Hello,
platform x86_64-redhat-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu svn rev 63987 version.string R version 3.0.2 (2013-09-25)
I am trying to run the "exomePeak" package on Texas Advanced computing Center (TACC). The configurations of TACC cluster can be found in very bottom of the post.
library (exompeack)
library(IRanges)
exomepeak(GENE_ANNO_GTF=gtf,IP_BAM=IP_BAM,INPUT_BAM=INPUT_BAM,TREATED_IP_BAM=TREATED_IP_BAM,TREATED_INPUT_BAM=TREATED_INPUT_BAM,EXPERIMENT_NAME=EXPERIMENT_NAME)
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
Error in .Call2("svn_time", PACKAGE = "IRanges") :
IRanges internal error in svn_time(): get_svn_time() failed
I've IRanges package installed in R, but I don't know why still I have this problem. Any suggestions?
The similar problem using "TxDbPackageFromUCSC" packages in reported before, but they were not helpful in my case:
'version' is missing error when running makeTxDbPackageFromUCSC
'version' is missing error when running makeTxDbPackageFromUCSC
===== Processor composition on TACC=====
Processor name : Intel(R) Xeon(R) E5-2680 @ 2.70GHz
Architectures: x86_64
Cores: 16
Processors (CPUs): 16
Cores per package: 8
Threads per core: 1
CPU op-mode(s): 32-bit, 64-bit
Core(s) per socket: 8
Socket(s): 2
NUMA node(s): 2
CPU MHz: 2700.191
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 20480K
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15
Hi,
source("https://bioconductor.org/biocLite.R")
, that should have automatically set your installation to point to the latest BioC release (which is 3.1). You can check which BioC version you have by loading the BiocInstaller package in a fresh session.svn_time()
function in this version doesn't work on your cluster right? You need to ask the people who manage the TACC cluster to update to the latest R/BioC. They need to understand the importance of ALWAYS RUNNING THE LATEST R/BioC.R CMD config CC
to see the compiler used by R to compile packages.Cheers,
H.