problems with mzmatchR installation in R version 3.0.2

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maria....@gmail.com

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Dec 4, 2013, 12:10:31 PM12/4/13
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Dear all,

Have you noticed any problem installing mzmatch.R package in R version 3.0.2?. Either installing it from MZMatch.R_1.0.tgz or  using install.packages("mzmatch.R", repos="http://R-Forge.R-project.org") I got the same error

Warning in install.packages :
  package ‘~/Downloads/mzmatch.R_1.0-2.tar’ is not available (for R version 3.0.2)

Are any of you aware about mzmatch.R package and R 3.0.2

Please find bellow my configuration

Any help would be appreciated

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.12.0

Andris Jankevics

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Dec 4, 2013, 2:18:25 PM12/4/13
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Dear Maria,

You should follow these instructions to install mzmatch.R:


Best Regards,
Andris
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Andris Jankevics

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Faculty of Life Sciences, Manchester Institute of Biotechnology, 
University of Manchester,
Manchester, United Kingdom

maria....@gmail.com

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Dec 5, 2013, 6:32:01 AM12/5/13
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Dear Andris,

Thank you very much for your quick response,

I've been trying to follow the instructions you mention with no success. However, it seems that there is firstable a problem with the connection. This is the error message 

Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  unable to connect to 'puma.ibls.gla.ac.uk' on port 80.

Alternatively I have download the tar.gz file package from (https://r-forge.r-project.org/R/?group_id=923)  and I install it in R from archive file, then it pops up the error that I in the previous message:  

 install.packages("~/Downloads/mzmatch.R_2.0-6-2.tar", repos = NULL)
Warning in install.packages :
  package ‘~/Downloads/mzmatch.R.0-6-2.tar’ is not available (for R version 3.0.2)
Error in install.packages : file ‘~/Downloads/mzmatch.R_2.0-6-2.tar’ is not an OS X binary package

Finally, I have tried to  add the unzipped mzmatch.R library package folder directly to my R library folder  and when I call it from R, this is the result:

library("mzmatch.R")
Error: package ‘mzmatch.R’ was built before R 3.0.0: please re-install it

Therefore, I think that the problem might be related to R version. I that so?. Have you ever noticed such installation issues with mzmatch?

Thanks a lot for your help and cooperation.
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Gavin Blackburn

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Dec 5, 2013, 7:07:54 AM12/5/13
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Hi Maria,

 

Try running this code first when you open R and then repeat what you have been doing previously:

 

setInternet2()

 

Cheers,

 

Gavin.

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Andris Jankevics

Research associate

Faculty of Life Sciences, Manchester Institute of Biotechnology, 

University of Manchester,

Manchester, United Kingdom

 

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maria....@gmail.com

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Dec 5, 2013, 12:13:44 PM12/5/13
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Dear all,

Thank you very much for  your fast responses and kind help

I am happy to say that I have just found the workaround to the installation issues of mzmatch. The problem was trying to install this package using Rstudio. I am quite new to R so I really do not know what was exactly the issue. I just can say that finally I have been able to  instal mzmatch by by-passing Rstudio and using directly the R console and from file "mzmatch.R.0-6-2.tar" in my local downloads folder. 

So happy now to be finally ready to evaluate mzmatch performance with my own data 

Thanks again,

maria
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