[BioC] ABPkgBuilder trouble
John Zhang
jzhang at jimmy.harvard.edu
Tue Feb 20 16:16:28 CET 2007
Looking at the code, I did not see anything wrong. Do you have only GB ids in
your base file or it also contains RefSeq ids too. If it also contains RefSeq
ids or other ids, try to pick a correct base type.
>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=0.2 required=5.0 tests=AWL, BAYES_50, HTML_70_80,
HTML_MESSAGE autolearn=no version=3.1.7
>Mime-Version: 1.0 (Apple Message framework v752.3)
>To: bioconductor at stat.math.ethz.ch
>From: Johan Lindberg <johanl at biotech.kth.se>
>Date: Mon, 19 Feb 2007 14:54:18 +0100
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Content-Disposition: inline
>Subject: [BioC] ABPkgBuilder trouble
>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:
2007.2.19.54434
>X-PMX-Spam: Probability=7%, Report='__CD 0, __CP_URI_IN_BODY 0, __CT 0, __CTE
0, __CTYPE_CHARSET_QUOTED 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __HAS_X_MAILER 0,
__MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0'
>
>Dear list.
>
>I have ran into trouble when I was re-annotating some in-house
>arrays. Although I do not get any errors I have trouble due to that:
>1) the environments created are empty
>2) the GO-environemnts are missing
>
>Is the GO-annotation moved to another function/package within the
>Bioconductor?
>
>I would really appreciate any tips of what has gone wrong.
>
>Best regards
>
>// Johan Lindberg
>
>#############################
>#My file with identifiers looks like this, it is tab-separated:
>RG3-B1 R45056
>RG3-F1 AA031514
>RG3-B4 AA428335
>RG3-F4 AA143331
>RG3-B7 N52474
>.
>.
>.
>#############################
>#The package contains the following:
>ls("package:Hum30kbatch1to5")
>[1] "Hum30kbatch1to5" "Hum30kbatch1to5ACCNUM"
>[3] "Hum30kbatch1to5CHRLENGTHS" "Hum30kbatch1to5CHRLOC"
>[5] "Hum30kbatch1to5ENTREZID" "Hum30kbatch1to5ENZYME"
>[7] "Hum30kbatch1to5LOCUSID" "Hum30kbatch1to5MAPCOUNTS"
>[9] "Hum30kbatch1to5ORGANISM" "Hum30kbatch1to5PATH"
>[11] "Hum30kbatch1to5PFAM" "Hum30kbatch1to5PROSITE"
>[13] "Hum30kbatch1to5QC" "Hum30kbatch1to5QCDATA"
>#Where is the GO-environments?
>
>#############################
>#My code and sessionInfo:
> > AnnWd <- "/Volumes/Cartman_2/forAnnbuilder/GBbatch1to5.txt"
> > AnnWd2 <- "/Volumes/Cartman_2/forAnnbuilder/hum30k1to5"
> > mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
> > ABPkgBuilder(baseName=AnnWd, srcUrls=mySrcUrls, baseMapType =
>"gb",pkgName="Hum30kbatch1to5", pkgPath=AnnWd2, organism = "Homo
>sapiens", version = "1.1.1", author = list(author = "Johan Lindberg",
>maintainer = "johanl at biotech.kth.se"), fromWeb = TRUE)
>perl: warning: Setting locale failed.
>perl: warning: Please check that your locale settings:
> LC_ALL = (unset),
> LANG = "en_SE.UTF-8"
> are supported and installed on your system.
>Read 1 item
>Read 1 item
>Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/
>hsa/hsa00195.gene
>Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/
>hsa/hsa00196.gene
>Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/
>hsa/hsa00231.gene
>#I get this for many genes....
>.
>.
>.
>.
>[1] "4085 2 2"
>The following data sets have been added to the database and will be
>removed:
>[1] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5ACCNUM.rda"
>[2] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/
>Hum30kbatch1to5CHRLENGTHS.rda"
>[3] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5CHRLOC.rda"
>[4] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/
>Hum30kbatch1to5ENTREZID.rda"
>[5] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5ENZYME.rda"
>[6] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/
>Hum30kbatch1to5MAPCOUNTS.rda"
>[7] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/
>Hum30kbatch1to5ORGANISM.rda"
>[8] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5PATH.rda"
>[9] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5PFAM.rda"
>[10] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/
>Hum30kbatch1to5PROSITE.rda"
>[11] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5QC.rda"
>[12] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/
>forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5QCDATA.rda"
>Warning message:
>Some rda files were not removed, be sure to check the data dir before
>building in: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE)
>
>#Then I check and compile the package:
> R CMD check Hum30kbatch1to5
> R CMD build Hum30kbatch1to5
>#Everything seems to be fine
>
> > sessionInfo()
>R version 2.4.1 (2006-12-18)
>i386-apple-darwin8.8.1
>
>locale:
>C
>
>attached base packages:
>[1] "splines" "tools" "stats" "graphics" "grDevices"
>[6] "utils" "datasets" "methods" "base"
>
>other attached packages:
> GOstats Category genefilter survival
> "2.0.4" "2.0.3" "1.12.0" "2.30"
> KEGG RBGL GO graph
> "1.14.1" "1.10.0" "1.14.1" "1.12.0"
>Hum30kbatch1to5 AnnBuilder RSQLite DBI
> "1.1.1" "1.12.0" "0.4-19" "0.1-12"
> annotate XML Biobase
> "1.12.1" "1.4-1" "1.12.2"
>*********************************************
>Johan Lindberg
>Royal Institute of Technology
>AlbaNova University Center
>Stockholm Center for Physics, Astronomy and Biotechnology
>School of Molecular Biotechnology
>Department of Gene Technology
>Visiting address:
>Roslagstullsbacken 21, Floor 3
>106 91 Stockholm, Sweden
>Delivering address:
>Roslagstullsbacken 30B
>104 06 Stockholm, Sweden
>Phone (office) +46 8 553 783 44
>Fax + 46 8 553 784 81
>http://www.ktharray.se/
>http://www.arrayadvice.se/
>*********************************************
>
>
>
> [[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
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
More information about the Bioconductor
mailing list