[BioC] newbie problems with AnnBuilder

[Sean Davis]

On Wed, Oct 22, 2008 at 11:07 AM, Mark Kimpel <mwkimpel at gmail.com> wrote:
> 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?

You can just

R CMD INSTALL ragene10stv1.db

where ragene10stv1.db is the directory that contains the package
(right above the DESCRIPTION file).

Sean


> 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]]
>> >
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>> >
>>
>
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