Clipper fails to build in Windows - Nov 3 release candidate

[Tristan Croll]

Installed the Nov 3 release candidate and attempted to rebuild Clipper, leading to the following error:

c:\program files\chimerax\bin\lib\site-packages\chimerax\atomic_lib\include\atomstruct\string_types.h(20): fatal error C1083: Cannot open include file: 'chutil/CString.h': No such file or directory

Here's what my dependency specification currently looks like. Do I need something new in there?

  <Dependencies>
    <Dependency name="ChimeraX-Core" build="true" version="&gt;=1.5rc202211032258, &lt;1.6"/>
    <Dependency name="ChimeraX-Atomic" version="~=1.36"/>
    <Dependency name="ChimeraX-AtomicLibrary" build="true" version="~=8.0"/>
    <Dependency name="ChimeraX-Arrays" build="true" version="~=1.0"/>
  </Dependencies>

[Zach Pearson]

Can you post the full log here? This is surely something I changed recently in the Windows builds, but I'd like to see the invocation of the compiler so I know what directories were included.

[Tristan Croll]

Here you go.

On Mon, Nov 7, 2022 at 5:13 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

make.out​

[Tristan Croll]

Added by email2trac

[Zach Pearson]

We used to move the core headers and libraries up to the top-level application directory, but we have a new API to find header and library files that the core now uses with the new TOML bundle builder. XML bundle builder does not know how to find those libraries. I had made a half-baked attempt to teach it how, but I can see that I missed some edge cases. I'll download Clipper and ensure it builds on the daily build, then merge the changes into the release candidates to test again, and finally update this ticket when it builds on the RC.

Thanks for reporting this! I'd hate for this bug to have shipped.

[Tristan Croll]

Maybe I should also be exploring the TOML option (after 1.5 has shipped, of
course), if that’s your preferred option for the future!

On Mon, 7 Nov 2022 at 18:43, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Zach Pearson]

I would hold off on it until we're sure that it works with the toolshed, but once that's done I'd encourage a switch.

[Zach Pearson]

I backported the slightly smarter lib finder I put in XML bundle builder then built clipper with the latest release/v1.5 code. Should work tomorrow (or you can build ChimeraX to test).

[Tristan Croll]

I’ll wait for the new build. :)

On Mon, 7 Nov 2022 at 20:57, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Tried it in today's build ( built: 2022-11-08 02:21:20 PST committed:
2022-11-08 00:09:12 PST). Still fails with the same error, I'm afraid.

On Mon, Nov 7, 2022 at 8:59 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

I can get a successful build after copying C:\Program
Files\ChimeraX\bin\Lib\site-packages\chimerax\core\include to C:\Program
Files\ChimeraX\include. Doesn't fix the bug, but gives me a working bundle
for now. :)

On Tue, Nov 8, 2022 at 4:22 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Zach Pearson]

OK, the bundle builder code was working but the core on the release branch did not have the get_include/lib code that the core on the develop branch had. *Now* it should work tomorrow. :)

[Zach Pearson]

Did it build?

[Tristan Croll]

Sorry - haven't done a build since last Tuesday (the one I got to work by
manually copying the include directory). Got a bit sidetracked by other
things. Will download the latest ChimeraX tomorrow and see how it goes.

On Wed, Nov 16, 2022 at 9:31 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Still failing in the same way using the Nov 15 chimerax-rc build, I'm
afraid. Here's an example of the compiler command:


On Wed, Nov 16, 2022 at 9:38 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Sorry... accidentally hit shift-return (which apparently equates to "send
now" in GMail). *Here's* an example of the compiler command:

"C:\Program Files\Microsoft Visual
Studio\2022\Professional\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe"
/c /nologo /O2 /W3 /GL /DNDEBUG /MD -DCLIPPER_CX_EXPORTS -DCLIPPER_VERBOSE
-DNOMINMAX -DDYNAMIC_LIBRARY=1 "-Ic:\Program Files\ChimeraX\include"
"-Ic:\Program Files\ChimeraX\bin\lib\site-packages\numpy\core\include"
-Isrc/deps "-Ic:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\atomic_lib\include"
"-Ic:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\arrays\include"
"-Ic:\Program Files\ChimeraX\bin\include" "-IC:\Program Files\Microsoft
Visual Studio\2022\Professional\VC\Tools\MSVC\14.16.27023\include"
"-IC:\Program Files\Microsoft Visual
Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files
(x86)\Windows Kits\10\include\10.0.19041.0\ucrt" "-IC:\Program Files
(x86)\Windows Kits\10\\include\10.0.19041.0\\um" "-IC:\Program Files
(x86)\Windows Kits\10\\include\10.0.19041.0\\shared" "-IC:\Program Files
(x86)\Windows Kits\10\\include\10.0.19041.0\\winrt" "-IC:\Program Files
(x86)\Windows Kits\10\\include\10.0.19041.0\\cppwinrt" "-IC:\Program
Files\Microsoft Visual
Studio\2022\Professional\VC\Tools\MSVC\14.16.27023\include" "-IC:\Program
Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include"
"-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt"
"-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.19041.0\\um"
"-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.19041.0\\shared"
"-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.19041.0\\winrt"
"-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.19041.0\\cppwinrt"
/EHsc /Tpsrc/clipper_ext/xtal_mgr.cpp /Fosrc/clipper_ext/xtal_mgr.obj

On Thu, Nov 17, 2022 at 9:31 AM Tristan Croll <tcroll@altoslabs.com> wrote:

[Zach Pearson]

No problem, thanks for getting back to me. I can see that that core folder is still missing. I must not have pushed the change I made but
​it's definitely there now so fingers crossed.

[Zach Pearson]

Tristan reported this morning that his bundle builds without his previous workaround.