[Bioc-devel] unexpected build and check error

[Luo Weijun]

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 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 <dtenenba at 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" <dtenenba at 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" <dtenenba at 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
 > > 
 > > 
 >