[BioC] AnnBuilder/ABPkgBuilder: lots of Errors

John Zhang jzhang at jimmy.harvard.edu
Wed Sep 8 16:02:03 CEST 2004


Could you start a new R and try the code again to see if the problem persists? 

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>From: Floor Stam <fjstam at bio.vu.nl>
>Subject: Re: [BioC] AnnBuilder/ABPkgBuilder: lots of Errors
>Date: Wed, 8 Sep 2004 15:39:34 +0200
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>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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>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084



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