Installing Rplinkseq

[Priya]

Dear PlinkSEQers,

Forgive me for my naive question - I'm new to PlinkSEQ/Rplinkseq.

I am installing PlinkSEQ and Rplinkseq to a Linux server.  I installed PlinkSEQ without any issues (I think) and now I would like to install Rplinkseq.  

I downloaded protobuf 2.4.1 and installed using the directions provided on the PlinkSEQ installation page in my home directory on a large/community server at my workplace (/home/priya/protobuf-2.4.1)

I have my own instance of R 3.0.0 i and have that installed in the same directory (however to launch R I need to type /home/priya/R-3.0.0/bin/R in the command line)

Next I downloaded Rplinkseq-0.08.tar.gz into my home directory.

When I launch R and type install.packages("Rplinkseq-0.08.tar.gz") I am given MANY errors with the last being :

Warning message:

In install.packages("Rplinkseq-0.08.tar.gz") :

  installation of package ‘Rplinkseq-0.08.tar.gz’ had non-zero exit status

Have I installed protobuf 2.4.1 in the right place?  How can I install Rplinkseq so it works!?

Thanks in advance!

-Priya

[Mara]

I get the error 

> install.packages("Rplinkseq-0.08.tar.gz")

Warning message:

package ‘Rplinkseq-0.08.tar.gz’ is not available (for R version 3.0.0) 

Any idea if there will be an update to the Rplinkseq package that will allow it to work with R 3.0.0?

Thank you,
M

[Priya Bhatt]

I finally got it to work and was able to install Rplinkseq using R.3.0.0.    Did you install protobuf?

[tony.pa...@gmail.com]

I get the follow error when trying to install Rplinkseq in R (I'm running R verions 2.10.0)

> install.packages("Rplinkseq-0.08.tar.gz", configure.args="--with-protobuf=/home/tparrado/bin")

Warning in install.packages("Rplinkseq-0.08.tar.gz", configure.args = "--with-protobuf=/home/tparrado/bin") :

  argument 'lib' is missing: using '/usr/lib64/R/library'

Warning in install.packages("Rplinkseq-0.08.tar.gz", configure.args = "--with-protobuf=/home/tparrado/bin") :

  'lib = "/usr/lib64/R/library"' is not writable

Error in install.packages("Rplinkseq-0.08.tar.gz", configure.args = "--with-protobuf=/home/tparrado/bin") : 

  unable to install packages

Any helpful suggestions are greatly appreciated.

[dweek...@gmail.com]

Mara:

I think 

install.packages("Rplinkseq-0.08.tar.gz")

looks for the package on a remote CRAN repository.

Instead try this command:

install.packages("Rplinkseq-0.08.tar.gz",repos=NULL,type="source")

which tells R to try to install using the local source file "Rplinkseq-0.08.tar.gz"

[joe]

I got the same error on RHEL:

> install.packages("Rplinkseq-0.08.tar.gz",repos=NULL,type="source")

ERROR: cannot extract package from 'Rplinkseq-0.08.tar.gz'
Warning message:
In install.packages("Rplinkseq-0.08.tar.gz", repos = NULL, type = "source") :

  installation of package 'Rplinkseq-0.08.tar.gz' had non-zero exit status

I also tried:

# R CMD INSTALL Rplinkseq-0.07-x86_64.tar.gz
Warning: invalid package 'Rplinkseq-0.07-x86_64.tar.gz'
Error: ERROR: no packages specified

# R CMD INSTALL ./Rplinkseq-0.07-x86_64.tar.gz
Warning: invalid package './Rplinkseq-0.07-x86_64.tar.gz'
Error: ERROR: no packages specified

# R CMD INSTALL Rplinkseq-0.07-x86_64.tar.gz -l /data/src-others
Warning: invalid package 'Rplinkseq-0.07-x86_64.tar.gz'
Error: ERROR: no packages specified

By the way I have R version 2.10.0 (2009-10-26)

Any advice will be appreciated.

J