Question: Error in parseURI("") : cannot parse URI (rtracklayer package)
0
gravatar for Qiang
3.6 years ago by
Qiang70
Qiang70 wrote:

Hi Lawrence,

I got an error when testing the import function.

track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
Error in parseURI("") : cannot parse URI

I found the parseURI("") was used in the .parseURI function when it run in unix system (io.R line 200).

parsed <- parseURI("")
parsed$path <- uri

#Why just parsed <- parseURI(uri) ?

The parseURI("") acts different in my test. It return a list when It works in one computer, but it gives me the "cannot parse URI" error in another computer.

parseURI("") 
Error in parseURI("") : cannot parse URI

This problem will also affect BSgenome... package. Please help. Thanks!

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] XML_3.98-1.4         rtracklayer_1.30.2   GenomicRanges_1.22.4
[4] GenomeInfoDb_1.6.3   IRanges_2.4.8        S4Vectors_0.8.11    
[7] BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] Rsamtools_1.22.0           Biostrings_2.38.4         
 [3] GenomicAlignments_1.6.3    bitops_1.0-6              
 [5] futile.options_1.0.0       zlibbioc_1.16.0           
 [7] XVector_0.10.0             futile.logger_1.4.1       
 [9] lambda.r_1.1.7             BiocParallel_1.4.3        
[11] tools_3.2.3                Biobase_2.30.0            
[13] RCurl_1.95-4.8             SummarizedExperiment_1.0.2

 

 

rtracklayer • 1.0k views
ADD COMMENTlink written 3.6 years ago by Qiang70

What are the differences between the two computers? Same version of the XML package? How about the version of libxml2?

ADD REPLYlink written 3.6 years ago by Michael Lawrence11k

Both have the same XML_3.98-1.4 installed, but the libxml2 version are different.

The problem one:

/usr/lib/libxml2.so -> libxml2.so.2.6.26

The working one:

/usr/lib/x86_64-linux-gnu/libxml2.so -> libxml2.so.2.9.1

Do I have to upgrade the libxml2 to 2.9? I don't have permission to do that, so I can't send you the results now. Thanks!

 

ADD REPLYlink written 3.6 years ago by Qiang70

I don't know but libxml2 2.6.26 is 10 years old, so it might be time to update.

ADD REPLYlink written 3.6 years ago by Michael Lawrence11k

The problem is solved after updating libxml2 to 2.9.1. Thanks!

ADD REPLYlink written 3.6 years ago by Qiang70
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