On 26 November 2011 at 23:16, Paul Menzel wrote:
| Dear Dirk,
|
|
| thank you again for your quick response.
|
|
| Am Samstag, den 26.11.2011, 15:35 -0600 schrieb Dirk Eddelbuettel:
|
| > On 26 November 2011 at 22:10, Paul Menzel wrote:
|
| > | Am Samstag, den 26.11.2011, 12:42 -0600 schrieb Dirk Eddelbuettel:
| > | > On 26 November 2011 at 18:57, Paul Menzel wrote:
| > | > | Package: littler
| > | > | Version: 0.1.5-1
| > | > | Severity: normal
| > | > |
| > | > | Dear Debian folks,
| > | >
| > | > There is a single maintainer for the littler package, and his name is
Dirk.
| > |
| > | I am sorry. I used that term because all Debian developers and users
| > | should try to fix bugs. And sometimes the maintainers are not as devoted
| > | as you are.
| >
| > What makes you think all developers would read a bug report against one
| > particular package?
|
| not all. But for example for GNOME packages a lot of times Debian
| developers deal with bug reports although they are not the maintainer.
littler != Gnome
| > | > | since the package rbenchmark is not packaged in Debian I installed it
using `install.packages()`. Then it was installed in my home directory I
believe.
| > | >
| > | > Your problem. Always check what .libPaths() says:
| > | >
| > | > edd@max:~$ r -e 'print(.libPaths())'
| > | > [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
| > | > [3] "/usr/lib/R/library"
| > | > edd@max:~$
| > |
| > | It says the same on my system.
| > |
| > | > So on my system an installation __done with littler__ goes to
/usr/local/lib/R/site-library
| > |
| > | Well, since I have not changed anything by default using
| > | `install.packages()` it goes into `~/R/i486-pc-linux-gnu-library/2.14/`.
| >
| > You shouldn't have to change anything. Apart maybe from making sure you (and
| > not jyst root) can write into /usr/local/lib/R/site-library/
| >
| > This is set from /etc/R/Renviron
|
| Looking at `/etc/R/Renviron` I see the following line.
|
| R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.14'}
Would you mind reading the remaining five or so lines of that file too?
| Could that be added to littler’s default path when looking for packages?
Up to you to do locally as I told you twice. See help(Startup). I am getting
bored of repeating myself.
Littler knows that env var too:
edd@max:~$ r -e 'print(Sys.getenv("R_LIBS_USER"))'
[1] "~/R/x86_64-pc-linux-gnu-library/2.14"
edd@max:~$
I just don't like it. Linux is multi-user, and I see no reason not to use
/usr/local/lib/R/site-library.
If your scripts fail to read from a particular library directory, read
help(library) and/or help(Startup).
There is no maliciousness at my end. I do not tell littler to ignore certain
directories just because I feel like it.
So can we stop this now, please?
| > | > In fact littler comes with two short example scripts 'install.r' and
| > | > 'update.r' I use all the time. Eg (for a not-required re-installation:)
| > | >
| > | > edd@max:~$ ~/bin/install.r rbenchmark
| > | > trying URL 'http://cran.r-project.org/src/contrib/rbenchmark_0.3.tar.gz'
| > | > Content type 'application/x-gzip' length 3504 bytes
| > | > opened URL
| > | > ==================================================
| > | > downloaded 3504 bytes
| > | >
| > | > * installing *source* package ‘rbenchmark’ ...
| > | > ** R
| > | > ** preparing package for lazy loading
| > | > ** help
| > | > *** installing help indices
| > | > ** building package indices ...
| > | > ** testing if installed package can be loaded
| > | >
| > | > * DONE (rbenchmark)
| > | >
| > | > The downloaded packages are in
| > | > ‘/tmp/downloaded_packages’
| > | > edd@max:~$ r -lrbenchmark -e 'res <- benchmark(function() {});
print(res)'
| > | > test replications elapsed relative user.self sys.self
user.child
| > | > 1 function() { 100 0.001 1 0 0
0
| > | > sys.child
| > | > 1 0
| > | > edd@max:~$
| > |
| > | I did not know about these scripts and that they should be used for
| > | installing packages. See #648981 [3].
| >
| > "Should be used" is too strong. I wrote them for my use as I find them
convenient.
|
| I see. But not having a references to them in for example the README I
| will find them too late because I am not checking out everything before
| starting to use a program.
You can always demand your money back.
| > | > | Executing `R` and then `library(rbenchmark)` works.
| > | > |
| > | > | Now I wanted to try `fibonacci.r` from the examples of the Rcpp
package (`r-cran-rcpp` [2]).
| > | > |
| > | > | $ cp /usr/lib/R/site-library/Rcpp/examples/Misc/fibonacci.r
/tmp/
| > | > | $ r fibonacci.r # includes `library(rbenchmark)`
| > | > |
| > | > | This aborts with an error that the package `rbenchmark` cannot be
found.
| > | > |
| > | > | $ LANG=C r fibonacci.r
| > | > | Loading required package: inline
| > | > | Loading required package: methods
| > | > | Loading required package: compiler
| > | > | Error in library(rbenchmark) : there is no package called
'rbenchmark'
| > | > | Execution halted
| > | > |
| > | > | Is littler supposed to work in such a setup?
| > | >
| > | > Well, yes. I use littler for all the blog posts you refer to.
| > | >
| > | > Read help(Startup) and figure out your paths.
| > | >
| > | > Not a bug. Next time, just ask on r-sig-debian, please.
| > |
| > | Is there a way to get that working by default? Should the path `~/R/`
| > | which gets used by default for installing packages be added somewhere?
| > | Or a new item to the FAQ in `README.gz`?
| >
| > Please do read 'help(Startup)' and how you can influence .ldPaths() -- and
if
| > you prefer to install in ~/R you have to figure out how to make sure littler
| > looks there too.
|
| As written above, that path seems to be taken from `/etc/R/Renviron`.
Not going to explain it another time.
Amities, Dirk
| Amicalement,
|
| Paul
| xapplication/pgp-signature [Click mouse-2 to save to a file]
--
"Outside of a dog, a book is a man's best friend. Inside of a dog, it is too
dark to read." -- Groucho Marx
--
To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
