Message-ID: <1396900552.26662.YahooMailBasic@web164705.mail.gq1.yahoo.com>
Date: 2014-04-07T19:55:52Z
From: Luo Weijun
Subject: [Bioc-devel] unexpected build and check error
In-Reply-To: <1801097057.1387810.1396836012551.JavaMail.root@fhcrc.org>
Hi Dan,
Thanks for the reminder. They are not the same indeed, all my questions got answers now.
Weijun
--------------------------------------------
On Sun, 4/6/14, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
Subject: Re: [Bioc-devel] unexpected build and check error
Cc: bioc-devel at r-project.org, "Martin Morgan" <mtmorgan at fhcrc.org>
Date: Sunday, April 6, 2014, 10:00 PM
Hi Weijun,
----- Original Message -----
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>,
"Martin Morgan" <mtmorgan at fhcrc.org>
> Cc: bioc-devel at r-project.org
> Sent: Sunday, April 6, 2014 6:51:17 PM
> Subject: Re: [Bioc-devel] unexpected build and check
error
>
> Martin,
> Your observation on re-uses the same environment to
build all
> vignettes is very helpful. The pre-existence of another
copy of bods
> does explain why I had problem with bods. What I
don?t understand is
> that this pre-existence copy should be identical
because I?ve
> updated both copies in pathview and gage package at the
same time.
> The error does make sense in the first round of
check/build when the
> R server has not updated its pathview package which
I?ve
> communicated with Dan. But now pathview package has
already been
> updated, why I still see the old bods data being loaded
from
[[elided Yahoo spam]]
You might want to double-check that the two datasets are
indeed identical; they don't appear to be to me:
load("gage/data/bods.rda")
ls()
gage.bods <- bods
load("pathview/data/bods.rda")
pathview.bods <- bods
identical(gage.bods, pathview.bods)
# returns FALSE
> all.equal(gage.bods, pathview.bods)
[1] "Attributes: < Component ?dimnames?: Component 2:
1 string mismatch >"
> dimnames(gage.bods)
[[1]]
NULL
[[2]]
[1]
"package"???"species"???"kegg
code" "id.type"?
> dimnames(pathview.bods)
[[1]]
NULL
[[2]]
[1]
"package"???"species"???"kegg
code" "gene.id"?
Look like one has id.type and the other has gene.id.
> packageVersion("gage")
[1] ?2.13.5?
> packageVersion("pathview")
[1] ?1.3.4?
Dan
> Weijun
>
> --------------------------------------------
> On Sat, 4/5/14, Martin Morgan <mtmorgan at fhcrc.org>
wrote:
>
>? Subject: Re: [Bioc-devel] unexpected build and
check error
"Dan Tenenbaum"
>? <dtenenba at fhcrc.org>
>? Cc: bioc-devel at r-project.org
>? Date: Saturday, April 5, 2014, 1:26 PM
>?
>? 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 <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??
[[elided Yahoo spam]]
>? >???> > Weijun
>? >???> >
>? >???> >
>? >???>
>? >
>? >
_______________________________________________
>? > Bioc-devel at r-project.org
>? mailing list
>? > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>? >
>?
>?
>? --
>? Computational Biology / Fred Hutchinson Cancer
Research
>? Center
>? 1100 Fairview Ave. N.
>? PO Box 19024 Seattle, WA 98109
>?
>? Location: Arnold Building M1 B861
>? Phone: (206) 667-2793
>
>