Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-09 Thread Henrik Bengtsson
On Wed, Oct 8, 2014 at 12:20 PM, Martin Morgan wrote: > On 10/08/2014 11:41 AM, Henrik Bengtsson wrote: >> >> You may want to make those function local to latex(). I haven't >> verified it works (won't have time), but I bet a beer that it will >> work. > > > I'll take you up on the bet, at least

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-08 Thread Martin Morgan
On 10/08/2014 11:41 AM, Henrik Bengtsson wrote: You may want to make those function local to latex(). I haven't verified it works (won't have time), but I bet a beer that it will work. I'll take you up on the bet, at least for some definition of 'work'. For instance when debugging a vignette

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-08 Thread Henrik Bengtsson
On Mon, Oct 6, 2014 at 7:03 PM, Henrik Bengtsson wrote: > On Mon, Oct 6, 2014 at 6:48 PM, Henrik Bengtsson > wrote: >> On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan wrote: >>> On 10/06/2014 04:52 PM, Henrik Bengtsson wrote: Maybe you could use \RequirePackage{Bioconductor} >

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Henrik Bengtsson
On Mon, Oct 6, 2014 at 6:48 PM, Henrik Bengtsson wrote: > On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan wrote: >> On 10/06/2014 04:52 PM, Henrik Bengtsson wrote: >>> >>> Maybe you could use >>> >>> \RequirePackage{Bioconductor} >>> >>> and then set the TEXINPUTS environment variable via Sys.seten

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Henrik Bengtsson
On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan wrote: > On 10/06/2014 04:52 PM, Henrik Bengtsson wrote: >> >> Maybe you could use >> >> \RequirePackage{Bioconductor} >> >> and then set the TEXINPUTS environment variable via Sys.setenv(). >> Internally tools::texi2dvi() is used that that "listens to

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Martin Morgan
On 10/06/2014 04:52 PM, Henrik Bengtsson wrote: Maybe you could use \RequirePackage{Bioconductor} and then set the TEXINPUTS environment variable via Sys.setenv(). Internally tools::texi2dvi() is used that that "listens to" TEXINPUTS. Thanks; I think that would require 'us' to run texi2dvi (o

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Henrik Bengtsson
Maybe you could use \RequirePackage{Bioconductor} and then set the TEXINPUTS environment variable via Sys.setenv(). Internally tools::texi2dvi() is used that that "listens to" TEXINPUTS. Just FYI: I use this trick in https://github.com/HenrikBengtsson/R.rsp/blob/master/R/compileLaTeX.R to set/fi

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Martin Morgan
On 10/6/2014 2:44 PM, James W. MacDonald wrote: Hi Steffen, It looks like you are running R as an administrator, rather than as a regular user (or you are on something really old like XP). By default R should try to create a user-level library directory in your Documents folder. It is probably n

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread James W. MacDonald
Hi Steffen, It looks like you are running R as an administrator, rather than as a regular user (or you are on something really old like XP). By default R should try to create a user-level library directory in your Documents folder. It is probably not such a good idea to run R as administrator if y

[Bioc-devel] BiocStyle on windows with spaces in path names

2014-10-06 Thread Neumann, Steffen
Hi, sometimes I am forced to R CMD check packages on windows, and my problem is that both the system-wide library and the personal library with BiocStyle contain spaces, so that BiocStyle::latex() results in: \RequirePackage{C:/Program Files/R/R-3.1.0/library/BiocStyle/sty/Bioconductor} which c