[package - main-i386-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_7 in build
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Date: Thu, 29 Jun 2023 05:23:41 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p8c7f3e19a83a_se495600ce3/logs/ncbi-toolkit-2017.01.06_7.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p8c7f3e19a83a_se495600ce3
Log:
=>> Building biology/ncbi-toolkit
build started at Thu Jun 29 05:16:06 UTC 2023
port directory: /usr/ports/biology/ncbi-toolkit
package name: ncbi-toolkit-2017.01.06_7
building for: FreeBSD main-i386-default-job-12 14.0-CURRENT FreeBSD 14.0-CURRENT 1400092 i386
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400092
Job Id: 12
!!! Jail is newer than host. (Jail: 1400092, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---End Environment---
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PORT_FLAGS=
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FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for ncbi-toolkit-2017.01.06_7:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
MOTIFLIB="-L/usr/local/lib -lXm" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasi
ng -DLIBICONV_PLUG " 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"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/ncbi-toolkit" EXAMPLESDIR="share/examples/ncbi-toolkit" DATADIR="share/ncbi-toolkit" WWWDIR="www/ncbi-toolkit" ETCDIR="etc/ncbi-toolkit"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-toolkit DOCSDIR=/usr/local/share/doc/ncbi-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-toolkit WWWDIR=/usr/local/www/ncbi-toolkit ETCDIR=/usr/local/etc/ncbi-toolkit
--End SUB_LIST--
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MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
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# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
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#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
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file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
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pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_2.pkg
[main-i386-default-job-12] Installing pkg-1.19.1_2...
[main-i386-default-job-12] Extracting pkg-1.19.1_2: .......... done
===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-toolkit-2017.01.06_7
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
===> Extracting for ncbi-toolkit-2017.01.06_7
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for ncbi-toolkit-2017.01.06_7
===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_7 from /usr/ports/biology/ncbi-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
<snip>
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF get.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF maketables.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pcre.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pcreposix.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF study.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
rm -f libregexp.a
ar cru libregexp.a chartables.o get.o maketables.o pcre.o pcreposix.o study.o
cp -p libregexp.a ../lib
ranlib ../lib/libregexp.a
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF aa_ungapped.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_diagnostics.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_engine.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_extend.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_filter.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_gapalign.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hits.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_itree.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_lookup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_message.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_options.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seg.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seqsrc.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_sw.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_setup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_stat.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_traceback.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_util.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gapinfo.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF greedy_align.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF link_hsps.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup_wrap.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF na_ungapped.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ncbi_math.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ncbi_std.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pattern.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_extend.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_lookup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup_util.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_encoding.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_psi.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_psi_priv.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_kappa.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF matrix_freq_ratios.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hspstream.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_parameters.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_posit.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_gapalign.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_program.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_query_info.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_tune.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_aalookup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_nalookup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
blast_nalookup.c:901:5: warning: array index 4294967295 refers past the last possible element for an array in 32-bit address space containing 32-bit (4-byte) elements (max possible 1073741824 elements) [-Warray-bounds]
mb_lt->hashtable[(Int8)0xffffffff] = 0;
^ ~~~~~~~~~~~~~~~~
../include/algo/blast/core/blast_nalookup.h:253:5: note: array 'hashtable' declared here
Int4* hashtable; /**< Array of positions */
^
../include/ncbistd.h:178:21: note: expanded from macro 'Int4'
#define Int4 Nlm_Int4
^
1 warning generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_aascan.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_nascan.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_dynarray.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF split_query.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gencode_singleton.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF index_ungapped.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF hspfilter_collector.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hspstream_mt_utils.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_traceback_mt_priv.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF boost_erf.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF jumper.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
rm -f libblast.a
ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.o
cp -p libblast.a ../lib
ranlib ../lib/libblast.a
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_api.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_input.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_format.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
blast_format.c:160:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'BlastOutput *' (aka 'struct struct_BlastOutput *') [-Wnon-literal-null-conversion]
return FALSE;
^~~~~
../include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
1 warning generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_mtlock.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_options_api.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_prelim.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_returns.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seq.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seqalign.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_tabular.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF repeats_filter.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF seqsrc_multiseq.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF seqsrc_readdb.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF twoseq_api.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF dust_filter.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_message_api.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF hspfilter_queue.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
hspfilter_queue.c:157:24: error: incompatible function pointer types assigning to 'BlastHSPWriterInitFn' (aka 'int (*)(void *, void *)') from 'int (*)(void *, BlastHSPResults *)' (aka 'int (*)(void *, struct BlastHSPResults *)') [-Wincompatible-function-pointer-types]
writer->InitFnPtr = &s_BlastHSPQueueInit;
^ ~~~~~~~~~~~~~~~~~~~~
hspfilter_queue.c:158:24: error: incompatible function pointer types assigning to 'BlastHSPWriterFinalFn' (aka 'int (*)(void *, void *)') from 'int (*)(void *, BlastHSPResults *)' (aka 'int (*)(void *, struct BlastHSPResults *)') [-Wincompatible-function-pointer-types]
writer->FinalFnPtr = &s_BlastHSPQueueFinal;
^ ~~~~~~~~~~~~~~~~~~~~~
hspfilter_queue.c:189:26: error: incompatible function pointer types assigning to 'BlastHSPWriterNewFn' (aka 'struct BlastHSPWriter *(*)(void *, struct BlastQueryInfo *, struct BLAST_SequenceBlk *)') from 'BlastHSPWriter *(*)(void *, BlastQueryInfo *)' (aka 'struct BlastHSPWriter *(*)(void *, struct BlastQueryInfo *)') [-Wincompatible-function-pointer-types]
writer_info->NewFnPtr = &s_BlastHSPQueueNew;
^ ~~~~~~~~~~~~~~~~~~~
3 errors generated.
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/build
Fatal error building NCBI core libraries.
Please be sure that you have X11 and Motif libraries installed.
The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-toolkit