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Bioconductor / VariantAnnotation

Annotation of Genetic Variants
https://bioconductor.org/packages/VariantAnnotation
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installation fail with error undefined symbol: hts_get_bgzfp #37

Closed rladiesPHL closed 4 years ago

rladiesPHL commented 4 years ago

Hi I tried to install VariantAnnotation by BiocManager from bioconductor at R 3.6.0 (I have to use R 3.6 to compatible for another VariantAnnotation dependent package). I kept getting error 

Error: package or namespace load failed for ‘VariantAnnotation’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/suc1/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs/VariantAnnotation.so':
  /home/suc1/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs/VariantAnnotation.so: undefined symbol: hts_get_bgzfp

Anyone had similar problem and solved it before?

hts_get_bgzfp should be a part of htslib. it is loaded in my system. Still not working.

hpages commented 4 years ago

We need a full transcript of what you did i.e. please show the command that you used for installing VariantAnnotation and the full output.

We also need to see the output of your sessionInfo().

Thanks!

lshep commented 4 years ago

With no follow up information we are closing this issue. If this continues to be an issue request the issue be reopened with the additional information requested.