Hi, I have the same problem in https://stat.ethz.ch/pipermail/bioconductor/2004-August/thread.html#57 52 described by Margaret Gardiner. Running the first AnnBuilder vignette (Windows OS, R 2.0.1, BioC 1.5, Active PERL, Environment variables and PATH modified), I obtain: Error in readURL(infoUrl) : Can't read from url: ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info Could someone help me? Here is the code: >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: XML 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 <- c(LL = >"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz", + UG = "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz", + GO = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml") > > >read.table(file.path(.path.package("AnnBuilder"), "data", "srca"), + sep = "\t", header = FALSE, as.is = TRUE) V1 V2 1 32468_f_at NA 2 32469_at 2 3 32481_at NA 4 33825_at 9 5 35730_at 1576 6 36512_at NA 7 38912_at 10 8 38936_at NA 9 39368_at NA >read.table(file.path(.path.package("AnnBuilder"), "data", "srcb"), + sep = "\t", header = FALSE, as.is = TRUE) V1 V2 1 32468_f_at NA 2 32469_at NA 3 32481_at 7051 4 33825_at NA 5 35730_at NA 6 36512_at 1084 7 38912_at NA 8 38936_at NA 9 39368_at 89 >myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), + "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), + "data", "srcb")) > > >myDir <- "H:/DATI/pkg" > >ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "human", version = "1.1.0", makeXML = TRUE, + author = list(author = "myname", maintainer = "myname@myemail.com"), + fromWeb = TRUE) Error in readURL(infoUrl) : Can't read from url: ftp://ftp.ncbi.nih.gov/repository/UniGene/.info > Thanks a lot. Giulio Di Giovanni.

>described by Margaret Gardiner. >Running the first AnnBuilder vignette (Windows OS, R 2.0.1, BioC 1.5, Active >PERL, Environment variables and PATH modified), >I obtain: > >Error in readURL(infoUrl) : Can't read from url: >ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info The URL is valid. UniGene was down when you were trying to read the file? Were you behind a fire wall that prevented you from accessing the URL? > >Could someone help me? > >Here is the code: > >>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: XML >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 <- c(LL = >>"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz", >+ UG = "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz", >+ GO = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml") >> >> >>read.table(file.path(.path.package("AnnBuilder"), "data", "srca"), >+ sep = "\t", header = FALSE, as.is = TRUE) > V1 V2 >1 32468_f_at NA >2 32469_at 2 >3 32481_at NA >4 33825_at 9 >5 35730_at 1576 >6 36512_at NA >7 38912_at 10 >8 38936_at NA >9 39368_at NA >>read.table(file.path(.path.package("AnnBuilder"), "data", "srcb"), >+ sep = "\t", header = FALSE, as.is = TRUE) > V1 V2 >1 32468_f_at NA >2 32469_at NA >3 32481_at 7051 >4 33825_at NA >5 35730_at NA >6 36512_at 1084 >7 38912_at NA >8 38936_at NA >9 39368_at 89 >>myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), >+ "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), >+ "data", "srcb")) >> >> >>myDir <- "H:/DATI/pkg" >> >>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >>myBaseType, >+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, >+ organism = "human", version = "1.1.0", makeXML = TRUE, >+ author = list(author = "myname", maintainer = "myname@myemail.com"), >+ fromWeb = TRUE) >Error in readURL(infoUrl) : Can't read from url: >ftp://ftp.ncbi.nih.gov/repository/UniGene/.info >> > >Thanks a lot. > >Giulio Di Giovanni. > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Giulio Di Giovanni wrote: >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >> myBaseType, > > + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, > + organism = "human", version = "1.1.0", makeXML = TRUE, > + author = list(author = "myname", maintainer = "myname@myemail.com"), > + fromWeb = TRUE) > Error in readURL(infoUrl) : Can't read from url: > ftp://ftp.ncbi.nih.gov/repository/UniGene/.info Change organism="human" to organism="Homo sapiens" and it should work. Jim > >> > > Thanks a lot. > > Giulio Di Giovanni. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109