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R 3.2 and AnalyzeCovariates

AlexanderVAlexanderV BerlinMember
edited July 2015 in Ask the GATK team

Hi,

I'm running R 3.2.0
There is no package reshape, which is required by GATK.

install.packages("reshape")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
[...]
package ‘reshape’ is not available (for R version 3.2.0)

What would be a solution to this?

Best Answer

  • KurtKurt ✭✭✭
    Accepted Answer

    It looks like you can load those in manually with
    R CMD INSTALL

    you can pull down reshape from a cran mirror (and you'll have to have plyr as well).

    R CMD INSTALL /isilon/sequencing/Kurt/temp/plyr_1.8.3.tar.gz

    R CMD INSTALL /isilon/sequencing/Kurt/temp/reshape_0.8.5.tar.gz

    R
    sessionInfo()

    R version 3.2.0 (2015-04-16)
    Platform: x86_64-unknown-linux-gnu (64-bit)
    Running under: Red Hat Enterprise Linux Server release 6.0 (Santiago)

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] reshape_0.8.5

    loaded via a namespace (and not attached):
    [1] plyr_1.8.3 Rcpp_0.11.6

Answers

  • AlexanderVAlexanderV BerlinMember

    Hi @pdexheimer, unfortunately I don't know what you want to tell me with that.
    I am describing the situation that I can't install this library, because the library is not available/existing. How can your link help me with this problem?

  • pdexheimerpdexheimer Member ✭✭✭✭

    I apologize, I didn't read your post carefully enough - I got as far as "there is no package reshape"

    I don't know enough about installing packages in R to help debugging your actual problem, unfortunately

  • KurtKurt Member ✭✭✭
    Accepted Answer

    It looks like you can load those in manually with
    R CMD INSTALL

    you can pull down reshape from a cran mirror (and you'll have to have plyr as well).

    R CMD INSTALL /isilon/sequencing/Kurt/temp/plyr_1.8.3.tar.gz

    R CMD INSTALL /isilon/sequencing/Kurt/temp/reshape_0.8.5.tar.gz

    R
    sessionInfo()

    R version 3.2.0 (2015-04-16)
    Platform: x86_64-unknown-linux-gnu (64-bit)
    Running under: Red Hat Enterprise Linux Server release 6.0 (Santiago)

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] reshape_0.8.5

    loaded via a namespace (and not attached):
    [1] plyr_1.8.3 Rcpp_0.11.6

  • AlexanderVAlexanderV BerlinMember

    @Kurt, my Hero! Thank you!

  • KurtKurt Member ✭✭✭
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