Problem with svn_time() function on IRanges package - trying to run "exomePeak" package
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0
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@mghanatbari-8842
Last seen 8.5 years ago
United States

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

iranges • 1.2k views
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@herve-pages-1542
Last seen 12 hours ago
Seattle, WA, United States

Hi,

Please always show your sessionInfo() when you report a problem: it's way more useful than "Processor composition".  It seems to me that you're lagging at least 2 or 3 Bioconductor versions behind (current release is BioC 3.1, BioC 3.2 is going to be released next month). Make sure you always use the latest release. Older versions are not supported. If you read carefully the issue you mention where your problem was already discussed

'version' is missing error when running makeTxDbPackageFromUCSC

you can see that I posted the following update 25 days ago:

  • I just made a change to S4Vectors that might address this. The change is in versions 0.6.4 (release) and 0.7.14 (devel) which should become available via biocLite() in the next 24 hours or less. I don't have access to the Intel Compiler though so I was not able to test this.

Are you using the Intel Compiler to compile your packages? If so, your problem might just go away by installing the latest BioC release. If that doesn't help, please let us know. Note that starting with BioC 3.0, svn_time() is in the S4Vectors package. 

Thanks,

H.

 

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@mghanatbari-8842
Last seen 8.5 years ago
United States

Hi

Thank you very much. Actually, I've read your previous post regarding to svn_time() function, but I couldn't find my answer, that is why I submitted a new post. 

I am only a user of TACC cluster, so I couldn't update the R (current version 3.0.2). But I installed the newest version of R (3.2.2) on my own directory, then the BioC 3.0.1. It is working perfectly, and I don't have that error. But the running time for the code as equal as my PC, I mean I try to use the R on TACC cluster to reduce the running time needed fro that code due TACC's computational power.

1. Do you think it is because of that I am using my own R installed not the R available on core of Cluster installed by the admin?

2. What is the version of BioC compatible with R 3.0.2? How can I install that specific version on R? I think when I use biocLite(), it installs the newest version of BioC on R 3.0.2, which causes the svn.ime() function in IRanges packages failure.

3. How can I check whether or not I am using Intel compiler to compile my packages?  

 

 

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Hi,

  1. I doubt you installed BioC 3.0.1 on your laptop as there is no such version of Bioconductor. You said you installed R 3.2.2, which is good, because it's the latest R release. So when you did 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.
  2. The version of BioC compatible with a 2-year old version of R (R 3.0.2) is a version that is lagging 4 releases behind the current BioC release! Knowing which version it is exactly will be of little use to you because it's an old and unsupported version anyway. Furthermore, it's probably the version you have on your cluster already so you can check which version it is by loading the BiocInstaller package in a fresh session. But we already know that the 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.
  3. Do R CMD config CC to see the compiler used by R to compile packages.

Cheers,

H.

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Entering edit mode
@mghanatbari-8842
Last seen 8.5 years ago
United States

I found that on TACC, R runs using  intel 15 compiler and mvapich2. Also, the they have installed R3.2.1. Now I could install the most version of BioC and svn_time() works perfectly.

 

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Glad to hear that the most recent version works with the Intel Compiler. Thanks for the feedback!

H.

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