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"
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
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
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!!
Make sure you are actually loading the rtracklayer 1.33.9 by
sessionInfo()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.
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
#===========
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)?
#========
Recommended practice is to use all packages from the same version of Bioconductor. So yes, use all packages from devel.
Thank you !
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 ??
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.
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
Also, I would make sure that I was installing packages using biocLite() and checking my installation using BiocInstaller::biocValid()