Dear List, I am trying to use the homoPkgBuilder-function from the AnnBuilder- package but did not yet succeed in getting it to work. I used AnnBuilder-1.4.2 on R-1.8.1 first. The function exits with an error about the object "tempList" not being defined. As far as I can see from the 1.4.2 code, this variable is used in the mapPS function but never defined. So I switched to R-1.9.1 and AnnBuilder-1.4.6 because the mapPS function looked like the problem got fixed. This time the function exits with Error in getClass(Class, where = topenv(parent.frame())) : "homoData" is not a defined class Looking at the code I assume that the function "getHomoData" tries to return an object of a class that has not been defined in the AnnBuilder package. Do I have to install another developmental package to get the class definition? I did look at Biobase but did not find anything there. Any help would greatly appreciated. Best regards Gunnar -- ---------------------------------------------- Gunnar Wrobel Divisions of Bioinformatics and Biochemistry Swiss Institute of Bioinformatics/Biozentrum Klingelbergstrasse 50/70 CH-4056 Basel / Switzerland Tel.: +41 61 267 1579 Fax: +41 61 267 3398 e-mail: bioc@gunnarwrobel.de -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-keys Size: 1486 bytes Desc: =?utf-8?b?w5ZmZmVudGxpY2hlciA=?= =?utf-8?b?UEdQLVNjaGzDvHNzZWw=?= Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040629/32ee66f5/attachment.bin

What version of annotate do you have? The class defination is in the devel version of annotate. > >I am trying to use the homoPkgBuilder-function from the AnnBuilder- package but >did not yet succeed in getting it to work. > >I used AnnBuilder-1.4.2 on R-1.8.1 first. The function exits with an error about >the object "tempList" not being defined. As far as I can see from the 1.4.2 >code, this variable is used in the mapPS function but never defined. > >So I switched to R-1.9.1 and AnnBuilder-1.4.6 because the mapPS function looked >like the problem got fixed. This time the function exits with > >Error in getClass(Class, where = topenv(parent.frame())) : > "homoData" is not a defined class > >Looking at the code I assume that the function "getHomoData" tries to return an >object of a class that has not been defined in the AnnBuilder package. Do I >have to install another developmental package to get the class definition? I >did look at Biobase but did not find anything there. > >Any help would greatly appreciated. > >Best regards > >Gunnar > >-- >---------------------------------------------- >Gunnar Wrobel > >Divisions of Bioinformatics and Biochemistry >Swiss Institute of Bioinformatics/Biozentrum >Klingelbergstrasse 50/70 >CH-4056 Basel / Switzerland >Tel.: +41 61 267 1579 >Fax: +41 61 267 3398 >e-mail: bioc@gunnarwrobel.de Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

While the development version of annotate did correct the problem with the class definition I came back to my original problem of the undefined "tempList" object. Looking at the code I guess the following typo ("tepList") in line 171 of file homoPkgBuilder.R causes the problem. saveOrgNameNCode <- function(pkgName, pkgPath, author, tepList) The code seems to work with the old homoloGene build (ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp) while I actually wanted to get a package from the new build (ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build36/hmlg.ftp). If I use that as url for the homoloGene information the function exits with: a <- homoPkgBuilder("homology",".","1.0","Gunnar Wrobel","ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build36/hmlg.ftp") [1] "Processing organism: 10090" Error in validObject(.Object) : Invalid "homoData" object: Invalid object for slot "homoOrg" in class "homoData": got class "NULL", should be or extend class "character" Should the code work in principle with the new homoloGene data? If that is the case I would try to debug the code until I get the package. Thanks for your help. Best regards Gunnar -- ---------------------------------------------- Gunnar Wrobel Divisions of Bioinformatics and Biochemistry Swiss Institute of Bioinformatics/Biozentrum Klingelbergstrasse 50/70 CH-4056 Basel / Switzerland Tel.: +41 61 267 1579 Fax: +41 61 267 3398 e-mail: bioc@gunnarwrobel.de -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-keys Size: 1486 bytes Desc: =?utf-8?b?w5ZmZmVudGxpY2hlciA=?= =?utf-8?b?UEdQLVNjaGzDvHNzZWw=?= Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040629/4ad4e876/attachment.bin