[package - head-amd64-default][biology/seaview] Failed for seaview-5.0.4, 1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Dec 19 07:35:04 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://beefy18.nyi.freebsd.org/data/head-amd64-default/p558421_s368710/logs/seaview-5.0.4,1.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p558421_s368710
Log:
=>> Building biology/seaview
build started at Sat Dec 19 07:34:44 UTC 2020
port directory: /usr/ports/biology/seaview
package name: seaview-5.0.4,1
building for: FreeBSD head-amd64-default-job-04 13.0-CURRENT FreeBSD 13.0-CURRENT 1300132 amd64
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: 1300132, Host: 1300121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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bofh at FreeBSD.org
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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-amd64-default-job-04] Installing pkg-1.15.10...
[head-amd64-default-job-04] 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
=> SHA256 Checksum OK for seaview_5.0.4.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by seaview-5.0.4,1 for building
===> Extracting for seaview-5.0.4,1
=> SHA256 Checksum OK for seaview_5.0.4.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for seaview-5.0.4,1
/usr/bin/sed -i.bak -e 's|^\(CC\) |#\1 | ; s|-ldl || ; s|^\(CXX\) |#\1 |' /wrkdirs/usr/ports/biology/seaview/work/seaview/Makefile
===========================================================================
=======================<phase: build-depends >============================
===> seaview-5.0.4,1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-amd64-default-job-04] Installing gmake-4.3_2...
[head-amd64-default-job-04] `-- Installing gettext-runtime-0.21...
[head-amd64-default-job-04] | `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done
[head-amd64-default-job-04] `-- Extracting gettext-runtime-0.21: .......... done
[head-amd64-default-job-04] Extracting gmake-4.3_2: .......... done
<snip>
[head-amd64-default-job-04] | | `-- Extracting libdrm-2.4.103,1: .......... done
[head-amd64-default-job-04] | | `-- Installing libunwind-20200331_1...
[head-amd64-default-job-04] | | `-- Extracting libunwind-20200331_1: .......... done
[head-amd64-default-job-04] | | `-- Installing libxshmfence-1.3...
[head-amd64-default-job-04] | | `-- Extracting libxshmfence-1.3: ......... done
[head-amd64-default-job-04] | | `-- Installing wayland-1.18.0_4...
[head-amd64-default-job-04] | | `-- Installing libepoll-shim-0.0.20200602...
[head-amd64-default-job-04] | | `-- Extracting libepoll-shim-0.0.20200602: .......... done
[head-amd64-default-job-04] | | `-- Installing libffi-3.3_1...
[head-amd64-default-job-04] | | `-- Extracting libffi-3.3_1: .......... done
[head-amd64-default-job-04] | | `-- Extracting wayland-1.18.0_4: .......... done
[head-amd64-default-job-04] | | `-- Installing zstd-1.4.5_1...
[head-amd64-default-job-04] | | `-- Installing liblz4-1.9.3,1...
[head-amd64-default-job-04] | | `-- Extracting liblz4-1.9.3,1: .......... done
[head-amd64-default-job-04] | | `-- Extracting zstd-1.4.5_1: .......... done
[head-amd64-default-job-04] | `-- Extracting mesa-libs-20.2.3: .......... done
[head-amd64-default-job-04] `-- Extracting libGLU-9.0.1: ...... done
[head-amd64-default-job-04] 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'
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/raa_acnuc.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/parser.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/md5.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/zsockr.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/misc_acnuc.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/dnapars.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/protpars.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/seq.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/phylip.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/lwl.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/bionj.c
cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dunix -Icsrc csrc/phyml_util.c
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+0x190)
ld: error: duplicate symbol: ancseq
>>> defined at dnapars.c
>>> dnapars.o:(ancseq)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x7B6)
ld: error: duplicate symbol: bestrees
>>> defined at dnapars.c
>>> dnapars.o:(bestrees)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x810)
ld: error: duplicate symbol: chars
>>> defined at dnapars.c
>>> dnapars.o:(chars)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x3C8)
ld: error: duplicate symbol: col
>>> defined at dnapars.c
>>> dnapars.o:(col)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x798)
ld: error: duplicate symbol: enterorder
>>> defined at dnapars.c
>>> dnapars.o:(enterorder)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x800)
ld: error: duplicate symbol: firstplotblock
>>> defined at dnapars.c
>>> dnapars.o:(firstplotblock)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x459)
ld: error: duplicate symbol: firstset
>>> defined at dnapars.c
>>> dnapars.o:(firstset)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x418)
ld: error: duplicate symbol: fsteps
>>> defined at dnapars.c
>>> dnapars.o:(fsteps)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x808)
ld: error: duplicate symbol: garbage
>>> defined at dnapars.c
>>> dnapars.o:(garbage)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x400)
ld: error: duplicate symbol: infilename
>>> defined at dnapars.c
>>> dnapars.o:(infilename)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x460)
ld: error: duplicate symbol: inseed
>>> defined at dnapars.c
>>> dnapars.o:(inseed)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x7A0)
ld: error: duplicate symbol: inseed0
>>> defined at dnapars.c
>>> dnapars.o:(inseed0)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x7A8)
ld: error: duplicate symbol: intreename
>>> defined at dnapars.c
>>> dnapars.o:(intreename)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x600)
ld: error: duplicate symbol: ith
>>> defined at dnapars.c
>>> dnapars.o:(ith)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x438)
ld: error: duplicate symbol: javarun
>>> defined at dnapars.c
>>> dnapars.o:(javarun)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x458)
ld: error: duplicate symbol: jumb
>>> defined at dnapars.c
>>> dnapars.o:(jumb)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x440)
ld: error: duplicate symbol: jumble
>>> defined at dnapars.c
>>> dnapars.o:(jumble)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x428)
ld: error: duplicate symbol: justwts
>>> defined at dnapars.c
>>> dnapars.o:(justwts)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x7B5)
ld: error: duplicate symbol: lastrearr
>>> defined at dnapars.c
>>> dnapars.o:(lastrearr)
>>> defined at protpars.c
>>> protpars.o:(.bss+0x840)
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'
===> 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 /usr/ports/biology/seaview
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