Support on using in Windows?

[realzehuali]

Seurat V5 is coming, but my installation of BPCells in Windows never suceeded. Do you have any plan for support using BPCells in Windows?

[bnprks]

Thanks for your interest in BPCells! I have good news which is that we fully support Windows. It can be a bit tricky to set up the first time since BPCells is not yet on CRAN, but I'll share my memory what I did when first setting up. Hopefully it will also work for you and if not please reply and I can try to improve my instructions :)

The basic ingredients you need to install BPCells on any system (Windows or otherwise) are a C++ compiler, and the hdf5 libraries. On my windows machine, I have BPCells installed both in Windows itself, and in WSL (Ubuntu running within Windows).

If you use want to install on Windows (most likely):

1. Download and install the appropriate version of R tools for windows: https://cran.r-project.org/bin/windows/Rtools/. This includes both a C++ compiler and hdf5 libraries, and is a truly excellent tool provided by the R core team.
2. Running installation from R or Rstudio should just work after that.

If you want to install in WSL:

1. Install WSL if you haven't already
2. I recommend also installing Windows Terminal as well for convenience
3. Run a WSL terminal, then from within linux, install R, install hdf5 with sudo apt-get install libhdf5-dev
4. From there, BPCells should install fine.
5. I would also recommend installing RStudio server, which you can start from WSL using sudo rstudio-server start, then load http://localhost:8787 in your Windows web browser and log in as your user. This will connect you to an R session running in linux

[realzehuali]

Thank you for the quick response. Here is my bug information:

remotes::install_github("bnprks/BPCells")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo bnprks/BPCells@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\MSI\AppData\Local\Temp\Rtmpy8DLCj\remotes124c22144b\bnprks-BPCells-62c5726/DESCRIPTION' ...
─ preparing 'BPCells': (420ms)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building 'BPCells_0.1.0.tar.gz'
Warning: file 'BPCells/cleanup' did not have execute permissions: corrected
Warning: file 'BPCells/configure' did not have execute permissions: corrected

Installing package into ‘D:/4.0’
(as ‘lib’ is unspecified)

• installing source package 'BPCells' ...
  ** using staged installation
  Testing hdf5 by compiling example program...
  C:\rtools42/x86_64-w64-mingw32.static.posix/bin/ld.exe: cannot find -lsz
  collect2.exe: error: ld returned 1 exit status

Unable to locate libhdf5. Please install manually or edit compiler flags.
ERROR: configuration failed for package 'BPCells'

• removing 'D:/4.0/BPCells'
  Warning message:
  In i.p(...) :
  installation of package ‘C:/Users/MSI/AppData/Local/Temp/Rtmpy8DLCj/file124c3e1c14d5/BPCells_0.1.0.tar.gz’ had non-zero exit status

I was using R 4.2.3 and Rtools42. I can find Hdf5 in my Rtools42 folder. But there is still this bug.

[realzehuali]

I upgraded my R to devel version and Rtools42 to Rtools43, it works. Thank you very much!