Opened 7 years ago

Closed 6 years ago

#1521 closed defect (fixed)

'devel install' failing for RedHat rpm builds

Reported by: Tristan Croll Owned by: Conrad Huang
Priority: major Milestone:
Component: Tool Shed Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: Linux64 (X11)
Project: ChimeraX

Description

Trying to get closer to the bottom of #1516 by building Clipper using devel install . in the GUI and came across a new problem: the base ChimeraX include directory is missing from the build options (see below).

Was fine in Windows last time I checked. 

compile options: '-std=c++11 -DDYNAMIC_LIBRARY=1 -I/home/tic20/include -I/opt/UCSF/ChimeraX-daily/lib/python3.6/site-packages/numpy/core/include -I/opt/UCSF/ChimeraX-daily/lib/python3.6/site-packages/chimerax/atomic/include -I/opt/UCSF/ChimeraX-daily/include/python3.6m -c'
gcc: src/symmetry_cpp/symmetry.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cc1plus: warning: command line option ‘-std=gnu99’ is valid for C/ObjC but not for C++
In file included from /opt/UCSF/ChimeraX-daily/lib/python3.6/site-packages/chimerax/atomic/include/atomstruct/Atom.h:37:0,
from src/symmetry_cpp/symmetry.cpp:22:
/opt/UCSF/ChimeraX-daily/lib/python3.6/site-packages/chimerax/atomic/include/atomstruct/string_types.h:20:28: fatal error: chutil/CString.h: No such file or directory
#include <chutil/CString.h>

Change History (6)

comment:1 by Tristan Croll, 7 years ago

OK, looks like this is a problem specific to the RedHat RPM. The build fails if I run ChimeraX from /usr/bin/chimerax-daily, but succeeds if I run it directly from /opt/UCSF/ChimeraX-daily/bin/ChimeraX.

comment:2 by Tristan Croll, 7 years ago

Component: Tool Shed → Build System
Owner: set to Greg Couch
Status: new → assigned
Summary: 'devel install' does not know ChimeraX include path → 'devel install' failing for RedHat rpm builds

in reply to:  3 ; comment:3 by tic20@…, 7 years ago 

Looks like this is more a ToolShed problem after all (sorry - emailing from my phone so can’t reassign). In an Ubuntu system today (using the generic Linux build), running ChimeraX from a symlink placed in /usr/local/bin caused the installed ISOLDE plugin to fail with linking errors. Running direct from the executable worked fine.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY

comment:4 by Eric Pettersen, 7 years ago

Component: Build System → Tool Shed
Owner: changed from Greg Couch to Conrad Huang

in reply to:  5 ; comment:5 by tic20@…, 7 years ago 

Question: is there any way I can monkey-patch around this issue for the ChimeraX 0.8/ISOLDE 1.0b2 release? If not, I can foresee quite the flood of bug reports from RedHat and Ubuntu users when the ISOLDE release goes live.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY

comment:6 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

The include files are now in the CentOS 7 rpm.

Note: See TracTickets for help on using tickets.