[package - 120powerpc64-quarterly][science/coot] Failed for coot-0.8.9.1_2 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed May 15 01:25:59 UTC 2019
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: yuri at FreeBSD.org
Ident: $FreeBSD: branches/2019Q2/science/coot/Makefile 490524 2019-01-17 05:59:38Z yuri $
Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/501608/logs/coot-0.8.9.1_2.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=501608
Log:
=>> Building science/coot
build started at Wed May 15 01:22:26 UTC 2019
port directory: /usr/ports/science/coot
package name: coot-0.8.9.1_2
building for: FreeBSD 120powerpc64-quarterly-job-16 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 powerpc
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q2/science/coot/Makefile 490524 2019-01-17 05:59:38Z yuri $
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=======================<phase: check-sanity >============================
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> coot-0.8.9.1_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[120powerpc64-quarterly-job-16] Installing pkg-1.10.5_5...
[120powerpc64-quarterly-job-16] Extracting pkg-1.10.5_5: .......... done
===> coot-0.8.9.1_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of coot-0.8.9.1_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
=> SHA256 Checksum OK for coot/coot-0.8.9.1.tar.gz.
=> SHA256 Checksum OK for coot/refmac-monomer-library.tar.gz.
=> SHA256 Checksum OK for coot/reference-structures.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
===> Extracting for coot-0.8.9.1_2
=> SHA256 Checksum OK for coot/coot-0.8.9.1.tar.gz.
=> SHA256 Checksum OK for coot/refmac-monomer-library.tar.gz.
=> SHA256 Checksum OK for coot/reference-structures.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for coot-0.8.9.1_2
===> Applying FreeBSD patches for coot-0.8.9.1_2
===========================================================================
=======================<phase: build-depends >============================
===> coot-0.8.9.1_2 depends on executable: update-desktop-database - not found
===> Installing existing package /packages/All/desktop-file-utils-0.23.txz
[120powerpc64-quarterly-job-16] Installing desktop-file-utils-0.23...
[120powerpc64-quarterly-job-16] `-- Installing gettext-runtime-0.19.8.1_2...
[120powerpc64-quarterly-job-16] | `-- Installing indexinfo-0.3.1...
[120powerpc64-quarterly-job-16] | `-- Extracting indexinfo-0.3.1: .... done
[120powerpc64-quarterly-job-16] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120powerpc64-quarterly-job-16] `-- Installing glib-2.56.3_3,1...
[120powerpc64-quarterly-job-16] | `-- Installing gcc8-8.3.0_2...
[120powerpc64-quarterly-job-16] | | `-- Installing binutils-2.32,1...
<snip>
===> coot-0.8.9.1_2 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so)
===> coot-0.8.9.1_2 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===> coot-0.8.9.1_2 depends on shared library: libgtk-x11-2.0.so - found (/usr/local/lib/libgtk-x11-2.0.so)
===> coot-0.8.9.1_2 depends on shared library: libart_lgpl_2.so - not found
===> Installing existing package /packages/All/libart_lgpl-2.3.21_3,1.txz
[120powerpc64-quarterly-job-16] Installing libart_lgpl-2.3.21_3,1...
[120powerpc64-quarterly-job-16] Extracting libart_lgpl-2.3.21_3,1: .......... done
===> coot-0.8.9.1_2 depends on shared library: libart_lgpl_2.so - found (/usr/local/lib/libart_lgpl_2.so)
===> Returning to build of coot-0.8.9.1_2
===> coot-0.8.9.1_2 depends on shared library: libglade-2.0.so - not found
===> Installing existing package /packages/All/libglade2-2.6.4_9.txz
[120powerpc64-quarterly-job-16] Installing libglade2-2.6.4_9...
[120powerpc64-quarterly-job-16] `-- Installing xmlcatmgr-2.2_2...
[120powerpc64-quarterly-job-16] `-- Extracting xmlcatmgr-2.2_2: ......... done
+ Creating /usr/local/share/sgml/catalog
+ Registering CATALOG catalog.ports (SGML)
+ Creating /usr/local/share/sgml/catalog.ports
+ Creating /usr/local/share/xml/catalog
+ Registering nextCatalog catalog.ports (XML)
+ Creating /usr/local/share/xml/catalog.ports
[120powerpc64-quarterly-job-16] Extracting libglade2-2.6.4_9: .......... done
Message from xmlcatmgr-2.2_2:
The following catalogs are installed:
1) /usr/local/share/sgml/catalog
The top level catalog for SGML stuff. It is not changed
by any ports/packages except textproc/xmlcatmgr.
2) /usr/local/share/sgml/catalog.ports
This catalog is for handling SGML stuff installed under
/usr/local/share/sgml. It is changed by ports/packages.
3) /usr/local/share/xml/catalog
The top level catalog for XML stuff. It is not changed
by any ports/packages except textproc/xmlcatmgr.
4) /usr/local/share/xml/catalog.ports
This catalog is for handling XML stuff installed under
/usr/local/share/xml. It is changed by ports/packages.
===> coot-0.8.9.1_2 depends on shared library: libglade-2.0.so - found (/usr/local/lib/libglade-2.0.so)
===> Returning to build of coot-0.8.9.1_2
===> coot-0.8.9.1_2 depends on shared library: libgnomecanvas-2.so - not found
===> Installing existing package /packages/All/libgnomecanvas-2.30.3_4.txz
[120powerpc64-quarterly-job-16] Installing libgnomecanvas-2.30.3_4...
[120powerpc64-quarterly-job-16] Extracting libgnomecanvas-2.30.3_4: .......... done
===> coot-0.8.9.1_2 depends on shared library: libgnomecanvas-2.so - found (/usr/local/lib/libgnomecanvas-2.so)
===> Returning to build of coot-0.8.9.1_2
===> coot-0.8.9.1_2 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===> coot-0.8.9.1_2 depends on shared library: libpango-1.0.so - found (/usr/local/lib/libpango-1.0.so)
===> coot-0.8.9.1_2 depends on shared library: libpangox-1.0.so - found (/usr/local/lib/libpangox-1.0.so)
===> coot-0.8.9.1_2 depends on shared library: libsqlite3.so - not found
===> Installing existing package /packages/All/sqlite3-3.28.0.txz
[120powerpc64-quarterly-job-16] Installing sqlite3-3.28.0...
[120powerpc64-quarterly-job-16] Extracting sqlite3-3.28.0: .......... done
===> coot-0.8.9.1_2 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so)
===> Returning to build of coot-0.8.9.1_2
===========================================================================
=======================<phase: configure >============================
===> Configuring for coot-0.8.9.1_2
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/macros/libtool.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/configure
configure: loading site script /usr/ports/Templates/config.site
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 for style of include used by gmake... GNU
checking for gcc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
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 dependency style of cc... gcc3
checking for library containing strerror... none required
checking for gcc... (cached) cc
checking whether we are using the GNU C compiler... (cached) yes
checking whether cc accepts -g... (cached) yes
checking for cc option to accept ISO C89... (cached) none needed
checking dependency style of cc... (cached) gcc3
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 whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking build system type... powerpc64-portbld-freebsd12.0
checking host system type... powerpc64-portbld-freebsd12.0
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... (cached) /usr/bin/fgrep
checking for ld used by cc... /usr/local/bin/ld
checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm
checking the name lister (/usr/local/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... (cached) 262144
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... no
checking for /usr/local/bin/ld option to reload object files... -r
checking for objdump... /usr/local/bin/objdump
checking how to recognize dependent libraries... pass_all
checking for ar... /usr/local/bin/ar
checking for strip... strip
checking for ranlib... /usr/local/bin/ranlib
checking command to parse /usr/local/bin/nm output from cc object... ok
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 dlfcn.h... (cached) yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether c++ accepts -g... (cached) yes
checking dependency style of c++... (cached) gcc3
checking how to run the C++ preprocessor... c++ -E
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by c++... /usr/local/bin/ld
checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC -DPIC
checking if c++ PIC flag -fPIC -DPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking which libtool initialization strategy to adopt... AC-PROG-LIBTOOL
checking what warning flags to pass to the C compiler... -Wall -Wunused
checking what language compliance flags to pass to the C compiler...
checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused
checking what language compliance flags to pass to the C++ compiler...
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for OpenMP flag of C compiler... -fopenmp
checking pkg-config is at least version 0.9.0... yes
checking for GLIB... yes
checking if this is MINGW on Windows... no
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no
checking for prefixed single-precision FFTW2 (sfftw.h)... yes
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Not using guile
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checking for GSL - version >= 1.3... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/local/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program compiled, but did not run. This usually means
*** that the run-time linker is not finding GtkGLExt or finding the wrong
*** version of GtkGLExt. If it is not finding GtkGLExt, you'll need to set your
*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point
*** to the installed location Also, make sure you have run ldconfig if that
*** is required on your system
***
*** If you have an old version installed, it is best to remove it, although
*** you may also be able to get things to work by modifying LD_LIBRARY_PATH
===> Script "configure" failed unexpectedly.
Please report the problem to yuri at FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/config.log" including the
output of the failure of your make command. Also, it might be a good idea to
provide an overview of all packages installed on your system (e.g. a
/usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1
Stop.
make: stopped in /usr/ports/science/coot
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