Error while using AnnBuilder
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@textoris-julien-1412
Last seen 9.6 years ago
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/rep ository/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 n?cessit? le package : Biobase Le chargement a n?cessit? 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 n?cessit? le package : XML Le chargement a n?cessit? 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) inutilis?(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 allis.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" >
Annotation GO Organism annotate AnnBuilder Annotation GO Organism annotate AnnBuilder • 1.3k views
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 3.0 years ago
United States
I did not follow much of the rest of your message, but the warning below means that you have overwritten some of the built-in functions or data by loading or creating an object with the same name. There was some discussion a couple of weeks ago about how to avoid this when loading libraries - sorry I do not have the exact e-mails, but they should be in the recent archives. --Naomi At 12:02 PM 1/28/2006, TEXTORIS Julien wrote: >What does it mean "The following object(s) are masked from >package:AnnBuilder :" ? Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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@ting-yuan-liu-fhcrc-1221
Last seen 9.6 years ago
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 allis.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? > $> mySrcUrls <- > c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/rep ository/UniGene/Homo_s$ > 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/r epository/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 n?cessit? le package : Biobase > Le chargement a n?cessit? 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 n?cessit? le package : XML > Le chargement a n?cessit? 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) inutilis?(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 allis.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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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 n?cessit? le package : Biobase Le chargement a n?cessit? 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 n?cessit? le package : XML Le chargement a n?cessit? le package : annotate Le chargement a n?cessit? le package : RSQLite Le chargement a n?cessit? 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 r?soudre '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 ?crit?: > 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 allis.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? > > > $> mySrcUrls <- > > c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/r eposito >ry/UniGene/Homo_s$ > > > 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 n?cessit? le package : Biobase > > Le chargement a n?cessit? 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 n?cessit? le package : XML > > Le chargement a n?cessit? 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) inutilis?(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 allis.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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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi Julien, On 30 Jan 2006, julien.textoris at gmail.com wrote: > thanks for the answers. But the error is still there ! It looks to me like a *different* error is giving you trouble now. It may be the same for you since, in the end, AnnBuilder isn't doing what you want. But for us, we like to call this progress; one error resolved and another in its place ;-) > Here is the log this time : Thanks, the output is helpful. >> 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 r?soudre 'www.godatabase.org'. I get the same thing, I think the GO site is down. > So the message about masked packages is still there ? Yes, we are working on a fix for this warning message, but we do not believe it is related to the problems you are having. + seth
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