User: vladislav.kim

gravatar for vladislav.kim
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Location:
Germany
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 1 month ago
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v************@embl.de

Posts by vladislav.kim

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Libgomp error in IHW
... Hey, the error indeed originates from upsteram of IHW in lpsymphony. By deault `lpsymphony` is compiled with --enable-openmp flag. Do you make targeted use of OpenMP threading? Vlad       ...
written 4 months ago by vladislav.kim10
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Comment: C: lpsymphony compilation trouble
... Hey Mark, I am happy to hear that you managed to install the package. No those files are not necessary for package install. Vlad       ...
written 4 months ago by vladislav.kim10
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Answer: A: lpsymphony compilation trouble
... Hi Mark, I built a minimalistic Docker image with Ubuntu Trusty Tahr and I can't reproduce your error. I deposited my Dockerfile on Github. Check out the branch 'lpsym' (not master) To try it out quickly, maybe you can pull the Docker image from the docker hub (https://hub.docker.com/r/vladkim/lpsy ...
written 4 months ago by vladislav.kim10
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Answer: A: biocLite("lpsymphony") consistently fails with linker errors (can't find static
... Dear Frank, I can't reproduce this installation error. The `prefix` directory is one of the first variables to be set; it is passed on to the configure script and subsequently passed to all configure/Makefile scripts. As basic as it is, I am pretty sure that the `prefix` is carried over correctly b ...
written 7 months ago by vladislav.kim10
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Answer: A: how to specify the number of cores used by IHW
... Hi Charlotte, I assume this problem arises because of the lpsymphony package, on which IHW depends. On Linux machines SYMPHONY is built with '--enable-openmp' flag by default.  I think it is possible to set the number of threads by export OMP_NUM_THREADS=2 (if you want only 2 threads). Otherwise ...
written 9 months ago by vladislav.kim10
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Comment: C: lpsymphony install on Ubuntu
... Hi Holger, can you please send me the output of your `R CMD config CFLAGS` and `R CMD config CXXFLAGS`?          ...
written 13 months ago by vladislav.kim10
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Comment: C: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
... Thank you! This works ...
written 18 months ago by vladislav.kim10
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Comment: C: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
... I am facing a similar issue: my BAM files are also in non-UCSC format. Plotting the `AlignmentTrack` alone works, but combining it with the `BiomartGeneRegionTrack` fails because chromosome names don't match. Is there an easy way to change the chromosome names of the `BiomartGeneRegionTrack` object? ...
written 18 months ago by vladislav.kim10

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