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installing DESeq2 on Windows

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 :(

r rstudio deseq2 windows
• 2,488 views • link
updated by Ram Ram • written by Aurinko • Aurinko

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

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written by JC JC

1 answer

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.

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written by i.sudbery i.sudbery

where can I find precompiled version?

• 0 views • link
written by Aurinko • Aurinko

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

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updated by Ram Ram • written by i.sudbery i.sudbery

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