Entering edit mode
John Zhang
★
2.9k
@john-zhang-6
Last seen 10.3 years ago
I just fixed the problem in AnnBuilder (1.1.3.12). If you can not
access the new
version here is the solution for now.
mySrcUrls <- AnnBuilder:::getSrcUrl("all", "Homo sapiens")
then the code should run.
The short versions of source files do not work any more due to a
switch from
LocusLink to Entrez Gene.
>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>X-Spam-Checker-Version: SpamAssassin 3.1.7 (2006-10-05) on
hypatia.math.ethz.ch
>X-Spam-Level:
>X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_50 autolearn=no
version=3.1.7
>X-Notes-Item: NOT CHECKED; name=$DNSBLSite
>Date: Thu, 11 Jan 2007 11:43:47 +0100
>From: Martin Kircher <kirmar at="" mpi-inf.mpg.de="">
>User-Agent: Icedove 1.5.0.8 (X11/20061128)
>MIME-Version: 1.0
>To: bioconductor at stat.math.ethz.ch
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>X-Mailman-Approved-At: Fri, 12 Jan 2007 19:18:25 +0100
>Subject: [BioC] ABPkgBuilder error: unable to find an inherited
method for
function "baseFile<-"
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.9
>List-Id: The Bioconductor Project Mailing List
<bioconductor.stat.math.ethz.ch>
>List-Unsubscribe:
<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe">
>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor="">
>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch="">
>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help">
>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe">
>Content-Transfer-Encoding: 7bit
>X-PMX-Version: 5.2.0.266434, Antispam-Engine: 2.5.0.283055, Antispam-
Data:
2007.1.12.100933
>X-PMX-Spam: Probability=7%, Report='__CP_URI_IN_BODY 0, __CT 0, __CTE
0,
__CTYPE_CHARSET_QUOTED 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0,
__MIME_TEXT_ONLY 0,
__MIME_VERSION 0, __SANE_MSGID 0, __USER_AGENT 0'
>
>Hi!
>
>I try to use the ABPkgBuilder method in the AnnBuilder library. After
>trying it with my one data without success, I used the example given
in
>the vignette
>(http://bioconductor.org/packages/1.9/bioc/vignettes/AnnBuilder/inst/
doc/ABPrim
er.pdf)
>and in the help for ABPkgBuilder with the same result.
>
>library(AnnBuilder)
>library(GO)
>
>myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
>myBaseType <- "gb"
>
>mySrcUrls <- c(LL =
>"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
> UG = "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
> GO = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")
>
>myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"),
> "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"),
> "data", "srcb"))
>
>myDir <- tempdir()
>
>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>myBaseType,
> otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
> organism = "Homo sapiens", version = "1.1.0", author = list(authors
=
>"myname",
> maintainer = "myname at myemail.com"), fromWeb = TRUE)
>
>I result with the following error, which I do not understand:
>
># # # # # # # # # # # # #
>Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "baseFile<-",
>for signature "NULL"
># # # # # # # # # # # # #
>
>I am using R version 2.4.1 (2006-12-18) and Bioconductor 0.9... The
>libraries mentioned in the vignette, I have installed in the
following
>versions:
>"AnnBuilder" "1.12.0", "RSQLite" "0.4-18", "DBI" "0.1-12",
"annotate"
>"1.12.1", "XML" "1.4-1", "Biobase" "1.12.2"
>
>I also got an error testing this with R 2.2.0 and Bioconductor 0.8 on
a
>different machine and platform... Both systems came up with a message
>containing "baseFile<-"...
>
>It would be great, if someone could help me! Thanks in advance!
>
>Martin Kircher
>
>_______________________________________________
>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
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
