On 04/04/2014 10:36 AM, Luo Weijun wrote:
Dan,
Thanks for the followup. That’s wired. I use R 3.0.0 here. It is different from 
R-3.1.0, but I don’t think it would make such a difference in generating the 
error below:
Error in bods[idx, "id.type"] : subscript out of bounds

I run the exact same build command on my local machine (as below), I got the 
same error indeed:
R CMD build --keep-empty-dirs --no-resave-data gage

But if I install gage package first, then then create vignettes manually, 
everything is fine.
sudo R CMD INSTALL gage
cd gage/vignettes/
R CMD Sweave gage.Rnw
R CMD texi2dvi -p gage.tex

I am not sure, why there is such a difference. Do you have any idea on this?

I can reproduce this providing the path to the gage source tree

  tools::buildVignettes(dir="path/to/gage", quiet=FALSE)

you'll see that this builds the dataPrep vignette first, and then the gage vignette. It seems like dataPrep loads data bods from pathview into the global environment, and when the gage vignette is being processed it attempts to load an identically named data set into the (same) global environment.

The (partial) output of buildVignettes is in gage/vignettes/gage.tex; editing gage.Rnw to include a print(ls()) early in the vignette confirms that an object 'bods' already exists.

It's surprising to me that R re-uses the same environment to build each vignette, and I'll take this up on the R-devel mailing list.

The data() function can arrange to load data into an arbitrary environment; for a function it seems better not to write to the global environment, and something like

  env = new.env(parent=emptyenv())
  obj = data("bods",envir=env)
  bods = env[[obj]]

is better.

Hopefully this helps to address your problem.

Martin


I suspected that bods data file (bods.rda in the data directory) was not 
updated or have some problem somehow. Below is the problematic code chunk in 
the go.gset.R file:

…
       idx=which(bods[,"species"] == species)
       if(length(idx)!=1) stop("bad species value")
       pkg.name = bods[idx, "package"]
       id.type=toupper(bods[idx, "id.type"])
…

I tried to insert the following two lines:
       print(head(bods))
       print(idx)
before the last line above and rerun rerun: R CMD build --keep-empty-dirs 
--no-resave-data gage
The error still exists, but I don’t see the printed out results from the newly 
added lines, hence not able to figure out what happened there.
so far, I can think of anything wrong with gage package. because the manual 
install and vignette creating worked. The only problem I am sure is that R CMD 
build --keep-empty-dirs --no-resave-data behave differently from the manual 
process. Could you help to check into the problem here? Thank you! I am cc’ing 
the devel list see if other people got the same problem.
Weijun

--------------------------------------------
On Fri, 4/4/14, Dan Tenenbaum <dtene...@fhcrc.org> wrote:

  Subject: Re: unexpected build and check error

  Date: Friday, April 4, 2014, 12:24 PM

  Hi Weijun,

  gage is still broken today:

  
http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/gage/zin2-buildsrc.html

  It seems to be using the latest versions:

  > packageVersion("gage")
  [1] ‘2.13.5’
  > packageVersion("pathview")
  [1] ‘1.3.4’

  So maybe the cause of the problem is different? Have you
  tried using the most recent R? (R-3.1.0 RC)?

  Dan



  ----- Original Message -----
  > From: "Dan Tenenbaum" <dtene...@fhcrc.org>

  > Sent: Thursday, April 3, 2014 10:24:10 AM
  > Subject: Re: unexpected build and check error
  >
  > No, I think it will be ok tomorrow. If not I'll make
  sure it gets
  > fixed.
  > Thanks,
  > Dan
  >
  >
  > ----- Original Message -----

  > > To: "Dan Tenenbaum" <dtene...@fhcrc.org>
  > > Sent: Thursday, April 3, 2014 10:19:16 AM
  > > Subject: unexpected build and check error
  > >
  > > Dear Dan,
  > > I got the following error in the bioc 2.14 build
  report:
  > > 
http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/zin2-buildsrc.html
  > >
  > > Error: processing vignette 'gage.Rnw' failed with
  diagnostics:
  > >  chunk 12 (label = go.gsets)
  > > Error in bods[idx, "id.type"] : subscript out of
  bounds
  > > Execution halted
  > >
  > > I believe this is due to the loading of the old
  pathview package at
  > > that time, which carries a copy of obsolete bods
  hence interfered
  > > the build/check. But since pathview and gage was
  updated at the
  > > same
  > > time. This error will be gone in the next
  building/checking cycle.
  > > My local copy does get through the
  building/checking free of error.
  > > Shall we do something given that the today is
  “Deadline for
  > > packages
  > > passing R CMD build and check without warning”?
  thanks!
  > > Weijun
  > >
  > >
  >

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