Compiling bundles on Windows error LNK2001 for python functions
Hello, I have successfully compiled and tested my Privateer for ChimeraX bundle on MacOS and Linux but am having issues trying to compile on Windows. I apologise in advance if my questions are naive or silly; I feel like a complete beginner when it comes to developing in the Windows environment. Following the guide here ( https://www.cgl.ucsf.edu/chimerax/docs/devel/environment.html) I ensured I have Visual Studio 2019. I tried compiling in Visual Studio directly using a make_win.bat file. I also tried installing MinGW and installing the necessary packages with pacman (as outlined in the guide) and compiling from there using a standard Makefile. In both cases I get the same issue, whereby all my C++ library dependencies compile, and my own C++ code compiles into .obj files, but when it comes to building the wheel, it fails due to linker errors (LNK2001: unresolved external symbol) which all seem linked to Python (e.g. error LINK2001: unresolved external symbol __imp__PyThread_tss_create and many more similar ones too) and relate to the .obj file for the C++ file which contains the python bindings with pybind11. I tried explicitly adding a link argument to python311.lib in case that was the issue, but it didn't help. I do not have this issue on MacOS or on LInux. I was just wondering if this is something anyone else has come across or can point me in the right direction. Any help is much appreciated. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
Hi Lou, Are you using ChimeraX to build your bundle? Try opening ChimeraX, using its command line and the cd command to navigate to your bundle directory, and then using the ‘devel' command: ‘devel build .’ — Zach
On 11 Feb 2026, at 07:52, Lou Holland via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:
Hello,
I have successfully compiled and tested my Privateer for ChimeraX bundle on MacOS and Linux but am having issues trying to compile on Windows. I apologise in advance if my questions are naive or silly; I feel like a complete beginner when it comes to developing in the Windows environment.
Following the guide here (https://www.cgl.ucsf.edu/chimerax/docs/devel/environment.html) I ensured I have Visual Studio 2019. I tried compiling in Visual Studio directly using a make_win.bat file. I also tried installing MinGW and installing the necessary packages with pacman (as outlined in the guide) and compiling from there using a standard Makefile. In both cases I get the same issue, whereby all my C++ library dependencies compile, and my own C++ code compiles into .obj files, but when it comes to building the wheel, it fails due to linker errors (LNK2001: unresolved external symbol) which all seem linked to Python (e.g. error LINK2001: unresolved external symbol __imp__PyThread_tss_create and many more similar ones too) and relate to the .obj file for the C++ file which contains the python bindings with pybind11.
I tried explicitly adding a link argument to python311.lib in case that was the issue, but it didn't help. I do not have this issue on MacOS or on LInux. I was just wondering if this is something anyone else has come across or can point me in the right direction. Any help is much appreciated.
Best wishes, Lou Holland (Pronouns: they/them)
Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK _______________________________________________ Chimera-dev mailing list -- chimera-dev@cgl.ucsf.edu To unsubscribe send an email to chimera-dev-leave@cgl.ucsf.edu
Hi Zach Thanks for your response. Apologies, I'm now realising all the details I left out of my initial message. Yes, I've tried building from within ChimeraX but it fails at the same point. When not building within ChimeraX I'm still building with it from my Makefile or .bat file depending on whether building from within Visual Studio or MinGW (e.g. ChimeraX-console.exe --nogui --safemode --exit --cmd "devel install ."). The non-zero exit status in all cases is 1120 (appearing after all the LNK2001 errors). This error does not appear when I compile on Mac or Linux. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK On Fri, 13 Feb 2026, 00:42 Zach Pearson, <zjp@cgl.ucsf.edu> wrote:
Hi Lou,
Are you using ChimeraX to build your bundle? Try opening ChimeraX, using its command line and the cd command to navigate to your bundle directory, and then using the ‘devel' command: ‘devel build .’
— Zach
On 11 Feb 2026, at 07:52, Lou Holland via Chimera-dev < chimera-dev@cgl.ucsf.edu> wrote:
Hello,
I have successfully compiled and tested my Privateer for ChimeraX bundle on MacOS and Linux but am having issues trying to compile on Windows. I apologise in advance if my questions are naive or silly; I feel like a complete beginner when it comes to developing in the Windows environment.
Following the guide here ( https://www.cgl.ucsf.edu/chimerax/docs/devel/environment.html) I ensured I have Visual Studio 2019. I tried compiling in Visual Studio directly using a make_win.bat file. I also tried installing MinGW and installing the necessary packages with pacman (as outlined in the guide) and compiling from there using a standard Makefile. In both cases I get the same issue, whereby all my C++ library dependencies compile, and my own C++ code compiles into .obj files, but when it comes to building the wheel, it fails due to linker errors (LNK2001: unresolved external symbol) which all seem linked to Python (e.g. error LINK2001: unresolved external symbol __imp__PyThread_tss_create and many more similar ones too) and relate to the .obj file for the C++ file which contains the python bindings with pybind11.
I tried explicitly adding a link argument to python311.lib in case that was the issue, but it didn't help. I do not have this issue on MacOS or on LInux. I was just wondering if this is something anyone else has come across or can point me in the right direction. Any help is much appreciated.
Best wishes, Lou Holland (Pronouns: they/them)
Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK _______________________________________________ Chimera-dev mailing list -- chimera-dev@cgl.ucsf.edu To unsubscribe send an email to chimera-dev-leave@cgl.ucsf.edu
Hi Lou, I looked up your project and cloned it, then tried to build the chimeraX_bundle branch with ChimeraX 1.11.1. I encountered the same errors you did, LINK2001 followed by exit code 1120. After reading the error log, it looks to me like the privateer_core CModule depends on the mmdb2 and ccp4 libraries you build, but does not link to them. Add <Library>mmdb2</Library> and <Library>ccp4</Library> after <Library>clipper</Library> in your bundle_info.xml — Zach
On 13 Feb 2026, at 01:23, Lou Holland <lou.holland@york.ac.uk> wrote:
Hi Zach
Thanks for your response. Apologies, I'm now realising all the details I left out of my initial message.
Yes, I've tried building from within ChimeraX but it fails at the same point.
When not building within ChimeraX I'm still building with it from my Makefile or .bat file depending on whether building from within Visual Studio or MinGW (e.g. ChimeraX-console.exe --nogui --safemode --exit --cmd "devel install .").
The non-zero exit status in all cases is 1120 (appearing after all the LNK2001 errors). This error does not appear when I compile on Mac or Linux.
Best wishes, Lou Holland (Pronouns: they/them)
Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
On Fri, 13 Feb 2026, 00:42 Zach Pearson, <zjp@cgl.ucsf.edu> wrote: Hi Lou,
Are you using ChimeraX to build your bundle? Try opening ChimeraX, using its command line and the cd command to navigate to your bundle directory, and then using the ‘devel' command: ‘devel build .’
— Zach
On 11 Feb 2026, at 07:52, Lou Holland via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:
Hello,
I have successfully compiled and tested my Privateer for ChimeraX bundle on MacOS and Linux but am having issues trying to compile on Windows. I apologise in advance if my questions are naive or silly; I feel like a complete beginner when it comes to developing in the Windows environment.
Following the guide here (https://www.cgl.ucsf.edu/chimerax/docs/devel/environment.html) I ensured I have Visual Studio 2019. I tried compiling in Visual Studio directly using a make_win.bat file. I also tried installing MinGW and installing the necessary packages with pacman (as outlined in the guide) and compiling from there using a standard Makefile. In both cases I get the same issue, whereby all my C++ library dependencies compile, and my own C++ code compiles into .obj files, but when it comes to building the wheel, it fails due to linker errors (LNK2001: unresolved external symbol) which all seem linked to Python (e.g. error LINK2001: unresolved external symbol __imp__PyThread_tss_create and many more similar ones too) and relate to the .obj file for the C++ file which contains the python bindings with pybind11.
I tried explicitly adding a link argument to python311.lib in case that was the issue, but it didn't help. I do not have this issue on MacOS or on LInux. I was just wondering if this is something anyone else has come across or can point me in the right direction. Any help is much appreciated.
Best wishes, Lou Holland (Pronouns: they/them)
Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK _______________________________________________ Chimera-dev mailing list -- chimera-dev@cgl.ucsf.edu To unsubscribe send an email to chimera-dev-leave@cgl.ucsf.edu
participants (3)
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Lou Holland -
Zach Pearson -
Zachary Pearson