Build log -j4

coot.log (text/plain), 14.74 KB, created by David Kredba on 2012-03-07 18:33:32 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/coot-0.7_pre4040
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        amd64 consolekit elibc_glibc kernel_linux multilib openmp policykit userland_GNU
[32;01m * [39;49;00mFEATURES:   nostrip preserve-libs sandbox
>>> Unpacking source...
>>> Unpacking coot-0.7_pre4040.tar.xz to /var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work/coot-0.7_pre4040 ...
 [32;01m*[0m Applying coot-0.7_pre4040-clipper-config.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-goocanvas.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-gl.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-mmdb-config.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-test.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-ssm.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.7_pre4040-libpng-1.5.patch ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Autoreconfiguring '/var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work/coot-0.7_pre4040' ...
 [32;01m*[0m Running libtoolize --copy --force --install --automake ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running aclocal -I macros ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[171C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running elibtoolize in: coot-0.7_pre4040/
 [32;01m*[0m   Applying portage/1.2.0 patch ...
 [32;01m*[0m   Applying sed/1.5.6 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work/coot-0.7_pre4040 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work/coot-0.7_pre4040"
 * econf: updating coot-0.7_pre4040/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating coot-0.7_pre4040/config.sub with /usr/share/gnuconfig/config.sub
/var/tmp/portage/sci-chemistry/coot-0.7_pre4040/work/coot-0.7_pre4040/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-dependency-tracking --docdir=/usr/share/doc/coot-0.7_pre4040 --enable-shared --disable-static --includedir=${prefix}/include/coot --with-goocanvas-prefix=/usr --with-guile --with-python=/usr --with-guile-gtk --with-gtk2 --with-pygtk --enable-openmp
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
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 x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for library containing strerror... none required
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for sysroot... no
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checking for mt... no
checking if : is a manifest tool... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux 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 how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
checking for x86_64-pc-linux-gnu-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GLIB... yes
checking if this is MINGW on Windows... no
checking for MMDB... yes
checking for CISPEP in MMDB... yes
checking for MMDBSSM... yes
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... /usr/bin/guile
checking for guile-config... /usr/bin/guile-config
checking for guile-tools... /usr/bin/guile-tools
checking libguile compile flags...  -pthread
checking libguile link flags... -pthread -L/usr/lib64 -lguile -lltdl -lgmp -lcrypt -lm -lltdl
checking for Guile-Lib... yes
checking for guile-gui... yes
checking GUILE_VERSION: 1.8
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.3... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0)
checking for GLUT... yes
checking for Python... checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
Cool, using Python
checking for PYGTK... yes
Good we have pygtk
checking for guile-gtk... 
checking libglade... yes
checking for GOOCANVAS... yes
yes
Not using database
checking for curl >= 7.9.7... 7.24.0
checking build type... [31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.001
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
error: cannot open Name index using db4 - Permission denied (13)
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.001
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
error: cannot open Name index using db4 - Permission denied (13)
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.001
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
error: cannot open Name index using db4 - Permission denied (13)
[31;01mACCESS DENIED[0m  open_wr:      /var/lib/rpm/__db.Name
Linux-GenuineIntel---python-gtk2
configure: creating ./config.status
config.status: creating Makefile
config.status: creating macros/Makefile
config.status: creating pdb-templates/Makefile
config.status: creating scheme/Makefile
config.status: creating python/Makefile
config.status: creating compat/Makefile
config.status: creating utils/Makefile
config.status: creating coot-utils/Makefile
config.status: creating protein_db/Makefile
config.status: creating ccp4mg-utils/Makefile
config.status: creating coords/Makefile
config.status: creating db-main/Makefile
config.status: creating density-contour/Makefile
config.status: creating surface/Makefile
config.status: creating coot-surface/Makefile
config.status: creating angles/Makefile
config.status: creating mini-mol/Makefile
config.status: creating skeleton/Makefile
config.status: creating ligand/Makefile
config.status: creating geometry/Makefile
config.status: creating ideal/Makefile
config.status: creating build/Makefile
config.status: creating analysis/Makefile
config.status: creating high-res/Makefile
config.status: creating tw/Makefile
config.status: creating cootaneer/Makefile
config.status: creating greg-tests/Makefile
config.status: creating python-tests/Makefile
config.status: creating lidia-core/Makefile
config.status: creating libgtkgraph/Makefile
config.status: creating goograph/Makefile
config.status: creating lbg/Makefile
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/coot
config.status: creating python/coot_load_modules.py
config.status: creating data/Makefile
config.status: creating rama-data/Makefile
config.status: creating auxil/Makefile
config.status: creating auxil/catcheck/Makefile
config.status: creating auxil/rama/Makefile
config.status: creating auxil/sec-str/Makefile
config.status: creating auxil/strand-analysis/Makefile
config.status: creating auxil/vectors/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
[31;01m--------------------------- ACCESS VIOLATION SUMMARY ---------------------------[0m
[31;01mLOG FILE[0m "/var/log/sandbox/sandbox-14872.log"

VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line

F: open_wr
S: deny
P: /var/lib/rpm/__db.001
A: /var/lib/rpm/__db.001
R: /var/lib/rpm/__db.001
C: rpm -q --qf %{name} fedora-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} fedora-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} fedora-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.001
A: /var/lib/rpm/__db.001
R: /var/lib/rpm/__db.001
C: rpm -q --qf %{name} redhat-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} redhat-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} redhat-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.001
A: /var/lib/rpm/__db.001
R: /var/lib/rpm/__db.001
C: rpm -q --qf %{name} centos-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} centos-release 

F: open_wr
S: deny
P: /var/lib/rpm/__db.Name
A: /var/lib/rpm/__db.Name
R: /var/lib/rpm/__db.Name
C: rpm -q --qf %{name} centos-release 
[31;01m--------------------------------------------------------------------------------[0m