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Topic: R myDSL effort - dependancy problem

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clacker

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Posts: 570
Joined: June 2004

Posted: Mar. 19 2005,19:13

I submitted the tar.gz , so first k4nt1 needs to check it out, then he puts it into the testing section of the repository. After some people have had a chance to try it out and make sure it's OK, it gets moved, probably to apps. So look for it in testing.

Doofer

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Posts: 12
Joined: Mar. 2005

Posted: Mar. 20 2005,09:25

Many thanks. I note from cran.r-project.org/doc/manuals/R-admin.html that running rsync.recommended looks as if it should get the packages in r-recommended okay. But of course the recommended 'R INSTALL pkg' methods _won't_ work in DSL unless one has all the compilers loaded.

Just as at Section 5.3 'Removing packages' they point out you can deinstall by just remove the package directory, so one could just compile a new package for DSL and pop that directory in R/libs... adding the sprinkling of whatever linux libs the new R library might need...

However, I'm not sure your process does this, since one only finds out which libs an R library needs, when one R INSTALLs the package. So, surely, to find out you'd have to R INSTALL each of the packages in r-recommended in turn, to find out which linux libs are needed?

(Not that r-recommended contains too many R packages to make this practical, but I don't see how else one could determine which libs are needed to R INSTALL - in some cases, compile - them.)

In summary, k4nt1 should be able to type at the R-prompt:
library(KernSmooth)
library(VR)
library(boot)
library(cluster)
library(foreign)
library(lattice)
library(mgcv)
library(nlme)
library(rpart)
library(survival)
and if these R-libraries all load without errors, all is well with r-recommended. I just suspect they will have to be R INSTALLed first.

(I _think_ what I've just said makes sense.... still metabolizing last night's real ales...)

softgun

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Posts: 120
Joined: Dec. 2004

Posted: Mar. 21 2005,16:03

This is great stuff Clacker!
It must go into the documentation.
A few questions
Quote:
Then you need to choose between making a *.dsl, a *.tar.gz, or a *.uci.

If we need to do some post install configuration which is the best choice?

quote:
If your program requires other directories, you need to make a dsl instead of a tar.gz.

Does other directories mean say /var/lib ?

I am trying to make postgresql as an extension and it can be put into one directory with ./configure --prefix=/opt/oio/postgresql

but it also creates a /var/lib/postgresql....

clacker

Group: Members
Posts: 570
Joined: June 2004

Posted: Mar. 21 2005,22:56

Doofer, that link looked great. I can't get to it before the end of the week but that page had lots of good info on compiling and using the libraries. I might not have been running ./tools/rsync-recommended from the top of my source directory but rsync-recommended from within the tools directory.

softgun, I believe that you can do post installation instructions for any of the three (dsl, tar.gz, uci). You would need to write a script and call it from the menu you create. If you need to change or modify any file within /opt/yourdir then it can't be a uci. One of the features of the uci is it lets the user uninstall it, so if your script modifies or adds files into other directories, they won't get uninstalled like the user expects. If you make a script to call you program, and set the PATH and LD_LIBRARY_PATH variables before calling your program, any of the 3 is fine.

As far as I know, if the files in the package aren't all under either the /opt, /home, or /tmp directories you can 't make a tar.gz or uci. So I don't think you can include a /var/lib directory in a tar.gz or uci file. Some packages don't lend themselves well to being placed into /opt because other programs need to call them and would need the PATH variable set to /opt/yourdir all the time to find them. I have gotten around this by making a menu option that opens a new bash shell that runs the export commands as part of it's initialization.

I've had fairly good luck using ./configure --prefix=/opt/yourdir to put my files into the /opt directory. Many times I've had problems not with the binaries but the libraries they look for. Is the /var/lib/postgresql directory created so that other programs can use the postgresql libraries as well as postgresql itself? have you tried moving them under the /opt/oio/postgresql directory and setting LD_LIBRAY_PATH? something like:

export LD_LIBRAY_PATH=$LD_LIBRAY_PATH:/opt/oio/postgresql/lib

and then calling your binary?