[BioC] newbie problems with AnnBuilder

[Mark Kimpel]

Build with AnnotationDbi was uneventful, but I have been unable to
install the package or use it as is.

If the package is just placed in my site-library, I get:
   'ragene10stv1.db' is not a valid package -- installed < 2.0.0?

If I tar the package and try R CMD INSTALL, I get:
   cannot extract package from 'ragene10stv1.db.tar.gz'

What approach should I be using?

Mark

------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do."
-- B. F. Skinner
******************************************************************


On Tue, Oct 21, 2008 at 6:41 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>
> Hi Mark,
>
> AnnBuilder is on its way out.  Please have a look at the SQLforge.pdf
> vignette which can be found here:
>
> http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html
>
> If you have further questions after reading this, then please just ask,
> and we should be able to help you out.
>
>
>  Marc
>
>
>
> Mark Kimpel wrote:
> > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST
> > array data supplied by Affy. Using the code chunk below, I am able to get
> > AnnBuilder to create the annotation object, but it crashes, I believe, when
> > it tries to save it. I should also mention that I had a previous crash when
> > I had a madecdfenv package directory in place that used the same name. I got
> > a "file lock" error, so I temporarily renamed the directory to see if this
> > fixed the problem. As below, the error changed, but I still can't get the
> > script to work.
> >
> > I suspect that there is a fundamental misunderstaning on my part related to
> > how the annotation package should relate to the cdf package or some naming
> > convention related to one or both.
> >
> > Mark
> >
> >
> >> require(AnnBuilder); require(makecdfenv)
> >> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe-entrez_gene.csv"
> >> myBaseType <- "ll"
> >> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus")
> >>
> >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> >>
> > +           myBaseType, pkgName =
> > substring(cleancdfname("RaGene-1_0-st-v1"),
> > +                         1, (nchar(cleancdfname("RaGene-1_0-st-v1")) - 3)),
> > +           pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus
> > norvegicus", version = "1.0",
> > +           author = list(authors = "Mark W Kimpel", maintainer =
> > +                           "mkimpel at iupui.edu"), fromWeb = TRUE)
> > Read 1 item
> > Read 1 item
> > [1] "4450 2 2"
> > Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) :
> >   cannot open file
> > '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or
> > directory
> >
> > Enter a frame number, or 0 to exit
> >
> > 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > myBaseTy
> > 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE)
> > 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress)
> > 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,
> > envhook)
> > 5: function (e)
> > 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook)
> >
> > Selection: 1
> > Browse[1]> annotation[1:2,]
> >      ENTREZID    PROBE      ACCNUM GO
> > [1,] "100008565" "10766774" NA     NA
> > [2,] "100034253" "10937540" NA     "GO:0005525 at IEA;GO:0005622 at IEA"
> >      PMID                SYMBOL
> > [1,] "16804107;17292978" "Slc39a4l"
> > [2,] "8889548"           "Gnl3l"
> >      GENENAME                                                     CHR
> > [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA
> > [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X"
> >      MAP        REFSEQ                      UNIGENE     CHRLOC        PATH
> > [1,] NA         "NM_001101021;NP_001094491" "Rn.10120"  "NA"          NA
> > [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA
> >      ENZYME PFAM                  PROSITE
> > [1,] NA     "NA at IPI00817057"      "NA at IPI00817057"
> > [2,] NA     "PF01926 at IPI00362844" "NA at IPI00362844"
> > ------------------------------------------------------------
> > Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> > Indiana University School of Medicine
> >
> > 15032 Hunter Court, Westfield, IN  46074
> >
> > (317) 490-5129 Work, & Mobile & VoiceMail
> > (317) 399-1219  Home
> > Skype:  mkimpel
> >
> > "The real problem is not whether machines think but whether men do." -- B.
> > F. Skinner
> > ******************************************************************
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>