[BioC] Error while using AnnBuilder
TEXTORIS Julien
julien.textoris at gmail.com
Tue Jan 31 08:00:38 CET 2006
Hi,
thanks for the answers. But the error is still there !
I've updated the packages for :
- AnnBuilder
- Biobase
- GOstats
- goCluster
-go
Here is the log this time :
> library(AnnBuilder)
Le chargement a nécessité le package : Biobase
Le chargement a nécessité le package : tools
Welcome to Bioconductor
Vignettes contain introductory material.
To view, simply type 'openVignette()' or start with 'help(Biobase)'.
For details on reading vignettes, see the openVignette help page.
Le chargement a nécessité le package : XML
Le chargement a nécessité le package : annotate
Le chargement a nécessité le package : RSQLite
Le chargement a nécessité le package : DBI
> myDir <- tempdir()
> myBaseType <- "image"
> myBase <- "/home/jtextori/Documents/DEA/bioc/MC0311.txt"
> ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "myPkg",
pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author =
list(author = "Julien TEXTORIS", maintainer = "Julien.Textoris at gmail.com"),
fromWeb = TRUE)
Attachement du package : 'GO'
The following object(s) are masked from package:AnnBuilder :
GO
Erreur dans readLines(con) : impossible d'ouvrir la connexion
De plus : Warning message:
incapable de résoudre 'www.godatabase.org'.
> sessionInfo()
R version 2.2.1, 2005-12-20, i686-pc-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
GO AnnBuilder RSQLite DBI annotate XML Biobase
"1.10.0" "1.9.11" "0.4-1" "0.1-10" "1.8.0" "0.99-6" "1.9.2"
>
So the message about masked packages is still there ?
And for the second warning about not finding www.godatabase.org, i run a host
in a shell and that's true my DNS don't know this address :
[jtextori at diablotin Desktop]# host www.godatabase.org
;; Got SERVFAIL reply from 139.124.1.2, trying next server
;; connection timed out; no servers could be reached
[jtextori at diablotin Desktop]#
can these errors be linked ?
and do i have to run this : "mySrcUrls <- getSrcUrl("all", "Homo sapiens")"
Thanks for any clue,
sincerily
Julien
PS :
a part of the input file :
MDF023.001 NA
MDF019.295 303810
MDF019.350 313037
MDF019.376 314781
MDF019.339 337441
MDF018.001 368564
MDF018.002 368564
MDF018.017 368682
MDF018.018 368713
MDF018.033 368776
...
Le Lundi 30 Janvier 2006 19:44, vous avez écrit :
> Hi Julien,
>
> > What does it mean "The following object(s) are masked from
> > package:AnnBuilder :" ?
>
> This is not the reason why you cannot run ABPkgBuilder successfully. The
> function GO in the GO package is used to display some descriptive
> statistics for the environments, and the GO function in AnnBuilder is to
> define a new object of class "GO". It is OK to see this message.
>
> > Erreur dans all(is.na(annotation[, "GO"])) : indice hors limites
> > $>
>
> I think this bug has been fixed. Could you try the developmental version
> of AnnBuilder and see if you still get the same error message?
>
> > $> mySrcUrls <-
>
> c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/reposito
>ry/UniGene/Homo_s$
>
>
> This setting is not necessary. If you ignore the srcUrls argument,
> AnnBuilder will determine it for you.
>
> HTH,
> Ting-Yuan
> ______________________________________
> Ting-Yuan Liu
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> Seattle, WA, USA
> ______________________________________
>
> On Sat, 28 Jan 2006, TEXTORIS Julien wrote:
> > Hi,
> >
> > We are currently trying to develop a library to deal with nylon arrays.
> >
> > I wanted to build an annotation package for our chip, but i have an error
> > with GO. Here is the log :
> >
> > $> mySrcUrls <-
> > c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/reposi
> >tory/UniGene/Homo_sapiens/Hs.data.gz") $> myBase <-
> > "/home/jtextori/Documents/DEA/bioc/MC0311.txt.csv"
> > $> myBaseType <- "image"
> > $> myDir <- tempdir()
> > $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
> > organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author =
> > list(author = "Julien TEXTORIS", maintainer =
> > "Julien.Textoris at gmail.com"), fromWeb = TRUE)
> > Erreur : impossible de trouver la fonction "ABPkgBuilder"
> > $> library(AnnBuilder)
> > Le chargement a nécessité le package : Biobase
> > Le chargement a nécessité le package : tools
> >
> > Welcome to Bioconductor
> >
> > Vignettes contain introductory material.
> > To view, simply type 'openVignette()' or start with 'help(Biobase)'.
> > For details on reading vignettes, see the openVignette help page.
> >
> > Le chargement a nécessité le package : XML
> > Le chargement a nécessité le package : annotate
> > $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
> > organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author =
> > list(author = "Julien TEXTORIS", maintainer =
> > "Julien.Textoris at gmail.com"), fromWeb = TRUE)
> > Erreur dans ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls,
> > baseMapType = myBaseType, :
> > argument(s) inutilisé(s) (makeXML ...)
> > $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > myBaseType, , pkgName = "myPkg", pkgPath = myDir, organism = "Homo
> > sapiens", version = "1.1.0", author = list(author = "Julien TEXTORIS",
> > maintainer = "Julien.Textoris at gmail.com"), fromWeb = TRUE)
> >
> > Attachement du package : 'GO'
> >
> >
> > The following object(s) are masked from package:AnnBuilder :
> >
> > GO
> >
> >
> > Erreur dans all(is.na(annotation[, "GO"])) : indice hors limites
> > $>
> >
> > The file is a text file with two columns, separated by a tabulation.
> > First is the identifier from the chip, seond is the cloneId in the form
> > IMAGE:nnnnn
> >
> > I had the same error when i specified an URL for GO ?
> >
> > What does it mean "The following object(s) are masked from
> > package:AnnBuilder :" ?
> >
> > Thanks in advance for any help,
> >
> > Julien
> >
> > PS, sessionInfo() follows :
> > > sessionInfo()
> >
> > R version 2.2.1, 2005-12-20, i686-pc-linux-gnu
> >
> > attached base packages:
> > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
> > [7] "datasets" "base"
> >
> > other attached packages:
> > GO AnnBuilder annotate XML Biobase
> > "1.10.0" "1.8.0" "1.8.0" "0.99-6" "1.8.0"
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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