Re: [Bioc-devel] Linking to HTML documents in a package on the BioC web site
Hi Dan, How does this behave in a competing situation when both a html and pdf file with the same name are present? Will only be one of them linked or both? Best wishes Julian On 03/29/2013 11:16 PM, Dan Tenenbaum wrote: Hi all, I wanted to announce a small new feature of the Bioconductor web site--if there are HTML files in the inst/doc directory of a built package tarball they will (with the exception of index.html which is a special case) be linked to on the package landing page. For packages which have HTML files in inst/doc, all other files there (such as images) will be available so that the HTML documents will render correctly from our site. For example, if you go to the RGalaxy landing page: http://www.bioconductor.org/packages/2.12/bioc/html/RGalaxy.html In the Documentation section, you can click on HTML and see the HTML vignette for this package. This feature is in response to the greater support for non-Sweave vignettes in R 3.0, but you can link to any HTML documents using this feature, not just vignettes. Let me know if you have any questions or comments. Thanks, Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Linking to HTML documents in a package on the BioC web site
I remember that is not allowed in R if both are package vignettes, so perhaps you should avoid naming HTML and PDF files with the same base name. Of course, when it comes to linking on BioC website, that is totally up to the webmaster. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Thu, Oct 17, 2013 at 3:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Thursday, October 17, 2013 12:20:49 PM Subject: Re: [Bioc-devel] Linking to HTML documents in a package on the BioC web site Hi Dan, How does this behave in a competing situation when both a html and pdf file with the same name are present? Will only be one of them linked or both? I believe both of them wil be linked. Dan Best wishes Julian On 03/29/2013 11:16 PM, Dan Tenenbaum wrote: Hi all, I wanted to announce a small new feature of the Bioconductor web site--if there are HTML files in the inst/doc directory of a built package tarball they will (with the exception of index.html which is a special case) be linked to on the package landing page. For packages which have HTML files in inst/doc, all other files there (such as images) will be available so that the HTML documents will render correctly from our site. For example, if you go to the RGalaxy landing page: http://www.bioconductor.org/packages/2.12/bioc/html/RGalaxy.html In the Documentation section, you can click on HTML and see the HTML vignette for this package. This feature is in response to the greater support for non-Sweave vignettes in R 3.0, but you can link to any HTML documents using this feature, not just vignettes. Let me know if you have any questions or comments. Thanks, Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Rd] Parallel R expression evaluations
Hi all,
I am using R-3.0.1 under Linux platform to embed R into my C++ code.
I am facing an error while executing more than 1 R-expressions parallelly.
I am executing round(X) and abs(X) parallelly on a set of 50 input rows
which resulted in segmentation fault after getting the following errors.
Error: unprotect_ptr: pointer not found
Error: argument to 'findVar' is not an environment
I am using the following code snippet for initializing R, parsing and
evaluation of R expression
// For initialization
int res= Rf_initEmbeddedR(R_argc, (char**)R_argv);
// For parsing and evaluation
SEXP cmd1= Rf_mkChar(rscript);
SEXP cmdSexp, cmdexpr, sresult = R_NilValue;
ParseStatus status;
R_len_t i=0;
PROTECT(cmdSexp = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(cmdSexp, 0, cmd1);
// parsing vector for R expressions
cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, status, R_NilValue));
if (status != PARSE_OK) {
UNPROTECT(2);
// error handling
return;
}
for(i = 0; i Rf_length(cmdexpr); i++)
{
int error;
sresult = R_tryEval(VECTOR_ELT(cmdexpr, i), R_GlobalEnv,
error); // R
expression evaluation
if(error) // checking for error
{
// error handling
return;
}
}
UNPROTECT(2);
I wonder if R supports parallel evaluations within a single session. I have
seen parallel evaluations of R using Rserve package. As I am trying to
overcome the overhead (using Rserve) in creating new connection for each
evaluation, here I am trying using embeded R.
I tried Rf_endEmbeddedR each time after one evaluation and initializing R
for the next set of evaluation. Even that did't work.
Please suggest me possible solution if any.
Thanks in advance.
Jai
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Re: [Rd] Q-Q plot scaling in plot.lm(); bug or thinko?
I've been looking fairly carefully at the Q-Q plots produced by
plot.lm() and am having difficulty understanding why plot.lm()
is doing what it's doing, specifically scaling the standardized
residuals by the prior weights. Can anyone explain this to me ... ?
Because with ideal choice of prior weights the scaled residuals are expected to
be IID Normal (under the normality assumption for a linear model) and without
scaling they aren't IID, so a Q-Q plot would be meaningless without scaling.
S Ellison
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