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I am not able to install the Vennerable R package from https://r-forge.r-project.org/projects/vennerable/ on my Windows 7 with newest R (2.13.0).

I tried following:

  1. installed from RGui and selecting R-Forge repos:
    there was no Vennerable package in the list

  2. installed from RGui using "install package from local zip file": 

    can not open compressed file 'Vennerable.tar.gz/DESCRIPTION'

  3. converted tar.gz into zip and installed from RGui using "install package from local zip file":

    can not open compressed file 'Vennerable.tar.gz/DESCRIPTION'

  4. tried manual install: install.packages("D:/Downloads/Vennerable.tar.gz", repos = NULL)

    can not open compressed file 'Vennerable.tar.gz/DESCRIPTION'
Error in install.packages : cannot open the connection

Note: there is a file DESCRIPTION.

What should I do to install this package?

Links on package page are dead (to either Windows build and package source).

Marek
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user670186
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  • @Marek if I use install.packages this shows up: ""package ‘Vennerable’ is not available (for R version 2.13.0)"" – user670186 May 15 '11 at 13:42
  • I tried -- LINK DOES NOT WORK!!! https://r-forge.r-project.org/bin/windows/contrib/latest/Vennerable_2.0.zip – user670186 May 15 '11 at 13:44
  • The link to the Vennerable Windows binary file is DOWN https://r-forge.r-project.org/bin/windows/contrib/latest/Vennerable_2.0.zip does anyone have a mirror? thanks – user670186 May 15 '11 at 13:52
  • OK. My bad I don't check links. I edit your question a little. – Marek May 15 '11 at 21:04
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    Have you tried contacting the project admin person listed on the r-forge page? – Spacedman May 16 '11 at 11:52
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    I was able to compile it for R-2.13. You could checked if it works: http://www.filedropper.com/vennerable201. – Marek May 17 '11 at 21:25
  • [There is a chance it will be available again](http://r-forge.r-project.org/forum/message.php?msg_id=4470&group_id=474) – Marek May 20 '11 at 21:35

4 Answers4

5

You can checkout the source: open the terminal and run the following command

svn checkout svn://svn.r-forge.r-project.org/svnroot/vennerable

Then build without vignettes.

cd  vennerable/pkg
R CMD build Vennerable/ --no-build-vignettes

and finally to install it:

R CMD INSTALL Vennerable_3.0.tar.gz

(Your build might be in a different name than Vennerable_3.0.tar.gz).

For me it generated the following error:

ERROR: dependencies ‘graph’, ‘RBGL’, ‘xtable’ are not available for package ‘Vennerable’

Then I had to go to R, run the following command:

install.packages(c("graph", "RBGL", "xtable"))

and then go back to the terminal and run the R CMD INSTALL ... command again.

Ali
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Joshua Ulrich
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    Due to changes in `switch` (R-2.13) package no longer compiles. On other hand correction is simple. – Marek May 17 '11 at 21:23
3

I had the same problem and figured it out. The issue was with how the package is archived. There is a directory called 'Vennerable' within the top level directory which is called "Vennerable_2.2'. I unzipped the archive. Then I navigated to the 'Vennerable' subdirectory, and zipped that. Then I ran the installation using the new 'Vennerable.zip' archive. Worked like a charm.

orville jackson
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3

Vennerable package has been updated and now version 2.1 is available from R-forge using

install.packages("Vennerable", repos="http://R-Forge.R-project.org")
Marek
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  • Did not work for me, for anyone else failing when trying this: https://github.com/frankkramer/rBiopaxParser/blob/master/README.md – Stenemo Feb 26 '14 at 14:47
  • @Stenemo Works for me. There is no dependencies (from bioconductor) but it works. "package ‘Vennerable’ successfully unpacked and MD5 sums checked" – Marek Mar 18 '14 at 06:35
2

If you have a tar.gz archive, you likely have the package's source files. You must build it first before installing the package. See section 1.3 of the Writing R Extensions manual

See also your other related question, where I provided this link to the built package for R 2.13.0 x86_64:

http://commondatastorage.googleapis.com/jthetzel-public/Vennerable_1.1.1.1.zip

Community
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jthetzel
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