[R] what folder to run write_PACKAGES in?

Uwe Ligges ligges at statistik.tu-dortmund.de
Wed May 9 15:56:32 CEST 2012



On 09.05.2012 01:14, Jeff Newmiller wrote:
> I have not done this myself, but reading through your book I see no reference to actual sample file names. I mention this because UNIX-ish operating systems download the tar.gz source archives while Windows works with the zip binary packages, and I can't tell what files you are putting in the repository.
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>         Basics: ##.#.       ##.#.  Live Go...
>                                        Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> Paul Johnson<pauljohn32 at gmail.com>  wrote:
>
>> I set up a local repo for testing packages. My packages are not
>> showing up from the repository when viewed by Linux clients. I suspect
>> this is a web administrator/firewall issue, but it could be I created
>> the repo wrongly.  I am supposed to run write_PACKAGES separately in
>> each R-version folder. Right?
>>
>> Maybe other novices can use these scripts, if they are not wrong :)
>>
>> Here's the file structure. On the file space that the Web server can
>> see, I create a folder "/tools/kran" and directories
>>
>> bin
>>     macosx
>>          leopard
>>               contrib
>>                 2.13
>>                 2.14
>>                 2.15
>>
>>     windows
>>          contrib
>>                2.13
>>                2.14
>>                2.15
>> src
>>     contrib
>>                2.13
>>                2.14
>>                2.15



For source packages, you do not need the versioned subfolders and you 
have to have a PACKAGES (or a compressed alternative) in /src/contrib.

Uwe ligges


>> That's created by this:
>> #############################################
>> create_repo_tree<- function(local.repos, rversions){
>>
>>     folders<-  c("/bin/windows/contrib",
>> "/bin/macosx/leopard/contrib", "/src/contrib")
>>     for(dir in folders){
>>         dirs<- paste(local.repos, dir, "/", rversions, sep='')
>>         lapply(dirs, dir.create, recursive = TRUE, showWarnings = TRUE)
>>     }
>> }
>>
>> create_repo_tree("/tools/kran", c(2.13, 2.14, 2.15))
>> ###########################################
>>
>> My CRAN mirror is in a sister folder /tools/cran and that works
>> properly to be served at the address http://rweb.quant.ku.edu/cran.
>>
>> I want our local testing thing to show at similar
>> http://rweb.quant.ku.edu/kran.  Supposing the Apache web server magic
>> is done, I *believe* the following should work.
>>
>> I dropped packages in the right version folders, and I wrote a script
>> that goes separately to each version number folder and runs
>> write_PACKAGES.
>>
>> ### Researchers can upload
>> ### packages into the approrpriate folder.
>> ### Administratively, we schedule this run run every night
>> write_PACKAGES_wrapper<- function(local.repos) {
>>     require(tools)
>>
>>     rversions<-  dir(path = paste(local.repos,
>> "/bin/windows/contrib", sep=""), full.names = TRUE)
>>     for (i in rversions) write_PACKAGES(dir = i, subdirs=TRUE,
>> type="win.binary")
>>
>> #repeat
>>     rversions<-  dir(path = paste(local.repos,
>> "/bin/macosx/leopard/contrib", sep=""), full.names = TRUE)
>>     for (i in rversions) write_PACKAGES(dir = i, subdirs=TRUE,
>> type="mac.binary")
>>
>>     rversions<-  dir(path = paste(local.repos, "/src/contrib",
>> sep=""), full.names = TRUE)
>> for (i in rversions) write_PACKAGES(dir = i, subdirs=TRUE,
>> type="source")
>> }
>>
>>
>> write_PACKAGES_wrapper("/tools/kran")
>>
>> #############################
>>
>> Right?
>>
>> After running that, I do see the PACKAGES files appear under the
>> version number directories.
>>
>> However, from the linux clients I see this:
>>
>>> install.packages("rockchalk", repos="http://rweb.quant.ku.edu/kran")
>> Installing package(s) into
>> ‘/home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15’
>> (as ‘lib’ is unspecified)
>> Warning: unable to access index for repository
>> http://rweb.quant.ku.edu/kran/src/contrib
>> Warning message:
>> package ‘rockchalk’ is not available (for R version 2.15.0)
>>
>> The Web administrator here suggests I've done the write_PACKAGES
>> incorrectly because there is no PACKAGES file in
>> /tools/kran/src/contrib.  But I do have PACKAGES files in the
>> subfolders 2.15.
>>
>>
>> However, on a windows system, it does work.
>>
>>> install.packages("rockchalk", repos="http://rweb.quant.ku.edu/kran")
>> trying URL
>> 'http://rweb.quant.ku.edu/kran/bin/windows/contrib/2.15/rockchalk_1.5.5.06.zip'
>> Content type 'application/zip' length 486682 bytes (475 Kb)
>> opened URL
>> downloaded 475 Kb
>>
>> package ‘rockchalk’ successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>   C:\Users\pauljohn32\AppData\Local\Temp\Rtmpq0m3Id\downloaded_packages
>>
>> The Web admin folks say to me, "if we did it wrong, nothing would
>> work. Some does, so it is your fault."
>>
>> --
>> Paul E. Johnson
>> Professor, Political Science    Assoc. Director
>> 1541 Lilac Lane, Room 504     Center for Research Methods
>> University of Kansas               University of Kansas
>> http://pj.freefaculty.org            http://quant.ku.edu
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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