R devel - Jun 2006 - Building R package: make pdf & _masked_by_GlobalEnv

Hi....

I am assembling an R package (under Windows XP, R v.2.3) and have a very 
basic question.  Running R CMD build does not generate a pdf.  R CMD check 
generates a .dvi, but I cannot figure out how to automatically create the 
pdf.  I thought from reading the "writing r extensions' manual that R
CMD
build was supposed to generate the pdf.  I am having no success using 
various permutations of the Rd2dvi and texi2dvi, and I'm a bit 
frustrated.  I have miktex 2.4, which should (I thought) have the necessary 
pdftex tools to do this.  Maybe it does; I definitely have various 
directories named 'dvipdfm', 'pdftex', etc on my computer, but I
have no
idea whether there might be a problem.

When I install the package, I receive the message that most of my functions 
are "masked _by_ .GlobalEnv".  I have no idea what this means; I'm
sure
that this is amply documented, but I confess that I have a rather difficult 
time with much of the documentation on writing packages.

Apologies for the elementary level of these questions, and thanks in 
advance for your help!

~Dan Rabosky






Dan Rabosky
Department of Ecology and Evolutionary Biology
237 Corson Hall
Cornell University
Ithaca, NY14853-2701 USA
607 254 4262 (office)
607 592 4636  (cell)
DLR32 at cornell.edu
web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm

On 6/12/2006 9:47 PM, Dan Rabosky wrote:
> Hi....
> 
> I am assembling an R package (under Windows XP, R v.2.3) and have a very 
> basic question.  Running R CMD build does not generate a pdf.  R CMD check 
> generates a .dvi, but I cannot figure out how to automatically create the 
> pdf.  I thought from reading the "writing r extensions' manual
that R CMD
> build was supposed to generate the pdf.  I am having no success using 
> various permutations of the Rd2dvi and texi2dvi, and I'm a bit 
> frustrated.  I have miktex 2.4, which should (I thought) have the necessary
> pdftex tools to do this.  Maybe it does; I definitely have various 
> directories named 'dvipdfm', 'pdftex', etc on my computer,
but I have no
> idea whether there might be a problem.
You need to give a bit more detail.  What is the .pdf being created 
from?  What do things look like when you run a build?  Does install work?
> 
> When I install the package, I receive the message that most of my functions
> are "masked _by_ .GlobalEnv".  I have no idea what this means;
I'm sure
> that this is amply documented, but I confess that I have a rather difficult
> time with much of the documentation on writing packages.
This means that you have variables in your workspace with the same names 
as ones in your package.  You probably want to clean out your workspace, 
because most uses will find those versions before the ones in the 
package -- and that really messes up testing, etc.

Duncan Murdoch
> 
> Apologies for the elementary level of these questions, and thanks in 
> advance for your help!
> 
> ~Dan Rabosky
> 
> 
> 
> 
> 
> 
> Dan Rabosky
> Department of Ecology and Evolutionary Biology
> 237 Corson Hall
> Cornell University
> Ithaca, NY14853-2701 USA
> 607 254 4262 (office)
> 607 592 4636  (cell)
> DLR32 at cornell.edu
> web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

>>
>>I am assembling an R package (under Windows XP, R v.2.3) and have a very
>>basic question.  Running R CMD build does not generate a pdf.  R CMD 
>>check generates a .dvi, but I cannot figure out how to automatically 
>>create the pdf.  I thought from reading the "writing r
extensions' manual
>>that R CMD build was supposed to generate the pdf.  I am having no 
>>success using various permutations of the Rd2dvi and texi2dvi, and
I'm a
>>bit frustrated.  I have miktex 2.4, which should (I thought) have the 
>>necessary pdftex tools to do this.  Maybe it does; I definitely have 
>>various directories named 'dvipdfm', 'pdftex', etc on my
computer, but I
>>have no idea whether there might be a problem.
>
>You need to give a bit more detail.  What is the .pdf being created 
>from?  What do things look like when you run a build?  Does install work?
I guess I'm not sure what the .pdf is being created from - I don't know
how
this works.  I assumed that my set of .Rd files from the man dir would 
automatically be converted into .pdf, much like 'check' reads them into
a
dvi document.   When I run a build, I get an archive with all of my .R 
source files, the DESCRIPTION, the .Rd files, my datafiles, and any 
documentation I've placed in inst/doc.  When I install this from CMD, the 
html help & chtml files compile, examples are copied from the /man 
directory to their own .Rd files, and everything - to me - appears 
OK.  'Install' from R CMD works with no problem - it warns me that my 
'examples' directory is empty, but it proceeds to create the examples
from
my .Rd files anyway.

I only get a .dvi manual when running 'check'.

>>When I install the package, I receive the message that most of my 
>>functions are "masked _by_ .GlobalEnv".  I have no idea what
this means;
>>I'm sure that this is amply documented, but I confess that I have a 
>>rather difficult time with much of the documentation on writing
packages.
>
>This means that you have variables in your workspace with the same names 
>as ones in your package.  You probably want to clean out your workspace, 
>because most uses will find those versions before the ones in the package 
>-- and that really messes up testing, etc.
thanks for the clarification!