openmm / pdbfixer

PDBFixer fixes problems in PDB files
Other
461 stars 115 forks source link

Can build membranes #157

Closed peastman closed 6 years ago

peastman commented 6 years ago

Fixes #144

peastman commented 6 years ago

Has the OpenMM dev build not gotten rebuilt? Travis reports that it's installing OpenMM from omnia/label/dev, but it's not finding files that were added yesterday. According to https://anaconda.org/omnia/openmm/files, the last update to the dev build was two days ago.

peastman commented 6 years ago

Tagging @jchodera in case you aren't following this repository.

jchodera commented 6 years ago

Tagging @lnaden.

Looks like there is an error in the sphinx docs for OpenMM causing a build failure from a stray non-ASCII character:

! Package inputenc Error: Unicode char ϕ (U+3D5)
(inputenc)                not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.9879 ...ing improved sampling of the backbone ϕ
                                                  , \(\psi\) and side-chain ...
? 
! Emergency stop.
 ...                                              

l.9879 ...ing improved sampling of the backbone ϕ
                                                  , \(\psi\) and side-chain ...
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on OpenMMUsersGuide.log.
make[5]: *** [OpenMMUsersGuide.pdf] Error 1
make[4]: *** [latexpdf] Error 2
make[3]: *** [sphinx-docs/userguide/latex/OpenMMUsersGuide.pdf] Error 2
make[2]: *** [docs-source/CMakeFiles/sphinxpdf.dir/all] Error 2
make[1]: *** [docs-source/CMakeFiles/sphinxpdf.dir/rule] Error 2
make: *** [sphinxpdf] Error 2
Lnaden commented 6 years ago

Once the dev version is on conda, this PR's tests can be re-triggered and should pass

jchodera commented 6 years ago

I've re-triggered the dev package build which can be monitored here.

peastman commented 6 years ago

Rerunning the tests now.