[BioC] AnnBuilder/ABPkgBuilder: lots of Errors

Floor Stam fjstam at bio.vu.nl
Wed Sep 8 15:39:34 CEST 2004


I'm running R 1.9.1 on mac OSX using AnnBuilder 1.4.2.
When i try to build an annotation package using AnnBuilder i get an  
error using the following code:

 > myDir<-("/Data_analyse")
 > myBase<-file.path("GBbase.txt")
 > myBaseType<-"gb"


ShowmyBase<-read.table("GBbase.txt")
ShowmyBase[1:5,]
   V1        V2
1 91 NM_013184
2 92 NM_019255
3 93 NM_031055
4 94  AI236115
5 95  BI283260


 > mySrcUrls
                                                                          
          LL
                                 
"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz"
                                                                          
          UG
                               
"ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.data.gz"
                                                                          
          GO
"http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407- 
termdb.xml.gz"
                                                                          
        KEGG
                                           
"ftp://ftp.genome.ad.jp/pub/kegg/pathways"


 > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
+ myBaseType, pkgName = "GOFloor", pkgPath=myDir, organism = "rat",  
version = "1.1.0", makeXML = F, author =
+ list(author = "fjstam", maintainer = "fjstam at bio.vu.nl"), fromWeb =  
TRUE)
[1] "It may take me a while to process the data. Be patient!"
Error in file(con, "r") : All connections are in use
Error in ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls,  
baseMapType = myBaseType,  :
	Parsing LocusLink data failed because of:

  Error in file(con, "r") : All connections are in use

The error happens after about half an hour of processing. Using the  
urls and base file from the Vignette (except for the GO url that i was  
reporting about yesterday), this code does produce a package.

Can anyone tell me what's happening here? is there anything wrong with  
the source urls? the LL url points to an existing file on the ftp  
server but this file does not seem to contain rat information. If i  
point it to LL.out_rn.gz which does contain rat data then i get

Error in file(file, "r") : All connections are in use

after a few seconds.


Running the scirpt (with the LL_tmpl.gz url), a huge textfile (>200MB)  
that ends with _tmpl is created in the temp subdir of the AnnBuilder  
package. This file contains lots of info per LL ID and starts with LLID  
1 and goes on for ages. Also a perl file (? .pl ) is created. But no  
package.

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 7 Sep 2004 , at 12:29, Floor Stam wrote:

> 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
>>
> _______________________________________________
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