[Rd] Fixing the HDF5 package: the on.exit mystery

2011-03-04 Thread H C Pumphrey
Dear all, I'm trying to fix a subtle bug in the hdf5 package. This package provides an interfaces to the HDF5 library and hence allows one to load data into R from files in the HDF5 format. The bug appeared during a period in which R changed but the package did not. I include below both the

[Rd] Extending type list: names and inherited methods issue

2011-03-04 Thread Renaud Gaujoux
Hi, I want to extend the type list, but it looks like the names are not handled properly (in the show method), not the [ method. See below for code example. I imagine this comes from the S3/S4 mixing, but I would like to understand and the recommended work around (that avoid redefining all

[Rd] removing files on windows as part of vignette building

2011-03-04 Thread Kasper Daniel Hansen
This is about the Bioconductor package Genominator. As part of the vignette building process, we create two sizable sqlite3 databases, in the vignette directory (inst/doc). When we build the source tarball, these databases are deleted, but when a Windows binary is being made on the Bioconductor

Re: [Rd] Problem building R-2.13 r54645 on Windows

2011-03-04 Thread Dan Tenenbaum
On Thu, Mar 3, 2011 at 10:50 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: I am building R-2.13 r54645 from source as described here: http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source The make all recommended command ends as follows on both 32 and 64-bit Windows (Windows

Re: [Rd] Problem building R-2.13 r54645 on Windows

2011-03-04 Thread Dan Tenenbaum
On Fri, Mar 4, 2011 at 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Thu, Mar 3, 2011 at 10:50 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: I am building R-2.13 r54645 from source as described here: http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source The make all

Re: [Rd] Fixing the HDF5 package: the on.exit mystery

2011-03-04 Thread Prof Brian Ripley
Looks like you should be using finalizers instead. See the RODBC package for an example of this. On Fri, 4 Mar 2011, H C Pumphrey wrote: Dear all, I'm trying to fix a subtle bug in the hdf5 package. This package provides an interfaces to the HDF5 library and hence allows one to load data

[Rd] Minor typo in Writing R Extensions

2011-03-04 Thread Brian Diggs
In Writing R Extensions, section 1.1.1, the paragraph talking about the Depends field has an extra right parenthesis at the end of the second sentence (or is missing a left parenthesis somewhere). This is on line 392 of R-exts.texi (revision 54667). I have attached a diff, thought I don't

[Rd] Does R use computed gotos - a gcc extension of C?

2011-03-04 Thread Dr. David Kirkby
The R manual says R will not build with gcc on 64-bit Solaris x86 with gcc http://cran.r-project.org/doc/manuals/R-admin.html#Solaris Tests with gcc32 on ‘x86’ and ‘amd64’ have been less successful: ‘x86’ builds have failed on tests using complex arithmetic33, whereas on ‘amd64’ the builds

Re: [Rd] Does R use computed gotos - a gcc extension of C?

2011-03-04 Thread luke-tierney
On Fri, 4 Mar 2011, Dr. David Kirkby wrote: The R manual says R will not build with gcc on 64-bit Solaris x86 with gcc http://cran.r-project.org/doc/manuals/R-admin.html#Solaris Tests with gcc32 on ‘x86’ and ‘amd64’ have been less successful: ‘x86’ builds have failed on tests using complex