[package - head-i386-default][biology/viennarna] Failed for viennarna-2.4.14_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Aug 30 16:54:33 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: yuri at FreeBSD.org
Last committer: dinoex at FreeBSD.org
Ident: $FreeBSD: head/biology/viennarna/Makefile 533989 2020-05-04 21:31:39Z dinoex $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p546963_s364970/logs/viennarna-2.4.14_1.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p546963_s364970
Log:
=>> Building biology/viennarna
build started at Sun Aug 30 16:51:05 UTC 2020
port directory: /usr/ports/biology/viennarna
package name: viennarna-2.4.14_1
building for: FreeBSD head-i386-default-job-03 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/viennarna/Makefile 533989 2020-05-04 21:31:39Z dinoex $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
Jail OSVERSION: 1300113
Job Id: 03
!!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---Begin OPTIONS List---
===> The following configuration options are available for viennarna-2.4.14_1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
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444"
--End MAKE_ENV--
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/viennarna DOCSDIR=/usr/local/share/doc/ViennaRNA EXAMPLESDIR=/usr/local/share/examples/ViennaRNA WWWDIR=/usr/local/www/viennarna ETCDIR=/usr/local/etc/viennarna
--End SUB_LIST--
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ARCH=${MACHINE_ARCH}
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--End resource limits--
=======================<phase: check-sanity >============================
===> License ViennaRNALicense accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> viennarna-2.4.14_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-i386-default-job-03] Installing pkg-1.14.7...
[head-i386-default-job-03] Extracting pkg-1.14.7: .......... done
===> viennarna-2.4.14_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of viennarna-2.4.14_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.4.14_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.4.14_1 for building
=> SHA256 Checksum OK for ViennaRNA-2.4.14.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.4.14_1 for building
===> Extracting for viennarna-2.4.14_1
=> SHA256 Checksum OK for ViennaRNA-2.4.14.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for viennarna-2.4.14_1
===> Applying FreeBSD patches for viennarna-2.4.14_1 from /usr/ports/biology/viennarna/files
===========================================================================
=======================<phase: build-depends >============================
===> viennarna-2.4.14_1 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.0.18_3.txz
<snip>
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT distance_matrix.o -MD -MP -MF $depbase.Tpo -c -o distance_matrix.o distance_matrix.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cluster.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cluster.o -MD -MP -MF $depbase.Tpo -c -o cluster.o cluster.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo treeplot.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT treeplot.o -MD -MP -MF $depbase.Tpo -c -o treeplot.o treeplot.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo AD_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT AD_main.o -MD -MP -MF $depbase.Tpo -c -o AD_main.o AD_main.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo statgeom.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT statgeom.o -MD -MP -MF $depbase.Tpo -c -o statgeom.o statgeom.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo AS_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT AS_main.o -MD -MP -MF $depbase.Tpo -c -o AS_main.o AS_main.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo PS3D.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT PS3D.o -MD -MP -MF $depbase.Tpo -c -o PS3D.o PS3D.c &&\
mv -f $depbase.Tpo $depbase.Po
/usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib
/usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib
libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp
libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Cluster'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src'
gmake[4]: Nothing to be done for 'all-am'.
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src'
Making all in man
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/man'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/man'
Making all in misc
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/misc'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/misc'
Making all in doc
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/doc'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/doc'
Making all in RNA-Tutorial
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/RNA-Tutorial'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/RNA-Tutorial'
Making all in interfaces
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces'
gmake[4]: Nothing to be done for 'all-am'.
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces'
Making all in src/Kinfold
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
gmake all-recursive
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
Making all in Example
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold/Example'
gmake[5]: Nothing to be done for 'all'.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold/Example'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c
mv -f .deps/cache.Tpo .deps/cache.Po
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c
globals.c:333:5: warning: add explicit braces to avoid dangling else [-Wdangling-else]
else GTV.seed = 1;
^
globals.c:348:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[0],
^~~~~~~~~~~~~~~~~~
globals.c:349:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[1],
^~~~~~~~~~~~~~~~~~
globals.c:350:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[2]) == 0)
^~~~~~~~~~~~~~~~~~
globals.c:437:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[0],
^~~~~~~~~~~~~~~~~~
globals.c:438:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[1],
^~~~~~~~~~~~~~~~~~
globals.c:439:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]
&GAV.phi_bounds[2]) == 0)
^~~~~~~~~~~~~~~~~~
7 warnings generated.
mv -f .deps/globals.Tpo .deps/globals.Po
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
main.c:175:8: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (c=strchr(ctmp, '&')) {
~^~~~~~~~~~~~~~~~~~
main.c:175:8: note: place parentheses around the assignment to silence this warning
if (c=strchr(ctmp, '&')) {
^
( )
main.c:175:8: note: use '==' to turn this assignment into an equality comparison
if (c=strchr(ctmp, '&')) {
^
==
main.c:200:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (c=strchr(GAV.startform, '&')) {
~^~~~~~~~~~~~~~~~~~~~~~~~~~~
main.c:200:10: note: place parentheses around the assignment to silence this warning
if (c=strchr(GAV.startform, '&')) {
^
( )
main.c:200:10: note: use '==' to turn this assignment into an equality comparison
if (c=strchr(GAV.startform, '&')) {
^
==
main.c:224:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (c=strchr(ctmp, '&')) {
~^~~~~~~~~~~~~~~~~~
main.c:224:12: note: place parentheses around the assignment to silence this warning
if (c=strchr(ctmp, '&')) {
^
( )
main.c:224:12: note: use '==' to turn this assignment into an equality comparison
if (c=strchr(ctmp, '&')) {
^
==
3 warnings generated.
mv -f .deps/main.Tpo .deps/main.Po
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c
mv -f .deps/nachbar.Tpo .deps/nachbar.Po
cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c
mv -f .deps/baum.Tpo .deps/baum.Po
mv -f .deps/cmdline.Tpo .deps/cmdline.Po
cc -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -lm -L/usr/local/lib
ld: error: duplicate symbol: GAV
>>> defined at baum.c
>>> baum.o:(GAV)
>>> defined at globals.c
>>> globals.o:(.bss+0x0)
ld: error: duplicate symbol: GSV
>>> defined at baum.c
>>> baum.o:(GSV)
>>> defined at globals.c
>>> globals.o:(.bss+0x830)
ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>> baum.o:(GTV)
>>> defined at globals.c
>>> globals.o:(.bss+0x878)
ld: error: duplicate symbol: GAV
>>> defined at baum.c
>>> baum.o:(GAV)
>>> defined at main.c
>>> main.o:(.bss+0x0)
ld: error: duplicate symbol: GSV
>>> defined at baum.c
>>> baum.o:(GSV)
>>> defined at main.c
>>> main.o:(.bss+0x830)
ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>> baum.o:(GTV)
>>> defined at main.c
>>> main.o:(.bss+0x878)
ld: error: duplicate symbol: GAV
>>> defined at baum.c
>>> baum.o:(GAV)
>>> defined at nachbar.c
>>> nachbar.o:(.bss+0xC)
ld: error: duplicate symbol: GSV
>>> defined at baum.c
>>> baum.o:(GSV)
>>> defined at nachbar.c
>>> nachbar.o:(.bss+0x844)
ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>> baum.o:(GTV)
>>> defined at nachbar.c
>>> nachbar.o:(.bss+0x8A0)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[5]: *** [Makefile:486: Kinfold] Error 1
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
gmake[4]: *** [Makefile:571: all-recursive] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
gmake[3]: *** [Makefile:389: all] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold'
gmake[2]: *** [Makefile:668: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14'
gmake[1]: *** [Makefile:561: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14'
===> 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/viennarna
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