ABPkgBuilder trouble
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@johan-lindberg-815
Last seen 8.1 years ago
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 8.1 years ago
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.r da" >[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.r da" >[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.r da" >[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.r da" >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
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi Johan, I created a package by using your script and the probe-GenBank mapping (5 lines)showed in your email. It looks fine: Quality control information for Hum30kbatch1to5 Date built: Created: Tue Feb 20 17:43:09 2007 Number of probes: 5 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: Hum30kbatch1to5ACCNUM found 5 of 5 Hum30kbatch1to5CHRLOC found 4 of 5 Hum30kbatch1to5CHR found 4 of 5 Hum30kbatch1to5ENTREZID found 4 of 5 Hum30kbatch1to5ENZYME found 2 of 5 Hum30kbatch1to5GENENAME found 4 of 5 Hum30kbatch1to5GO found 4 of 5 ... I am using R 2.5 though (sessionInfo below). GO 1.51.1 and GO 1.14.1 are the same. AnnBuilder 1.12.0 should work well on R 2.4. And your script is fine. Maybe it is environment setting or network problem? hope this is helpful nianhua sessionInfo() R version 2.5.0 Under development (unstable) (2007-01-22 r40546) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US; LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C; LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.15.1" "1.13.14" "1.13.4" "1.4-0" "1.13.34"
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