Skip site navigation (1)Skip section navigation (2)
Date:      Tue, 15 Sep 2020 21:26:46 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-powerpc64-default][biology/viennarna] Failed for viennarna-2.4.14_1 in build
Message-ID:  <202009152126.08FLQk0A086251@pylon.nyi.freebsd.org>

next in thread | raw e-mail | index | archive | help

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
Last committer: dinoex@FreeBSD.org
Ident:          $FreeBSD: head/biology/viennarna/Makefile 533989 2020-05-04 21:31:39Z dinoex $
Log URL:        http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p547769_s365371/logs/viennarna-2.4.14_1.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p547769_s365371
Log:

=>> Building biology/viennarna
build started at Tue Sep 15 21:01:54 UTC 2020
port directory: /usr/ports/biology/viennarna
package name: viennarna-2.4.14_1
building for: FreeBSD head-powerpc64-default-job-08 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 powerpc
maintained by: yuri@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: 1300084
Jail OSVERSION: 1300113
Job Id: 08




!!! Jail is newer than host. (Jail: 1300113, Host: 1300084) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300113
UNAME_v=FreeBSD 13.0-CURRENT 1300113
UNAME_r=13.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-powerpc64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---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@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}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl  PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/viennarna/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work  HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/usr/local/bin/bash CONFIG_SHELL=/usr/local/bin/bash CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--

--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/viennarna/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work  HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib"  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include "  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="" PORTEXAMPLES="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0  PERL_VER=5.32  PERL5_MAN1=lib/perl5/site_perl/man/man1  PERL5_MAN3=lib/perl5/site_perl/man/man3  SITE_PERL=lib/perl5/site_perl  SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/ViennaRNA"  EXAMPLESDIR="share/examples/ViennaRNA"  DATADIR="share/viennarna"  WWWDIR="www/viennarna"  ETCDIR="etc/viennarna"
--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--

---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
#### /usr/local/etc/poudriere.d/make.conf ####
# 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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=powerpc64
PPC_ABI=ELFv2
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300113
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
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)  1024
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
--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-powerpc64-default-job-08] Installing pkg-1.14.7...
[head-powerpc64-default-job-08] 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
[head-powerpc64-default-job-08] Installing bash-5.0.18_3...
[head-powerpc64-default-job-08] `-- Installing gettext-runtime-0.21...
[head-powerpc64-default-job-08] |   `-- Installing indexinfo-0.3.1...
[head-powerpc64-default-job-08] |   `-- Extracting indexinfo-0.3.1: .... done
<snip>
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
nachbar.c:311:43: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
        sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1);
                            ~~                   ^~~~~~~~~~~~~~~~~~~~~~~~
                            %lu
1 warning generated.
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+0x860)

ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>>            baum.o:(GTV)
>>> defined at globals.c
>>>            globals.o:(.bss+0x8B0)

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+0x860)

ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>>            baum.o:(GTV)
>>> defined at main.c
>>>            main.o:(.bss+0x8B0)

ld: error: duplicate symbol: GAV
>>> defined at baum.c
>>>            baum.o:(GAV)
>>> defined at nachbar.c
>>>            nachbar.o:(.bss+0x18)

ld: error: duplicate symbol: GSV
>>> defined at baum.c
>>>            baum.o:(GSV)
>>> defined at nachbar.c
>>>            nachbar.o:(.bss+0x888)

ld: error: duplicate symbol: GTV
>>> defined at baum.c
>>>            baum.o:(GTV)
>>> defined at nachbar.c
>>>            nachbar.o:(.bss+0x8E8)
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



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202009152126.08FLQk0A086251>