[BioC] I have trouble running the AnnBuilder Vignette

Richard Friedman friedman at cancercenter.columbia.edu
Thu Nov 11 20:59:47 CET 2004


Dear John (and Everyone),

	Thank you very much for your quick reply. I tried what you said,
but I got a warrning and an error message but I still can't reachthe
object. The warning was that gzip was not found.
The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism
code

I got a list of entries in AnnInfo but could not find the files:
Here is what I did:
###########################################################################
>  ABPkgBuilder(baseName = "thgu95a", srcUrls = mySrcUrls, baseMapType =
"gb",
+              pkgName = "myPkg",
+              pkgPath = myDir, organism = "Homo sapiens", version =
"1.1.0",
+              makeXML = TRUE, author = list(author = "RichardFriedman",
maintainer =
+                              "friedman at cancercenter.columbia.edu"),
fromWeb = TRUE)
Warning: gzip not found
Warning: gzip not found
Error in parseKEGGGenome() : Faild to obtain KEGG organism code
>
> ls()
[1] "AnnInfo"      "last.warning" "myBase"       "myBaseType"   "myDir"
"mySrcUrls"
[7] "sourceURLs"
> library(gzip)
Error in library(gzip) : There is no package called 'gzip'
> ls(AnnInfo)
 [1] "#CHRNUM#END"    "#CHRNUM#START"  "#CHROMSEQ#"     "#EXON#"
"#HGID2GB#"
 [6] "#HGID2HGID#"    "#HGID2LL#"      "#HGID2PS#"      "#HOMODATA#"
"#ONETOMANYMAN#"
[11] "#ONETOONEMAN#"  "#REPLACEME#"    "#SEQUENCE#"     "ACCNUM"
"AFFY"
[16] "ALIAS"          "AnnInfo"        "ASSOCIATION"    "BPANCESTOR"
"BPCHILDREN"
[21] "BPID2TERM"      "BPOFFSPRING"    "BPPARENTS"      "CATEGORY"
"CCANCESTOR"
[26] "CCCHILDREN"     "CCID2TERM"      "CCOFFSPRING"    "CCPARENTS"
"CHR"
[31] "CHRLENGTHS"     "CHRLOC"         "CHRORI"         "CURRENTLOCUSID"
"CYTOLOC"
[36] "DESCRIPTION"    "ENZYME"         "ENZYME2PROBE"   "ENZYMEID2GO"
"ENZYMEID2NAME"
[41] "EXTID2PATHID"   "GENENAME"       "GO"             "GO2ALLLL"
"GO2ALLPROBES"
[46] "GO2ENZYMEID"    "GO2EVIDENCE"    "GO2LL"          "GO2PROBE"
"GRIF"
[51] "HGID"           "IMAGE"          "LL2GO"          "LL2HGID"
"LOCUSID"
[56] "LOCUSID2CHR"    "LOCUSTYPE"      "MAP"            "MFANCESTOR"
"MFCHILDREN"
[61] "MFID2TERM"      "MFOFFSPRING"    "MFPARENTS"      "NC"
"NG"
[66] "NM"             "NP"             "OMIM"           "ONTOLOGY"
"ORF"
[71] "ORGANISM"       "ORGCODE"        "PATH"           "PATH2PROBE"
"PATHID2EXTID"
[76] "PATHID2NAME"    "PATHNAME2ID"    "PMID"           "PMID2PROBE"
"PROBE"
[81] "PROBECOUNTS"    "PRODUCT"        "REFSEQ"         "SUMFUNC"
"SUMMARY"
[86] "SYMBOL"         "TERM"           "UNIGENE"
> list.files(file.path(myDir, "myPkg"))
Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is
not a readable directory
character(0)
> list.files(file.path(myDir, "myPkg", "data"))
Warning: list.files:
C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable
directory
character(0)
>
#############################################################################
I would appreciate any suggestion that you might have about
building the annotation files.

Best wishes.
Rich


On Wed, 10 Nov 2004, John Zhang wrote:

> The files were certainly not created since the code did not get to run under
> Windows. You have to remove "if(.Platform$OS.type != "windows" &&
> interactive()){" when you rn ABPkgBuilder(...). Since human interference is
> required to finish the vignette, I have to put the checking there to make the
> vignette pass the building process under Windows.
>
>
> >Date: Wed, 10 Nov 2004 15:22:23 -0500 (EST)
> >From: Richard Friedman <friedman at cancercenter.columbia.edu>
> >To: bioconductor at stat.math.ethz.ch
> >MIME-Version: 1.0
> >Received-SPF: none (hypatia: domain of bioconductor-bounces at stat.math.ethz.ch
> does not designate permitted sender hosts)
> >Received-SPF: none (hypatia: domain of friedman at cancercenter.columbia.edu does
> not designate permitted sender hosts)
> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
> >Subject: [BioC] I have trouble running the AnnBuilder Vignette
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> >
> >Dear Bioconductor Users,
> >
> >	I am trying to learn to use AnnBuilder in Bioconductor 1.5.0
> >under R2.0 under Windows XP Professional. Here is a transcript
> >of my session:
> >###################################################################
> >> library(XML)
> >> library(AnnBuilder)
> >Loading required package: Biobase
> >Loading required package: tools
> >Welcome to Bioconductor
> >         Vignettes contain introductory material.  To view,
> >         simply type: openVignette()
> >         For details on reading vignettes, see
> >         the openVignette help page.
> >Loading required package: annotate
> >Warning message:
> >'addPDF2Vig' is deprecated.
> >Use 'addVigs2WinMenu' instead.
> >See help("Deprecated")
> >> read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"),
> >+     sep = "\t", header = FALSE, as.is = TRUE)
> >          V1       V2
> >1 32468_f_at   D90278
> >2   32469_at   L00693
> >3   32481_at AL031663
> >4   33825_at   X68733
> >5   35730_at   X03350
> >6   36512_at   L32179
> >7   38912_at   D90042
> >8   38936_at   M16652
> >9   39368_at AL031668
> >> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
> >> myBaseType <- "gb"
> >> mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
> >> mySrcUrls
> >
> >LL
> >
> >"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz"
> >
> >GP
> >
> >"http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/"
> >
> >UG
> >
> >"ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz"
> >
> >GO
> >"http://www.godatabase.org/dev/database/archive/2004-09-01/go_200409-termdb.xml
> .gz"
> >
> >KEGG
> >
> >"ftp://ftp.genome.ad.jp/pub/kegg/pathways"
> >
> >YG
> >
> >"http://www.yeastgenome.org/DownloadContents.shtml"
> >
> >HG
> >
> >"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"
> >>
> >> myDir <- tempdir()
> >> if(.Platform$OS.type != "windows" && interactive()){
> >+         ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls,
> >baseMapType = g,
> >+              pkgName = "myPkg",
> >+              pkgPath = myDir, organism = "Homo sapiens", version =
> >"1.1.0",
> >+              makeXML = TRUE, author = list(author = "RichardFriedman",
> >maintainer =
> >+                              "friedman at cancercenter.columbia.edu"),
> >fromWeb = TRUE)
> >+ }
> >> ls()
> >[1] "last.warning" "myBase"       "myBaseType"   "myDir"
> >"mySrcUrls"    "sourceURLs"
> >> if(.Platform$OS.type != "windows"  && interactive()){
> >+         list.files(file.path(myDir, "myPkg"))
> >+         list.files(file.path(myDir, "myPkg", "data"))
> >+         list.files(file.path(myDir, "myPkg", "man"))
> >+         list.files(file.path(myDir, "myPkg", "R"))
> >+     }
> >>
> >>
> >> list.files(file.path(myDir, "myPkg"))
> >Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is
> >not a readable directory
> >character(0)
> >> list.files(file.path(myDir, "myPkg", "data"))
> >Warning: list.files:
> >C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable
> >directory
> >character(0)
> >##############################################################################
> >
> >Apparently the package was not created.
> >Am I correct in this?
> >If the package was created, how can I access it?
> >If the package was not created, how can I create it?
> >
> >Thanks and best wieshes,
> >Rich
> >------------------------------------------------------------
> >Richard A. Friedman, PhD
> >Associate Research Scientist
> >Herbert Irving Comprehensive Cancer Center
> >Oncoinformatics Core
> >Lecturer
> >Department of Biomedical Informatics
> >Box 95, Room 130BB or P&S 1-420C
> >Columbia University Medical Center
> >630 W. 168th St.
> >New York, NY 10032
> >(212)305-6901 (5-6901) (voice)
> >friedman at cancercenter.columbia.edu
> >http://cancercenter.columbia.edu/~friedman/
> >
> >"That was written by Felix Mendelsohn?
> >Did he start Mendelsohn's Pizza?"
> >-Rose Friedman, age 8
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>

------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"That was written by Felix Mendelsohn?
Did he start Mendelsohn's Pizza?"
-Rose Friedman, age 8



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