[BioC] newbie problems with AnnBuilder
Mark Kimpel
mwkimpel at gmail.com
Wed Oct 22 18:05:25 CEST 2008
Interesting, it works from a command line outside of R, but when I had
tried R> system('R CMD INSTALL ragene10stv1.db') I received an error
message. I have used this approach successfully with other packages to
avoid leaving R and starting a shell, but with this package I get:
'* Installing to library '/home/mkimpel/R_HOME/site-library-2.8.0'
ERROR: no packages specified'
Well, thanks, it now is installed. Any comment on why my system()
approach might not have worked?
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 Wed, Oct 22, 2008 at 11:53 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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]]
>>> >
>>> > _______________________________________________
>>> > Bioconductor mailing list
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>>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>> >
>>> >
>>>
>>
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