[package - main-amd64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_9 in build
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Date: Sat, 09 May 2026 07:28:42 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/beefy24/data/main-amd64-default/p142569cd0b2b_s1bef5535c1f/logs/ncbi-toolkit-2017.01.06_9.log
Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=p142569cd0b2b_s1bef5535c1f
Log:
=>> Building biology/ncbi-toolkit
build started at Sat May 9 07:23:34 UTC 2026
port directory: /usr/ports/biology/ncbi-toolkit
package name: ncbi-toolkit-2017.01.06_9
building for: FreeBSD main-amd64-default-job-28 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2813 Sep 30 2025 /usr/ports/biology/ncbi-toolkit/Makefile
Ports top last git commit: 142569cd0b2bd7c606dce1694dbcedeadfd212db
Ports top unclean checkout: no
Port dir last git commit: b64b73fd938d5b2788547d16ed6a76493acc9142
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8
Host OSVERSION: 1600014
Jail OSVERSION: 1600018
Job Id: 28
!!! Jail is newer than host. (Jail: 1600018, Host: 1600014) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1600018
UNAME_v=FreeBSD 16.0-CURRENT 1600018
UNAME_r=16.0-CURRENT
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=3.4.8
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
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OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.8
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 ncbi-toolkit-2017.01.06_9:
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 -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-poin
ter-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG " 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=16.0 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--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---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
pipebuf (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[main-amd64-default-job-28] Installing pkg-2.7.5...
[main-amd64-default-job-28] Extracting pkg-2.7.5: .......... done
===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-toolkit-2017.01.06_9
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_9 for building
===> Extracting for ncbi-toolkit-2017.01.06_9
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for ncbi-toolkit-2017.01.06_9
===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_9 from /usr/ports/biology/ncbi-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ncbi-toolkit-2017.01.06_9 depends on package: gettext-runtime>=0.26 - not found
===> Installing existing package /packages/All/gettext-runtime-1.0.pkg
[main-amd64-default-job-28] Installing gettext-runtime-1.0...
[main-amd64-default-job-28] `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-28] `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-28] Extracting gettext-runtime-1.0: .......... done
===> ncbi-toolkit-2017.01.06_9 depends on package: gettext-runtime>=0.26 - found
===> Returning to build of ncbi-toolkit-2017.01.06_9
===> ncbi-toolkit-2017.01.06_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===> Installing existing package /packages/All/libX11-1.8.13_1,1.pkg
[main-amd64-default-job-28] Installing libX11-1.8.13_1,1...
[main-amd64-default-job-28] `-- Installing libxcb-1.17.0...
[main-amd64-default-job-28] | `-- Installing libXau-1.0.12...
[main-amd64-default-job-28] | `-- Extracting libXau-1.0.12: .......... done
[main-amd64-default-job-28] | `-- Installing libXdmcp-1.1.5...
[main-amd64-default-job-28] | | `-- Installing xorgproto-2025.1...
<snip>
toporg.c:4796:12: note: add parentheses after the '!' to evaluate the comparison first
4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) {
| ^
| ( )
toporg.c:4796:12: note: add parentheses around left hand side expression to silence this warning
4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) {
| ^
| ( )
1 warning generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pobutil.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
pobutil.c:2380:44: warning: 'size' argument to memset is '0'; did you mean to transpose the last two arguments? [-Wmemset-transposed-args]
2380 | MemSet((Pointer) (&tmp), sizeof(ValNode), 0);
| ^
pobutil.c:2380:44: note: parenthesize the third argument to silence
pobutil.c:2381:42: warning: 'size' argument to memset is '0'; did you mean to transpose the last two arguments? [-Wmemset-transposed-args]
2381 | MemSet((Pointer) (&si), sizeof(SeqInt), 0);
| ^
pobutil.c:2381:42: note: parenthesize the third argument to silence
2 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF stsutil.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggadj.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggest.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF suggslp.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
blast.c:3179:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
3179 | if (virtual_oidlist = rdfp_chain->oidlist) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
blast.c:3179:29: note: place parentheses around the assignment to silence this warning
3179 | if (virtual_oidlist = rdfp_chain->oidlist) {
| ^
| ( )
blast.c:3179:29: note: use '==' to turn this assignment into an equality comparison
3179 | if (virtual_oidlist = rdfp_chain->oidlist) {
| ^
| ==
blast.c:3210:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blast.c:3210:29: note: place parentheses around the assignment to silence this warning
3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) {
| ^
| ( )
blast.c:3210:29: note: use '==' to turn this assignment into an equality comparison
3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) {
| ^
| ==
blast.c:10121:25: warning: add explicit braces to avoid dangling else [-Wdangling-else]
10121 | else if( del_index < new_index )
| ^
3 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastutl.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
blastutl.c:7554:12: warning: expression result unused [-Wunused-value]
7554 | stop_timer("after repeat filtering");
| ^~~~~~~~~~~~~~~~~~~~~~~~
blastutl.c:10282:12: warning: expression result unused [-Wunused-value]
10282 | stop_timer("after BlastGappedScoreInternal");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastool.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastconcat.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF splutil.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gapxdrop.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
gapxdrop.c:866:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
866 | else if ((t/10)%3 == 2) k = 3;
| ^
gapxdrop.c:869:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
869 | else if ((t/30) == 2) k = 3;
| ^
2 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg0.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
bandalg0.c:277:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
277 | } else {
| ^
1 warning generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg1.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
bandalg1.c:210:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
210 | else data->CD[leftd - 1].DD = e;
| ^
1 warning generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg2.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg3.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg4.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
bandalg4.c:828:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
828 | else if ((t/10)%3 == 2) k = 3;
| ^
bandalg4.c:831:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
831 | else if ((t/30) == 2) k = 3;
| ^
2 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalg5.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
bandalg5.c:294:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
294 | else if ((t/10)%3 == 2) k = 3;
| ^
bandalg5.c:297:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
297 | else if ((t/30) == 2) k = 3;
| ^
2 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF bandalgn.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blastkar.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
blastkar.c:4936:10: warning: implicit conversion from 'double' to 'Nlm_Int2' (aka 'short') changes value from 0.5 to 0 [-Wliteral-conversion]
4936 | return 0.5;
| ~~~~~~ ^~~
1 warning generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF actutils.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
actutils.c:3026:84: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
3026 | slp = SeqLocCopyRegion (sip, sfp->location, bsp, 0, bsp->length - 1, strand, FALSE);
| ^~~~~
../include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
247 | #define FALSE ((Nlm_Boolean)0)
| ^~~~~~~~~~~~~~~~
actutils.c:3035:88: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
3035 | slp = SeqLocCopyRegion (sip, cbp->loc, bsp, 0, bsp->length - 1, strand, FALSE);
| ^~~~~
../include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
247 | #define FALSE ((Nlm_Boolean)0)
| ^~~~~~~~~~~~~~~~
actutils.c:3047:94: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
3047 | slp = SeqLocCopyRegion (sip, trp->anticodon, bsp, 0, bsp->length - 1, strand, FALSE);
| ^~~~~
../include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
247 | #define FALSE ((Nlm_Boolean)0)
| ^~~~~~~~~~~~~~~~
3 warnings generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF posit.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
lookup.c:1198:56: warning: for loop has empty body [-Wempty-body]
1198 | index>0; index=mb_lt->next_pos[index], pcount++);
| ^
lookup.c:1198:56: note: put the semicolon on a separate line to silence this warning
1 warning generated.
cc -DNDEBUG -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF readdb.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
readdb.c:2506:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
2506 | else
| ^
readdb.c:2734:33: warning: 'memset' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess]
2734 | memset(blast_dir, 0, sizeof(blast_dir));
| ~~~~~~~~~ ^~~~~~~~~
readdb.c:2734:33: note: did you mean to provide an explicit length?
2734 | memset(blast_dir, 0, sizeof(blast_dir));
| ^~~~~~~~~
readdb.c:3167:37: warning: format specifies type 'long long *' but the argument has type 'Nlm_Int8 *' (aka 'long *') [-Wformat]
3167 | sscanf(ptr, "%lld", &(rdbap->len));
| ~~~~ ^~~~~~~~~~~~~
| %ld
readdb.c:4896:45: error: chained comparison 'X <= Y <= Z' does not behave the same as a mathematical expression [-Wparentheses]
4896 | if (rdfp_var->start <= oid <= rdfp_var->stop)
| ^
readdb.c:6366:34: warning: 'memset' call operates on objects of type 'char' while the size is based on a different type 'Nlm_CharPtr' (aka 'char *') [-Wsizeof-pointer-memaccess]
6366 | MemSet(defline, '\0', sizeof(defline));
| ~~~~~~~ ^~~~~~~
readdb.c:6366:34: note: did you mean to provide an explicit length?
6366 | MemSet(defline, '\0', sizeof(defline));
| ^~~~~~~
readdb.c:9804:26: warning: address of array 'srp->div' will always evaluate to 'true' [-Wpointer-bool-conversion]
9804 | srp->div ? srp->div : "N/A", (long) SequenceLen,
| ~~~~~^~~ ~
readdb.c:9853:45: warning: address of array 'pc->div' will always evaluate to 'true' [-Wpointer-bool-conversion]
9853 | (long) direc.owner, pc->div ? pc->div : "N/A",
| ~~~~^~~ ~
readdb.c:12404:26: warning: format specifies type 'int' but the argument has type 'Nlm_Int8' (aka 'long') [-Wformat]
12404 | fprintf(fp, "%d\n", gi->data.intvalue);
| ~~ ^~~~~~~~~~~~~~~~~
| %ld
7 warnings and 1 error generated.
*** Error code 1
Stop.
make[1]: stopped making "all" 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 making "build" in /usr/ports/biology/ncbi-toolkit