[Rd] Making a package CITATION file from BibTeX

2019-05-29 Thread Dr Gregory Jefferis
Dear Colleagues, I would like to provide a CITATION file for my package nat.nblast [1]. I have the correct citation in BibTeX format [2]. How can I convert this BibTeX to the format needed by R for a package CITATION file (I have a lot of other packages needing citations ...). I think what I

Re: [Rd] Making a package CITATION file from BibTeX

2019-05-29 Thread Dr Gregory Jefferis
list. All the best, Greg. On 29 May 2019, at 23:46, Achim Zeileis wrote: On Thu, 30 May 2019, Dr Gregory Jefferis wrote: Dear Colleagues, I would like to provide a CITATION file for my package nat.nblast [1]. I have the correct citation in BibTeX format [2]. How can I convert this BibT

Re: [Rd] Comments requested on "changedFiles" function

2013-09-05 Thread Dr Gregory Jefferis
Dear Duncan, This certainly looks useful. Might you consider adding the ability to supply an alternative digest function? Details below. I often use a homemade "make" type function which starts by looking at modification times e.g. in a private package https://github.com/jefferis/nat.utils/

[Rd] inflate zlib compressed data using base R or CRAN package?

2013-11-27 Thread Dr Gregory Jefferis
Hello, I have a binary file type that includes a zlib compressed data block (ie not gzip). Is anyone aware of a way using base R or a CRAN package to decompress this kind of data (from disk or memory). So far I have found Rcompression::decompress on omegahat, but I would prefer to keep depend

Re: [Rd] inflate zlib compressed data using base R or CRAN package?

2013-11-28 Thread Dr Gregory Jefferis
Dear Murray, On 28 Nov 2013, at 1:30, Murray Stokely wrote: I think none of these examples describe a zlib compressed data block inside a binary file that the OP asked about, as all of your examples are e.g. prepending gzip or zip headers. Greg, is memDecompress what you are looking for? Y

[Rd] possible bug: graphics::image seems to ignore getOption("preferRaster")

2014-03-19 Thread Dr Gregory Jefferis
the details section of ?image says: If useRaster is not specified, raster images are used when the getOption("preferRaster") is true, the grid is regular and either dev.capabilities("raster") is "yes" or it is "non-missing" and there are no missing values. but in my experience this is never

[Rd] subscripting a data.frame (without changing row order) changes internal row.names

2014-11-10 Thread Dr Gregory Jefferis
Dear R-devel, Can anyone help me to understand this? It seems that subscripting the rows of a data.frame without actually changing their order, somehow changes an internal representation of row.names that is revealed by e.g. dput/dump/serialize I have read the docs and inspected the (R) code

Re: [Rd] subscripting a data.frame (without changing row order) changes internal row.names

2014-11-10 Thread Dr Gregory Jefferis
Hi Kevin, Joshua, Many thanks for this additional information. On 10 Nov 2014, at 22:21, Kevin Ushey wrote: I believe the question here is related to the sign on the compact row names representation: why is it sometimes `c(NA, )` and sometimes `c(NA, )` -- why the difference in sign? It was

[Rd] depends/suggests when making a new generic to override a function in a user package

2012-07-06 Thread Dr Gregory Jefferis
Dear R developers, I would like to add a new S3 generic to override a function in a user package, specifically: STAR::as.repeatedTrain I have followed the recommendation here: http://cran.r-project.org/doc/manuals/R-exts.html#Adding-new-generics doing this: as.repeatedTrain<-

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

2013-03-05 Thread Dr Gregory Jefferis
On 5 Mar 2013, at 14:36, Cook, Malcolm wrote: So, even if I wanted to go where dragons lurked, it would not be possible to cobble a version of biocLite that installed specific versions of software. Thus, I might rather consider an approach that at 'publish' time tarzips up a copy of the R pa