[package - 114amd64-quarterly][biology/treekin] Failed for treekin-0.5.1_3 in build
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Date: Thu, 29 Jul 2021 01:23:36 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: http://beefy3.nyi.freebsd.org/data/114amd64-quarterly/03c599c1eb7a/logs/treekin-0.5.1_3.log
Build URL: http://beefy3.nyi.freebsd.org/build.html?mastername=114amd64-quarterly&build=03c599c1eb7a
Log:
=>> Building biology/treekin
build started at Thu Jul 29 01:23:19 UTC 2021
port directory: /usr/ports/biology/treekin
package name: treekin-0.5.1_3
building for: FreeBSD 114amd64-quarterly-job-09 11.4-RELEASE-p12 FreeBSD 11.4-RELEASE-p12 amd64
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License LatticeLib accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> treekin-0.5.1_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[114amd64-quarterly-job-09] Installing pkg-1.16.3...
[114amd64-quarterly-job-09] Extracting pkg-1.16.3: .......... done
===> treekin-0.5.1_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of treekin-0.5.1_3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LatticeLib accepted by the user
===> Fetching all distfiles required by treekin-0.5.1_3 for building
===========================================================================
=======================<phase: checksum >============================
===> License LatticeLib accepted by the user
===> Fetching all distfiles required by treekin-0.5.1_3 for building
=> SHA256 Checksum OK for Treekin-0.5.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LatticeLib accepted by the user
===> Fetching all distfiles required by treekin-0.5.1_3 for building
===> Extracting for treekin-0.5.1_3
=> SHA256 Checksum OK for Treekin-0.5.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for treekin-0.5.1_3
===> Applying FreeBSD patches for treekin-0.5.1_3 from /usr/ports/biology/treekin/files
===========================================================================
=======================<phase: build-depends >============================
===> treekin-0.5.1_3 depends on package: lapacke>0 - not found
===> Installing existing package /packages/All/lapacke-3.10.0.txz
[114amd64-quarterly-job-09] Installing lapacke-3.10.0...
[114amd64-quarterly-job-09] `-- Installing blas-3.10.0...
[114amd64-quarterly-job-09] | `-- Installing gcc10-10.3.0...
[114amd64-quarterly-job-09] | | `-- Installing binutils-2.33.1_4,1...
[114amd64-quarterly-job-09] | | `-- Installing gettext-runtime-0.21...
[114amd64-quarterly-job-09] | | | `-- Installing indexinfo-0.3.1...
[114amd64-quarterly-job-09] | | | `-- Extracting indexinfo-0.3.1: .... done
[114amd64-quarterly-job-09] | | `-- Extracting gettext-runtime-0.21: .......... done
[114amd64-quarterly-job-09] | | `-- Extracting binutils-2.33.1_4,1: .......... done
[114amd64-quarterly-job-09] | | `-- Installing gmp-6.2.1...
[114amd64-quarterly-job-09] | | `-- Extracting gmp-6.2.1: .......... done
[114amd64-quarterly-job-09] | | `-- Installing mpc-1.2.0...
[114amd64-quarterly-job-09] | | `-- Installing mpfr-4.1.0...
[114amd64-quarterly-job-09] | | `-- Extracting mpfr-4.1.0: .......... done
[114amd64-quarterly-job-09] | | `-- Extracting mpc-1.2.0: ......... done
[114amd64-quarterly-job-09] | `-- Extracting gcc10-10.3.0: .......... done
[114amd64-quarterly-job-09] `-- Extracting blas-3.10.0: ........ done
<snip>
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc10
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> treekin-0.5.1_3 depends on package: lapacke>0 - found
===> Returning to build of treekin-0.5.1_3
===> treekin-0.5.1_3 depends on executable: gfortran10 - found
===> treekin-0.5.1_3 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[114amd64-quarterly-job-09] Installing gmake-4.3_2...
[114amd64-quarterly-job-09] Extracting gmake-4.3_2: .......... done
===> treekin-0.5.1_3 depends on package: gmake>=4.3 - found
===> Returning to build of treekin-0.5.1_3
===> treekin-0.5.1_3 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===> treekin-0.5.1_3 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===> treekin-0.5.1_3 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for treekin-0.5.1_3
configure: loading site script /usr/ports/Templates/config.site
checking whether gmake supports nested variables... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking build system type... amd64-portbld-freebsd11.4
checking host system type... amd64-portbld-freebsd11.4
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking for style of include used by gmake... GNU
checking dependency style of c++... gcc3
checking for gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking for ranlib... /usr/local/bin/ranlib
checking whether gmake sets $(MAKE)... (cached) yes
checking for autoconf... autoconf
checking for aclocal... aclocal
checking for make... /wrkdirs/usr/ports/biology/treekin/work/.bin/make
checking for ar... /usr/local/bin/ar
checking whether c++ supports C++11 features with -std=gnu++11... yes
checking for gengetopt... no
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... yes
checking for dgemm_ in -ldgemm... no
checking for sgemm_ in -lmkl... no
checking for sgemm_... (cached) no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) yes
checking for sgemm_ in -lessl... no
checking for sgemm_ in -lblas... (cached) yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran10 accepts -g... yes
checking how to get verbose linking output from gfortran10... -v
checking for Fortran 77 libraries of gfortran10... -L/usr/local/lib -L/usr/local/lib/gcc10 -L/usr/local/bin -L/usr/local/lib/gcc10/gcc/x86_64-portbld-freebsd11.4/10.3.0 -L/usr/local/lib/gcc10/gcc/x86_64-portbld-freebsd11.4/10.3.0/../../../../../x86_64-portbld-freebsd11.4/lib -L/usr/local/lib/gcc10/gcc/x86_64-portbld-freebsd11.4/10.3.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking openblas/lapacke.h usability... no
checking openblas/lapacke.h presence... no
checking for openblas/lapacke.h... no
checking lapacke/lapacke.h usability... yes
checking lapacke/lapacke.h presence... yes
checking for lapacke/lapacke.h... yes
checking for ANSI C header files... (cached) yes
checking for errno.h... (cached) yes
checking for math.h... (cached) yes
checking for pkg-config... no
checking how to run the C++ preprocessor... c++ -std=gnu++11 -E
checking for mlapack... no
configure: WARNING:
**********************************************************************
Failed to setup linking the program against the MLAPACK library.
In case you have installed mlapack in a non-standard directory, consider
using the
--with-mlapack=/path/to/mlapack
parameter to specify the location where to find MLAPACK.
Otherwise, you can obtain the mlapack library from
https://github.com/RaumZeit/mlapack
**********************************************************************
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for size_t... (cached) yes
checking for help2man... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating packaging/treekin.spec
config.status: creating packaging/PKGBUILD
config.status: creating packaging/treekin-mlapack.spec
config.status: creating packaging/PKGBUILD-mlapack
config.status: creating man/Makefile
config.status: creating man/cmdlopt.sh
config.status: creating config.h
config.status: executing depfiles commands
configure:
======================================
Treekin 0.5.1
======================================
Configured successful with the following options:
Extra Libraries
---------------
* MLapack : no ( mlapack library missing or not of version 0.8 or higher )
Install Directories
-------------------
* Executables : /usr/local/bin
* Libraries : /usr/local/lib
* Header files : /usr/local/include
* Extra Data : /usr/local/share
* Man pages : /usr/local/man
Note, that the most recent version of the DrTransformer program requires Treekin to be linked against the MLAPACK library!
You can run make now.
===========================================================================
=======================<phase: build >============================
===> Building for treekin-0.5.1_3
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1'
/wrkdirs/usr/ports/biology/treekin/work/.bin/make all-recursive
make[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1'
Making all in src
make[3]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src'
c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-mxccm.o -MD -MP -MF .deps/treekin-mxccm.Tpo -c -o treekin-mxccm.o `test -f 'mxccm.cpp' || echo './'`mxccm.cpp
mv -f .deps/treekin-mxccm.Tpo .deps/treekin-mxccm.Po
c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-globals.o -MD -MP -MF .deps/treekin-globals.Tpo -c -o treekin-globals.o `test -f 'globals.cpp' || echo './'`globals.cpp
mv -f .deps/treekin-globals.Tpo .deps/treekin-globals.Po
c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-barparser.o -MD -MP -MF .deps/treekin-barparser.Tpo -c -o treekin-barparser.o `test -f 'barparser.cpp' || echo './'`barparser.cpp
mv -f .deps/treekin-barparser.Tpo .deps/treekin-barparser.Po
c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-calcpp.o -MD -MP -MF .deps/treekin-calcpp.Tpo -c -o treekin-calcpp.o `test -f 'calcpp.cpp' || echo './'`calcpp.cpp
In file included from calcpp.cpp:6:
./calcpp.h:317:74: error: too few arguments to function call, expected 23, have 20
(double *)z, ldz, (double *)work, lwork, iwork, ifail, info);
^
/usr/local/include/lapacke/lapack.h:17248:1: note: 'dsyevx_' declared here
void LAPACK_dsyevx_base(
^
In file included from calcpp.cpp:6:
./calcpp.h:373:33: error: too few arguments to function call, expected 27, have 23
lwork, iwork, info);
^
/usr/local/include/lapacke/lapack.h:1900:1: note: 'dgeevx_' declared here
void LAPACK_dgeevx_base(
^
2 errors generated.
make[3]: *** [Makefile:514: treekin-calcpp.o] Error 1
make[3]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src'
make[2]: *** [Makefile:411: all-recursive] Error 1
make[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1'
gmake[1]: *** [Makefile:344: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/treekin