Hi I'd be grateful for your help. I am having problems with creating an annotation packages. The errors are: gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed data--crc error gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed data--length error Can not open /tmp/RtmpQ29612/file66334873Hs.data at /tmp/RtmpQ29612/tempPerl238e1f29.pl line 6. Warning messages: 1: Built for UCSC is not valid! in: getUCSCBuilt(organism) 2: cannot open file '/tmp/RtmpQ29612/tempOut625558ec', reason 'No such file or directory' Error in if (!is.null(ug) && nrow(ugMapping) > 0) { : missing value where TRUE/FALSE needed In addition: Warning message: Failed to get or parse UniGene data becaus of: Error in file(file, "r") : unable to open connection in: unifyMappings(base, eg, ug, otherSrc) > traceback() 6: unifyMappings(base, eg, ug, otherSrc) 5: getUniMappings(baseName, srcObjs[["eg"]], srcObjs[["ug"]], NULL, baseMapType) 4: ABPkgBuilder(baseName = mybaseName, srcUrls = mySrcUrls, baseMapType = myBaseType, otherSrc = NULL, pkgName = "TIGR40K.mapGB", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = myauthor, fromWeb = TRUE) 3: eval.with.vis(expr, envir, enclos) 2: eval.with.vis(ei, envir) 1: source("AnnBuilder.R") My basefile looks like. V2 are genbank accesssion numbers V1 V2 1 489567 AA099162 2 46105 H09322 3 396145 AA757917 4 1755589 AI204424 5 1690935 AI091817 6 504207 AA132086 7 33150 R43822 8 1690655 AI143430 9 809876 AA455126 10 32175 R43463 > mySrcUrls GP "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/ database/" UG "ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz" GO "http://www.godatabase.org/dev/database/archive/latest/go_200602-termd b.rdf-xml.gz" HG "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" EG "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" Session Info R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: hgu133plus2 GO AnnBuilder annotate XML Biobase "1.10.0" "1.7.1" "1.8.0" "1.8.0" "0.99-6" "1.8.0" Thanks for your help Aedin

Hi Aedin, It seems that your gunzip function cannot unzip the Hs.data.gz file correctly. It could be (1) the gunzip function didn't work well, or (2) the Hs.data.gz is not compressed well. According to the website ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/, the file Hs.data.gz is put on Dec 30, 2005. When I was building packages between Dec 30, 2005, and today, I don't have any problem in this file. Therefore, I think the file Hs.data.gz is OK. Here is my gunzip version: tliu at gopher1:~/tmp> gunzip --version gunzip 1.3.5 (2002-09-30) This one works on the Hs.data.gz file. Today I used "wget" to download ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz and I can unzip it without any error messages. Could you also try wget ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz and gunzip Hs.data.gz to see if your gunzip function works? Could you also try to build the package again to see if you will have the same problem? It is also possible that the Hs.data.gz file was not downloaded completely (due to the network connection problem) so that the file cannot be uncompressed successfully. HTH, Ting ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Fri, 24 Feb 2006, Aedin Culhane wrote: > Hi > I'd be grateful for your help. I am having problems with creating an > annotation packages. The errors are: > > gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed > data--crc error > gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed > data--length error > Can not open /tmp/RtmpQ29612/file66334873Hs.data at > /tmp/RtmpQ29612/tempPerl238e1f29.pl line 6. > Warning messages: > 1: Built for UCSC is not valid! in: getUCSCBuilt(organism) > 2: cannot open file '/tmp/RtmpQ29612/tempOut625558ec', reason 'No such > file or directory' > Error in if (!is.null(ug) && nrow(ugMapping) > 0) { : > missing value where TRUE/FALSE needed > In addition: Warning message: > Failed to get or parse UniGene data becaus of: > > Error in file(file, "r") : unable to open connection > in: unifyMappings(base, eg, ug, otherSrc) > > > > traceback() > 6: unifyMappings(base, eg, ug, otherSrc) > 5: getUniMappings(baseName, srcObjs[["eg"]], srcObjs[["ug"]], NULL, > baseMapType) > 4: ABPkgBuilder(baseName = mybaseName, srcUrls = mySrcUrls, baseMapType > = myBaseType, > otherSrc = NULL, pkgName = "TIGR40K.mapGB", pkgPath = myDir, > organism = "Homo sapiens", version = "1.1.0", author = myauthor, > fromWeb = TRUE) > 3: eval.with.vis(expr, envir, enclos) > 2: eval.with.vis(ei, envir) > 1: source("AnnBuilder.R") > > > My basefile looks like. V2 are genbank accesssion numbers > > V1 V2 > 1 489567 AA099162 > 2 46105 H09322 > 3 396145 AA757917 > 4 1755589 AI204424 > 5 1690935 AI091817 > 6 504207 AA132086 > 7 33150 R43822 > 8 1690655 AI143430 > 9 809876 AA455126 > 10 32175 R43463 > > > > mySrcUrls > > GP > > "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapien s/database/" > > UG > > "ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz" > > GO > "http://www.godatabase.org/dev/database/archive/latest/go_200602-ter mdb.rdf-xml.gz" > > HG > > "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" > > EG > > "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" > > > > Session Info > R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > hgu133plus2 GO AnnBuilder annotate XML Biobase > "1.10.0" "1.7.1" "1.8.0" "1.8.0" "0.99-6" "1.8.0" > > > Thanks for your help > Aedin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >