Hmm, this one is trickier. I will have to look at it closely. What distribution are you running? Thanks, Ian — Sent from Mailbox On Mon, Dec 8, 2014 at 5:50 PM, Maxime Cuypers wrote:

Hi Ian, thanks for your suggestion, i installed the x11 headers and it passed the problem. however, now it gets stuck on gtk+ the logfile claims that libxrender can not be found. strange since this library is now installed on my system. "checking for XRenderQueryExtension... no configure: error: *** libXrender not found. Check 'config.log' for more details." config.log enclosed from dir .../gtk+-2.10.11/ any idea? thanks Installing gtk+... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/gtk+_install_log getting package gtk+-2.10.11.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/gtk+-2.10.11.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 541, in build_wxpython_dependencies_linux self.call("./configure %s" % " ".join(gtk_config_args), log=gtk_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base" --disable-cups --without-libjpeg' failed with exit code 1 2014-12-08 22:32 GMT+01:00 :

...

Xrender can fail for many reasons, but generally missing X11 libraries or headers on your system. Can you send the log file:

/pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log

Thanks, Ian

-- Sent from Mailbox https://www.dropbox.com/mailbox

On Mon, Dec 8, 2014 at 4:30 PM, Maxime Cuypers wrote:

...

hi all, am getting the following error installing phenix from source dev-1839. (tried with source from 1.9-1692 with same error) am on latest kubuntu.

any idea on how to debug? -see below report...

PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation.

cheerios,

.... Installing Xrender... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple log=pkg_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1

max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a Linux A7K 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

-- Dr. Maxime Cuypers

-- Dr. Maxime Cuypers

hi Nathaniel, 2- i just need to modify a file in : cctbx_project/cctbx/eltbx/neutron.cpp can you be more explicit on what i need to do to recompile from the binary package to take change into account please? " cd "`libtbx.show_build_path`" libtbx.scons -j NUMBER_OF_PROCESSORS " thanks in advance, cheerios, ------- 1- i tried the no-gui option and it gave the following error: ---------- Dependencies finished building. ****************************** * BASE INSTALLATION COMPLETE * ****************************** -------------------------------------------------------------------------------- Building core Phenix components unwrapping cctbx_bundle.tar.gz... unwrapping phenix.tar.gz... unwrapping solve_resolve.tar.gz... unwrapping elbow.tar.gz... unwrapping reel.tar.gz... unwrapping labelit.tar.gz... unwrapping annlib.tar.gz... unwrapping annlib_adaptbx.tar.gz... unwrapping Plex.tar.gz... unwrapping PyQuante.tar.gz... unwrapping pulchra.tar.gz... unwrapping ksdssp.tar.gz... unwrapping muscle.tar.gz... unwrapping Durandal.tar.gz... unwrapping phaser.tar.gz... unwrapping reduce.tar.gz... unwrapping probe.tar.gz... unwrapping king.tar.gz... unwrapping suitename.tar.gz... configuring PHENIX components with optimization... Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 352, in install_from_source call([python_bin, config_path] + config_args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base/bin/python /usr/local/phenix-dev-1839/cctbx_project/libtbx/configure.py --build=release --scan_boost --command_version_suffix=dev-1839 --current_working_directory="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64" phenix phaser solve_resolve labelit xfel dxtbx' failed with exit code 2 max@A7K:/pgmax/phenix-installer-dev-1839$ 2014-12-09 0:07 GMT+01:00 Nathaniel Echols :

I'm pretty sure I encountered something similar in the past; unfortunately I can't remember what the explanation was, except that it involved some poorly explained dependencies.

However, I think in this case it may be overkill, for two reasons:

1) If you don't plan on using the Phenix GUI, add "--no-gui" to the install arguments to skip this whole mess entirely.

2) Since the source code is distributed along with the binaries, you can probably just rebuild starting from the binary installation - all you need to do is this (I think):

cd "`libtbx.show_build_path`" libtbx.scons -j NUMBER_OF_PROCESSORS

and it will compile only the part that changed. If this works I definitely recommend avoiding the source installer.

On Mon, Dec 8, 2014 at 2:57 PM, wrote:

...

Hmm, this one is trickier. I will have to look at it closely. What distribution are you running?

Thanks, Ian

-- Sent from Mailbox https://www.dropbox.com/mailbox

On Mon, Dec 8, 2014 at 5:50 PM, Maxime Cuypers wrote:

...

Hi Ian,

thanks for your suggestion, i installed the x11 headers and it passed the problem. however, now it gets stuck on gtk+

the logfile claims that libxrender can not be found. strange since this library is now installed on my system. "checking for XRenderQueryExtension... no configure: error: *** libXrender not found. Check 'config.log' for more details."

config.log enclosed from dir .../gtk+-2.10.11/

any idea? thanks

Installing gtk+... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/gtk+_install_log getting package gtk+-2.10.11.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/gtk+-2.10.11.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 541, in build_wxpython_dependencies_linux self.call("./configure %s" % " ".join(gtk_config_args), log=gtk_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base" --disable-cups --without-libjpeg' failed with exit code 1

2014-12-08 22:32 GMT+01:00 :

Xrender can fail for many reasons, but generally missing X11 libraries

...

or headers on your system. Can you send the log file:

/pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log

Thanks, Ian

-- Sent from Mailbox https://www.dropbox.com/mailbox

On Mon, Dec 8, 2014 at 4:30 PM, Maxime Cuypers

...

wrote:

...

hi all, am getting the following error installing phenix from source dev-1839. (tried with source from 1.9-1692 with same error) am on latest kubuntu.

any idea on how to debug? -see below report...

PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation.

cheerios,

.... Installing Xrender... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple log=pkg_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1

max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a Linux A7K 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

-- Dr. Maxime Cuypers

-- Dr. Maxime Cuypers

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Dr. Maxime Cuypers 1, avenue des fauvettes 1341 Ceroux-Mousty Belgique fixed tel: +32 10 61 36 69 Mobile phones: Belgique: +32 499 23 09 42 USA: +1 208-589-6914

hello, so trying more: from the build directory: /usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/ $ sudo libtbx.scons -j 2 sudo: libtbx.scons: command not found is there a typo in the command? can someone help please? cheers, Maxime 2014-12-09 0:45 GMT+01:00 Nathaniel Echols :

On Mon, Dec 8, 2014 at 3:39 PM, Maxime Cuypers wrote:

...

2- i just need to modify a file in : cctbx_project/cctbx/eltbx/neutron.cpp can you be more explicit on what i need to do to recompile from the binary package to take change into account please?

I can't be much more explicit than (re-)stating the commands - no other action should be necessary:

"

...

cd "`libtbx.show_build_path`" libtbx.scons -j NUMBER_OF_PROCESSORS "

I'll let Ian deal with the --no-gui crash, but to start with you should look for a file named compile_phenix.log in the installer directory - this will probably have some kind of error message. (Which is very possibly a bug, since that particular installer feature is not regularly tested.)

-Nat

-- Dr. Maxime Cuypers

Did you set up the environment as usual? There will usually be a libtbx.scons command in the 'bin' subdirectory of the build directory. On Mon, Dec 8, 2014 at 4:50 PM, Maxime Cuypers wrote:

hello,

so trying more: from the build directory: /usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/

$ sudo libtbx.scons -j 2 sudo: libtbx.scons: command not found

is there a typo in the command?

can someone help please? cheers, Maxime

2014-12-09 0:45 GMT+01:00 Nathaniel Echols :

...

On Mon, Dec 8, 2014 at 3:39 PM, Maxime Cuypers wrote:

...

2- i just need to modify a file in : cctbx_project/cctbx/eltbx/neutron.cpp can you be more explicit on what i need to do to recompile from the binary package to take change into account please?

I can't be much more explicit than (re-)stating the commands - no other action should be necessary:

"

...

cd "`libtbx.show_build_path`" libtbx.scons -j NUMBER_OF_PROCESSORS "

I'll let Ian deal with the --no-gui crash, but to start with you should look for a file named compile_phenix.log in the installer directory - this will probably have some kind of error message. (Which is very possibly a bug, since that particular installer feature is not regularly tested.)

-Nat

-- Dr. Maxime Cuypers