installing DESeq2 on Windows

Question

[Aurinko]

I have a problem with installing DESeq2 on Windows. The problem started with installing libraries that DESeq2 uses so I'm installing them individually. I do it by: 'BiocManager::install('zlibbioc')' . I got an error that suggests that is something wrong with compilation:

   C:\rtools43\x86_64-w64-mingw32.static.posix\bin\windres.exe: can't popen `C:\rtools43\x86_64-w64-mingw32.static.posix\bin\gcc.exe -E -xc -DRC_INVOKED -DGCC_WINDRES win32/zlib1.rc': Bad file descriptor
    make[1]: *** [win32/Makefile.gcc:122: zlibrc.o] Error 1
    make[1]: Leaving directory '/c/Users/aurin/AppData/Local/Temp/RtmpovRpJD/R.INSTALL1d6814126e30/zlibbioc/src/zlib-1.2.5'
    make: *** [Makevars.win:7: libzbioc] Error 2
    ERROR: compilation failed for package 'zlibbioc'

As you can see I'm using rtools (the version is compatible with the version of R). I updated BiocManager, did a reinstallation of rtools, R, and Rstudio. I'm stuck, please help :(

[JC]

Avoid using R on Windows, use WSL and use a conda environment or use a docker container

[Aurinko]

thank you!

Answer 1

[i.sudbery]

If your aim is just to install DESeq2, then you are almost certainly better using the precompiled version in windows, rather than trying to compile it and its associated dependencies.

[Aurinko]

where can I find precompiled version?

[i.sudbery]

It's supposed to ask, but if it doesn't, you should be able to add type="win.binary" to your install() call.