:00