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 <dtene...@fhcrc.org> wrote: Subject: Re: [Bioc-devel] unexpected build and check error Cc: bioc-devel@r-project.org, "Martin Morgan" <mtmor...@fhcrc.org> Date: Sunday, April 6, 2014, 10:00 PM Hi Weijun, ----- Original Message ----- > To: "Dan Tenenbaum" <dtene...@fhcrc.org>, "Martin Morgan" <mtmor...@fhcrc.org> > Cc: bioc-devel@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 <mtmor...@fhcrc.org> wrote: > > Subject: Re: [Bioc-devel] unexpected build and check error "Dan Tenenbaum" > <dtene...@fhcrc.org> > Cc: bioc-devel@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 <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”? [[elided Yahoo spam]] > > > > Weijun > > > > > > > > > > > > > > > _______________________________________________ > > Bioc-devel@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 > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel