[BioC] AnnBuilder/ABPkgBuilder: lots of Errors

Floor Stam fjstam at bio.vu.nl
Tue Sep 7 12:29:24 CEST 2004


Hi

I'd like to build an Annotation package for the (custom made rat) array  
that i'm using.

I'm running R 1.9.1 on mac osx and have an installation failure of  
AnnBuilder 1.4.13
I installed the devel versions of biobase and annotate as well, xml  
0.95-6 is also installed.

install.from.file(pkg="/Users/fjstam/Desktop/AnnBuilder")
	npackage installation failed

If i go back to the current versions of annotate and biobase i get the  
same error.
If i install AnnBuilder 1.4.2 i get it installed but then the same  
thing happens that was reported earlier, see mail below.

 > 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")
 > myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"),  
"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"),   
"data", "srcb"))
 > myDir <- tempdir()
 > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =  
myBaseType, otherSrc = myOtherSrc, pkgName = "testPkg", pkgPath =  
myDir,  organism = "human", version = "1.1.0", makeXML = TRUE, author =  
list(author = "kees", maintainer = "kees at myemail.com"), fromWeb = TRUE)
[1] "It may take me a while to process the data. Be patient!"
Error in url(sourceURLs[["GO"]], open = "r") :
	Object "sourceURLs" not found

So if i want the ABPkgBuilder to work,
-which version of AnnBuilder should i install?
-Should i upgrade any other package to devel or have everything at the  
current level?

Earlier this week i tried the code from the ABPkgPrimer vignette (see  
mail below) in R 1.9.0, and then i got an error at the end, after my  
computer had been thinking about things for a while, which said  
something like: cannot parse rows and cannot open blabla.xml. The same  
thing happened when i used the 'real' urls and my own base file (it's  
just that it took my poor laptop an hour or so instead of a few minutes  
to give the error message). I decided that going to R 1.9.1 would  
probably solve my problem so i did not save the text from this session,  
and can therefore not be more exact (i don't feel like going back to R  
1.9.0 unless it is really necessary).

i hope anyone can help me with the installation and/or the source url  
problem.

When these things are fixed i will probably have the parsing/opening  
xml problem again but we'll cross that bridge when we get there.

floor


_______________________________________________________
Floor Stam

Vrije Universiteit Amsterdam
Faculty of Earth and Life Sciences
Department of Molecular and Cellular Neurobiology
De Boelelaan 1085
1081HV Amsterdam
The Netherlands

Ph: 	+31-20-4447114
	+31-20-5665512
Fax: 	+31-20-4447112
e-mail: fjstam at bio.vu.nl
_______________________________________________________
On 25 Aug 2004 , at 18:20, John Zhang wrote:

>
>> I'm running R 1.9.1 on Windows 2000 and tried to test some of the  
>> code in
>> the AnnBuilder (1.4.2) package from the vignette.
>> I'm encountering an error, which I'm not clear on how to fix. Code and
>> error are copied below. Note that I've tried to run the same code on  
>> Linux
>> (R version 1.9.0) and got the same error.
>> Any advice on this?
>
> I just noticed this bug and will have it fixed today. Thanks.
>
>
>> Thanks,
>> Elisabetta
>>
>> ---
>>> 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")
>>> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls,  
>>> baseMapType=myBaseType,
>> pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML=F)
>> [1] "It may take me a while to process the data. Be patient!"
>> Error in url(sourceURLs[["GO"]], open = "r") :
>>         Object "sourceURLs" not found
>> ---
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>


More information about the Bioconductor mailing list