[package - head-armv6-default][biology/seaview] Failed for seaview-5.0.4, 1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Nov 19 06:41:44 UTC 2020
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: bofh at FreeBSD.org
Last committer: bofh at FreeBSD.org
Ident: $FreeBSD: head/biology/seaview/Makefile 539893 2020-06-22 17:34:44Z bofh $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p555156_s367697/logs/seaview-5.0.4,1.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p555156_s367697
Log:
=>> Building biology/seaview
build started at Thu Nov 19 06:40:26 UTC 2020
port directory: /usr/ports/biology/seaview
package name: seaview-5.0.4,1
building for: FreeBSD head-armv6-default-job-07 13.0-CURRENT FreeBSD 13.0-CURRENT 1300129 arm
maintained by: bofh at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/seaview/Makefile 539893 2020-06-22 17:34:44Z bofh $
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!!! Jail is newer than host. (Jail: 1300129, Host: 1300121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> seaview-5.0.4,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[head-armv6-default-job-07] Installing pkg-1.15.10...
[head-armv6-default-job-07] Extracting pkg-1.15.10: .......... done
===> seaview-5.0.4,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seaview-5.0.4,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by seaview-5.0.4,1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by seaview-5.0.4,1 for building
<snip>
[head-armv6-default-job-07] | | `-- Extracting liblz4-1.9.2_1,1: .......... done
[head-armv6-default-job-07] | | `-- Extracting zstd-1.4.5_1: .......... done
[head-armv6-default-job-07] | `-- Extracting mesa-libs-20.2.0_1: .......... done
[head-armv6-default-job-07] `-- Extracting libGLU-9.0.1: ...... done
[head-armv6-default-job-07] Extracting fltk-1.3.5: .......... done
===> seaview-5.0.4,1 depends on shared library: libfltk.so - found (/usr/local/lib/libfltk.so)
===> Returning to build of seaview-5.0.4,1
===> seaview-5.0.4,1 depends on shared library: libfontconfig.so - found (/usr/local/lib/libfontconfig.so)
===> seaview-5.0.4,1 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so)
===> seaview-5.0.4,1 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for seaview-5.0.4,1
===========================================================================
=======================<phase: build >============================
===> Building for seaview-5.0.4,1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/seaview/work/seaview'
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF seaview.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF custom.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF use_mase_files.cxx
use_mase_files.cxx:396:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while(c != '\n' && c != '\r' && c != EOF) c = getc(in);
~ ^ ~~~
1 warning generated.
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF regions.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF load_seq.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF align.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF xfmatpt.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF comlines.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF resource.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF nexus.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF viewasprots.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF racnuc_fetch.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF concatenate.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF statistics.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF trees.cxx
trees.cxx:190:25: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while((c = fgetc(in)) != EOF) {
~~~~~~~~~~~~~~~ ^ ~~~
1 warning generated.
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF treedraw.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF addbootstrap.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF least_squares_brl.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF pseudoterminal.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF unrooted.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF pdf_or_ps.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF svg.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF threads.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF tbe.cxx
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF treerecs_draw.cxx
treerecs_draw.cxx:1007:33: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while( ( ch = fgetc(source) ) != EOF )
~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~
1 warning generated.
/nxb-bin/usr/bin/c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -I/usr/local/include -Icsrc -DDEFAULT_HELPFILE=\"/usr/local/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF FL/Fl_SVG_Image.cxx
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/raa_acnuc.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/parser.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/md5.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/zsockr.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/misc_acnuc.c
csrc/misc_acnuc.c:870:7: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if(c == EOF || c == '\n' || c == '\r') break;
~ ^ ~~~
1 warning generated.
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/dnapars.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/protpars.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/seq.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/phylip.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/lwl.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/bionj.c
/nxb-bin/usr/bin/cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/phyml_util.c
/nxb-bin/usr/bin/c++ -o seaview -fstack-protector-strong seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o treerecs_draw.o Fl_SVG_Image.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o `fltk-config --use-images --ldflags` -lpthread -lz
ld: error: duplicate symbol: progname
>>> defined at seaview.cxx
>>> seaview.o:(progname)
>>> defined at dnapars.c
>>> dnapars.o:(.bss+0x1B4)
ld: error: duplicate symbol: ancseq
>>> defined at dnapars.c
>>> dnapars.o:(ancseq)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x5EE)
ld: error: duplicate symbol: bestrees
>>> defined at dnapars.c
>>> dnapars.o:(bestrees)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x61C)
ld: error: duplicate symbol: chars
>>> defined at dnapars.c
>>> dnapars.o:(chars)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x260)
ld: error: duplicate symbol: col
>>> defined at dnapars.c
>>> dnapars.o:(col)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x5DC)
ld: error: duplicate symbol: enterorder
>>> defined at dnapars.c
>>> dnapars.o:(enterorder)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x614)
ld: error: duplicate symbol: firstplotblock
>>> defined at dnapars.c
>>> dnapars.o:(firstplotblock)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x2B9)
ld: error: duplicate symbol: firstset
>>> defined at dnapars.c
>>> dnapars.o:(firstset)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x28C)
ld: error: duplicate symbol: fsteps
>>> defined at dnapars.c
>>> dnapars.o:(fsteps)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x618)
ld: error: duplicate symbol: garbage
>>> defined at dnapars.c
>>> dnapars.o:(garbage)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x280)
ld: error: duplicate symbol: infilename
>>> defined at dnapars.c
>>> dnapars.o:(infilename)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x2BA)
ld: error: duplicate symbol: inseed
>>> defined at dnapars.c
>>> dnapars.o:(inseed)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x5E0)
ld: error: duplicate symbol: inseed0
>>> defined at dnapars.c
>>> dnapars.o:(inseed0)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x5E4)
ld: error: duplicate symbol: intreename
>>> defined at dnapars.c
>>> dnapars.o:(intreename)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x44A)
ld: error: duplicate symbol: ith
>>> defined at dnapars.c
>>> dnapars.o:(ith)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x29C)
ld: error: duplicate symbol: javarun
>>> defined at dnapars.c
>>> dnapars.o:(javarun)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x2B8)
ld: error: duplicate symbol: jumb
>>> defined at dnapars.c
>>> dnapars.o:(jumb)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x2A0)
ld: error: duplicate symbol: jumble
>>> defined at dnapars.c
>>> dnapars.o:(jumble)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x294)
ld: error: duplicate symbol: justwts
>>> defined at dnapars.c
>>> dnapars.o:(justwts)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x5ED)
ld: error: duplicate symbol: lastrearr
>>> defined at dnapars.c
>>> dnapars.o:(lastrearr)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x634)
ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile:46: seaview] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/seaview/work/seaview'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seaview
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