[package - main-amd64-default][biology/treekin] Failed for treekin-0.5.1_3 in build
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Date: Sun, 05 Sep 2021 04:21:36 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://beefy18.nyi.freebsd.org/data/main-amd64-default/pa985fc1b4ec1_scd85b97e0e/logs/treekin-0.5.1_3.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=pa985fc1b4ec1_scd85b97e0e
Log:
=>> Building biology/treekin
build started at Sun Sep 5 04:21:19 UTC 2021
port directory: /usr/ports/biology/treekin
package name: treekin-0.5.1_3
building for: FreeBSD main-amd64-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1400032
Job Id: 09
!!! Jail is newer than host. (Jail: 1400032, Host: 1400008) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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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-1.17.1.pkg
[main-amd64-default-job-09] Installing pkg-1.17.1...
[main-amd64-default-job-09] Extracting pkg-1.17.1: .......... 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.pkg
[main-amd64-default-job-09] Installing lapacke-3.10.0...
[main-amd64-default-job-09] `-- Installing blas-3.10.0...
[main-amd64-default-job-09] | `-- Installing gcc10-10.3.0...
[main-amd64-default-job-09] | | `-- Installing binutils-2.37_1,1...
[main-amd64-default-job-09] | | `-- Installing gettext-runtime-0.21...
[main-amd64-default-job-09] | | | `-- Installing indexinfo-0.3.1...
<snip>
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-freebsd14.0/10.3.0 -L/usr/local/lib/gcc10/gcc/x86_64-portbld-freebsd14.0/10.3.0/../../../../../x86_64-portbld-freebsd14.0/lib -L/usr/local/lib/gcc10/gcc/x86_64-portbld-freebsd14.0/10.3.0/../../.. -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
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-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-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-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-calcpp.o -MD -MP -MF .deps/treekin-calcpp.Tpo -c -o treekin-calcpp.o `test -f 'calcpp.cpp' || echo './'`calcpp.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-calc.o -MD -MP -MF .deps/treekin-calc.Tpo -c -o treekin-calc.o `test -f 'calc.cpp' || echo './'`calc.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:17248:6: note: 'dsyevx_' declared here
void LAPACK_dsyevx_base(
^
/usr/local/include/lapacke/lapack.h:17247:28: note: expanded from macro 'LAPACK_dsyevx_base'
#define LAPACK_dsyevx_base LAPACK_GLOBAL(dsyevx,DSYEVX)
^
/usr/local/include/lapacke/lapacke_mangling.h:5:34: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(name,NAME) name##_
^
<scratch space>:23:1: note: expanded from here
dsyevx_
^
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:1900:6: note: 'dgeevx_' declared here
void LAPACK_dgeevx_base(
^
/usr/local/include/lapacke/lapack.h:1899:28: note: expanded from macro 'LAPACK_dgeevx_base'
#define LAPACK_dgeevx_base LAPACK_GLOBAL(dgeevx,DGEEVX)
^
/usr/local/include/lapacke/lapacke_mangling.h:5:34: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(name,NAME) name##_
^
<scratch space>:565:1: note: expanded from here
dgeevx_
^
2 errors generated.
make[3]: *** [Makefile:514: treekin-calcpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from calc.cpp:6:
In file included from ./calc.h:30:
./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:17248:6: note: 'dsyevx_' declared here
void LAPACK_dsyevx_base(
^
/usr/local/include/lapacke/lapack.h:17247:28: note: expanded from macro 'LAPACK_dsyevx_base'
#define LAPACK_dsyevx_base LAPACK_GLOBAL(dsyevx,DSYEVX)
^
/usr/local/include/lapacke/lapacke_mangling.h:5:34: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(name,NAME) name##_
^
<scratch space>:346:1: note: expanded from here
dsyevx_
^
In file included from calc.cpp:6:
In file included from ./calc.h:30:
./calcpp.h:373:33: error: too few arguments to function call, expected 27, have 23
lwork, iwork, info);
^
/usr/local/include/lapacke/lapack.h:1900:6: note: 'dgeevx_' declared here
void LAPACK_dgeevx_base(
^
/usr/local/include/lapacke/lapack.h:1899:28: note: expanded from macro 'LAPACK_dgeevx_base'
#define LAPACK_dgeevx_base LAPACK_GLOBAL(dgeevx,DGEEVX)
^
/usr/local/include/lapacke/lapacke_mangling.h:5:34: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(name,NAME) name##_
^
<scratch space>:368:1: note: expanded from here
dgeevx_
^
2 errors generated.
make[3]: *** [Makefile:528: treekin-calc.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'
===> 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/treekin