Reputation:
10
Status:
New User
Location:
Germany
Last seen:
4 months, 2 weeks ago
Joined:
3 years, 4 months ago
Email:
v************@embl.de

<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 7 months ago by vladislav.kim10
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... 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 7 months ago by vladislav.kim10
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... 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 7 months ago by vladislav.kim10
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... 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 10 months ago by vladislav.kim10
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... 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 12 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 16 months ago by vladislav.kim10
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... Thank you! This works ...
written 21 months ago by vladislav.kim10
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... 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 21 months ago by vladislav.kim10