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 >>> > 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 >>> > >>> > >>> >> >> _______________________________________________ >> 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 >> >