R devel - Nov 2012 - paths and Rook problems only in OSX CRAN binary package?

Hi everyone,

I'm trying to diagnose a problem in my R package, but it is a little 
tricky since it seems to occur only with the Mac OSX CRAN binary build.

My package starts a Rook server and opens a browser. On my own system 
(details below), when I build the package, I have no trouble. The Rook 
server starts and the page loads in the browser.

However, if I've installed it from CRAN, I get the following error when 
trying to open my Rook interface:

######
Warning message:
In normalizePath(file.path(root, path_info)) :

path[1]="/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/BayesFactor/.//www/warning.html":
No such file or directory
######

I assume "Simon" refers to Simon Urbanek.

www/warning.html is the file Rook is attempting to open. This looks like 
a path from the CRAN build machine. How did this make it into my 
package? I'm sort of baffled, and I don't know how to diagnose it.

To replicate:
#########
install.packages('BayesFactor')
library(BayesFactor)
data(puzzles)
aovGUI(y = puzzles$RT, dataFixed = puzzles[,3:4], dataRandom = puzzles$ID)
#########

When I set
options(warning.expression = quote(recover()))

I see where the problem lies. In the frame "15:
file_server$call(env)",
the variable "root" is defined as:

Browse[1]> root
[1] 
"/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/BayesFactor/."

But "find" returns nothing for "root":
Browse[1]> find("root")
character(0)

In the Rook source here 
(https://github.com/jeffreyhorner/Rook/blob/master/Rook/R/File.R) is the 
reference to "root", but I'm not sure where the specific path
value
comes from.

Further information:
 > sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

loaded via a namespace (and not attached):
[1] tools_2.15.2


My Rook version is 1.0-8 and I'm running Mountain Lion (10.8.2). Any 
hints would be appreciated.

Best,
Richard



	[[alternative HTML version deleted]]

Richard,

I was away hence a late response.

The problem is that you are creating aovApp directly at compile time, so it will
hard-code the root path as the initialized object is lazy-loaded. This means
that the package will only work in the library that it was complied into, it
won't work anywhere else and thus it cannot be distributed as a binary
package.

There are many possible fixes, probably the easiest is to simply make aovApp a
function so the actual objects won't be lazy-loaded:

diff -ru BayesFactor/R/aovRook.R BayesFactor-fix/R/aovRook.R
--- BayesFactor/R/aovRook.R	2012-11-23 16:54:06.000000000 -0500
+++ BayesFactor-fix/R/aovRook.R	2012-11-26 09:32:48.000000000 -0500
@@ -119,7 +119,7 @@
     rookEnv$aov$s <- Rhttpd$new()
     rookEnv$aov$s$start(quiet=TRUE)
     rookEnv$aov$s$add(name="aov",
-          app=aovApp)
+          app=aovApp())
   }
   rookEnv$aov$s$browse("aov")
 }
@@ -262,7 +262,7 @@
   }
 }
 
-aovApp <- Builder$new(
+aovApp <- function() Builder$new(
   Static$new(
     urls = '/www',
     root = system.file('.', package='BayesFactor')


Cheers,
Simon


On Nov 21, 2012, at 3:57 PM, Richard D. Morey wrote:
> Hi everyone,
> 
> I'm trying to diagnose a problem in my R package, but it is a little
tricky since it seems to occur only with the Mac OSX CRAN binary build.
> 
> My package starts a Rook server and opens a browser. On my own system
(details below), when I build the package, I have no trouble. The Rook server
starts and the page loads in the browser.
> 
> However, if I've installed it from CRAN, I get the following error when
trying to open my Rook interface:
> 
> ######
> Warning message:
> In normalizePath(file.path(root, path_info)) :
> 
>
path[1]="/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/BayesFactor/.//www/warning.html":
> No such file or directory
> ######
> 
> I assume "Simon" refers to Simon Urbanek.
>  
> www/warning.html is the file Rook is attempting to open. This looks like a
path from the CRAN build machine. How did this make it into my package? I'm
sort of baffled, and I don't know how to diagnose it.
> 
> To replicate:
> #########
> install.packages('BayesFactor')
> library(BayesFactor)
> data(puzzles)
> aovGUI(y = puzzles$RT, dataFixed = puzzles[,3:4], dataRandom = puzzles$ID)
> #########
> 
> When I set 
> options(warning.expression = quote(recover()))
> 
> I see where the problem lies. In the frame "15:
file_server$call(env)", the variable "root" is defined as:
> 
> Browse[1]> root
> [1]
"/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/BayesFactor/."
> 
> But "find" returns nothing for "root":
> Browse[1]> find("root")
> character(0)
> 
> In the Rook source here
(https://github.com/jeffreyhorner/Rook/blob/master/Rook/R/File.R) is the
reference to "root", but I'm not sure where the specific path
value comes from.
> 
> Further information:
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
> 
> 
> My Rook version is 1.0-8 and I'm running Mountain Lion (10.8.2). Any
hints would be appreciated.
> 
> Best,
> Richard
> 
>