[Rd] install.packages deletes PACKAGES file in local repo

2014-12-05 Thread Renaud Gaujoux
Hi, running install.packages() to install a package from a local repository (i.e., starts with file:///) appears to delete the PACKAGES file that is in the src/contrib/ directory. This happens on a cluster running Scientific Linux release 6.4 (Carbon), but not on my Ubuntu local machine. Subseque

[Rd] Use of tools:::httpdPort in a package for CRAN.

2014-12-05 Thread Sven E. Templer
Hello, I wrote a function to show the help/index page of a package in a browser (and want to include this in an update for a CRAN package). I asked in R-help how to obtain the 00Index.html file, Duncan Murdoch suggested to inspect (see http://r.789695.n4.nabble.com/Obtain-00Index-html-tt4697661.ht

Re: [Rd] Use of tools:::httpdPort in a package for CRAN.

2014-12-05 Thread Duncan Murdoch
On 05/12/2014 11:24 AM, Sven E. Templer wrote: Hello, I wrote a function to show the help/index page of a package in a browser (and want to include this in an update for a CRAN package). I asked in R-help how to obtain the 00Index.html file, Duncan Murdoch suggested to inspect (see http://r.7896

Re: [Rd] Use of tools:::httpdPort in a package for CRAN.

2014-12-05 Thread Yihui Xie
Perhaps I missed something, but isn't this just a one-liner function? help.index = function (pkg) help(package = (pkg), help_type = "html") Regards, Yihui -- Yihui Xie Web: http://yihui.name On Fri, Dec 5, 2014 at 10:24 AM, Sven E. Templer wrote: > Hello, > > I wrote a function to show the he

Re: [Rd] install.packages deletes PACKAGES file in local repo

2014-12-05 Thread Gabriel Becker
Can you post exact code, i have not seen this behavior, and I work with local repositories quite extensively on my current project. ~G On Fri, Dec 5, 2014 at 7:45 AM, Renaud Gaujoux < ren...@mancala.cbio.uct.ac.za> wrote: > Hi, > > running install.packages() to install a package from a local rep

[Rd] R CMD check --as-cran and (a)spell checking

2014-12-05 Thread Henrik Bengtsson
Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package

[Rd] does parLapplyLB do load-balancing?

2014-12-05 Thread Chris Paciorek
Looking at parLapplyLB, one sees that it takes in X and then passes splitList(X, length(cl)) to clusterApplyLB, which then calls dynamicClusterApply. Thus while dynamicClusterApply does handle tasks in a load-balancing fashion, sending out individual tasks as previous tasks complete, parLapplyLB p

Re: [Rd] install.packages deletes PACKAGES file in local repo

2014-12-05 Thread Renaud Gaujoux
Hi, I was only doing install.packages('pkgname'), with the local repo being defined in the default repos option. After retrying it just now, this issue mysteriously suddenly disappeared, and things work as expected whether on the front node or in a job on a node. Really no idea of what happened. C

Re: [Rd] does parLapplyLB do load-balancing?

2014-12-05 Thread Ei-ji Nakama
Hello, In such cases, try the Rhpc package. The following is the result of the benchmark. http://prs.ism.ac.jp/~nakama/Rhpc/#benchmark # but tuning is not finished... 2014-12-06 10:36 GMT+09:00 Chris Paciorek : > Looking at parLapplyLB, one sees that it takes in X and then passes > splitList(X