Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6447 closed defect (fixed)

ChimeraX Mac build fails with Anaconda installed

Reported by: Tom Goddard Owned by: Tom Goddard
Priority: moderate Milestone:
Component: Build System Version:
Keywords: Cc: chimerax-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

With Anaconda installed on my macOS 12.3 laptop with M1 CPU in /opt/anaconda3 the ChimeraX build fails because PyPi package lxml shared library has a missing symbol _xmlFree. The lxml package is compiled by prereqs/pips and the compile works. Bundle builder uses it and when the first bundle addcharge is built lxml gives the missing symbol error halting the build.

Looking at prereqs/pips/pip.log revealed the compile of lxml uses /opt/anaconda3/include lxml header files! It found them apparently because /opt/anaconda/bin was in the executable search path. Taking the anaconda bin directory out of the search path made the build succeed.

Making this ticket just to document this problem since it took a half hour to debug it.

Change History (3)

comment:1 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed by taking /opt/anaconda3/bin out of the executable search path PATH variable in the shell where I build ChimeraX. Not a great solution.

comment:2 by Zach Pearson, 4 years ago

I appended a note to ​docs/devel/building.rst concerning this.

in reply to:  3 ; comment:3 by Tom Goddard, 4 years ago 

Good idea to put this info with the build instructions.  I gave a few more details in that documentation page.
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