sequenza does not work on WINDOWS

Create issue
Issue #8 resolved
Former user created an issue

Hi,

I have tried to run the sequenza.extract example on windows and by debugging into it I have seen it relies on running gzip and cut from commandline in the function gc.sample.stats. These tools are linux specific and they are not present by default on windows. I don't know if they can be installed or not, but please change your user Guide: it says you support Windows installations.

The test script:

library("sequenza") data.file = system.file("data", "example.seqz.txt.gz", package = "sequenza") test <- sequenza.extract(data.file)

Comments (3)

  1. Francesco Favero

    Hi,

    to run the version of sequenza currently on CRAN (2.1.2) you need to install Rtools, and make sure it is installed correctly. https://cran.r-project.org/bin/windows/Rtools

    We did work to solve the issue, and in the sequenza version that is soon be released, cut/gzip/sed commands are not required anymore. So, you may want to try to install the version in development (which is stable), or you can try to install Rtools.

    You can get the source zip of new sequenza from here: https://bitbucket.org/sequenza_tools/sequenza/get/1613884.zip

    and install it manually, or you can use the devtools package:

    library(devtools); install_bitbucket("sequenza_tools/sequenza@1613884")

  2. Log in to comment