Question: UCSC web service API
0
gravatar for Asma rabe
3.4 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Hi,

when i try to set the genome to hg19, I got the following error:

genome(session) <- "hg19"

Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'

# I set the proxy on my machine before i run R.

Thank you in advance

 

ADD COMMENTlink modified 3.4 years ago by Martin Morgan ♦♦ 24k • written 3.4 years ago by Asma rabe290
Answer: UCSC web service API
0
gravatar for Martin Morgan
3.4 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Use a mirror in the same region that you belong to or use rtracklayer from devel; see C: Gviz error 'Expectation Failed'

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Martin Morgan ♦♦ 24k

 

Thank you.

I installed devel version from

http://bioconductor.org/packages/devel/bioc/html/rtracklayer.html

source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")

but i still have the same error!!

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Asma rabe290

Make sure you are actually loading the rtracklayer 1.33.9 by sessionInfo()

ADD REPLYlink written 3.4 years ago by Tom10

See http://bioconductor.org/developers/how-to/useDevel/ but I wonder whether it is possible to point to an UCSC mirror that is 'in' Asia http://genome-asia.ucsc.edu. I'm not in Asia, so don't know whether that works.

ADD REPLYlink written 3.4 years ago by Martin Morgan ♦♦ 24k

Thank you Martin and Tom for kind help.

It seems the problem was related to rtracklayer version. devel version works well 

I can access  http://genome-asia.ucsc.edu using web browser. However, I got an error when I tried 

options(Gviz.ucscUrl="http://genome-asia.ucsc.edu")

session <- browserSession()

genome(session) <- "hg19"

Error in `genome<-`(`*tmp*`, value = "hg19") : 

  Failed to set session genome to 'hg19'

#===========

When I checked sessionInfo(), I found that rtracklayer_1.30.4 is running rather than rtracklayer 1.33.9.

I properly loaded rtracklayer 1.33.9 and it works now. Thank you very much...

I have one question:

 

1)To use devel version of one Bioconductor package (rtracklayer 1.33.9 for instance), Do i have to use all devel versions of all other packages I am using ?? (such as devel of  minfi for example)?

#========

sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
[1] C

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

other attached packages:
[1] rtracklayer_1.33.9   GenomicRanges_1.25.9 GenomeInfoDb_1.9.1  
[4] IRanges_2.7.11       S4Vectors_0.11.7     BiocGenerics_0.19.2 
[7] BiocInstaller_1.23.5

loaded via a namespace (and not attached):
 [1] lattice_0.20-33            XML_3.98-1.4              
 [3] Rsamtools_1.25.0           Biostrings_2.41.4         
 [5] GenomicAlignments_1.9.4    bitops_1.0-6              
 [7] grid_3.3.0                 zlibbioc_1.19.0           
 [9] XVector_0.13.6             Matrix_1.2-6              
[11] BiocParallel_1.7.4         tools_3.3.0               
[13] Biobase_2.33.0             RCurl_1.95-4.8            
[15] SummarizedExperiment_1.3.7
 session <- browserSession()
 genome(session) <- "hg19"

 

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Asma rabe290
1

Recommended practice is to use all packages from the same version of Bioconductor. So yes, use all packages from devel.

ADD REPLYlink written 3.4 years ago by Martin Morgan ♦♦ 24k

Thank you !

ADD REPLYlink written 3.4 years ago by Asma rabe290

I have downloaded another packages and restarted R session. Using session Info(), I found that old rtracklayer package is running rtracklayer_1.30.4 instead of rtracklayer 1.33.9

How to uninstall rtracklayer_1.30.4 ??

ADD REPLYlink written 3.4 years ago by Asma rabe290

You don't need to uninstall the old version of rtracklayer. Just set dev_mode(on=T) and load rtracklayer every time you need the development version.

ADD REPLYlink written 3.4 years ago by Tom10

dev_mode() is not a base R function, so you need to provide further context for your advice. Personally, I would instead make sure that .libPaths() is the same in the two R sessions, and perhaps confirm in more detail where rtracklayer is installed 

inst = installed.packages()
inst[ inst[,"Package"] == "rtracklayer", ]

Also, I would make sure that I was installing packages using biocLite() and checking my installation using BiocInstaller::biocValid()

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Martin Morgan ♦♦ 24k
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