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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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starting the trajectory Rmd #4

Closed stephaniehicks closed 4 years ago

stephaniehicks commented 5 years ago

@LTLA I think I understand how the OSCABase repo works, but I'd welcome your feedback

stephaniehicks commented 4 years ago

@LTLA so the hold up is that I'm running into some trouble with the TENxPBMCData data package. I deleted the cached dataset and downloaded a fresh copy to make sure that wasn't the problem. 

library(TENxPBMCData)
pbmc4k <- TENxPBMCData('pbmc4k')
/users/shicks1/.cache/ExperimentHub
  does not exist, create directory? (yes/no): yes
  |======================================================================| 100%

snapshotDate(): 2019-10-18
see ?TENxPBMCData and browseVignettes('TENxPBMCData') for documentation
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
  |======================================================================| 100%

  |======================================================================| 100%

HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: H5Dio.c line 199 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 601 in H5D__read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read failed
    major: Dataset
    minor: Filter operation failed
  #004: H5Z.c line 1301 in H5Z_pipeline(): required filter 'deflate' is not registered
    major: Data filters
    minor: Read failed
  #005: H5PLint.c line 270 in H5PL_load(): search in path table failed
    major: Plugin for dynamically loaded library
    minor: Can't get value
  #006: H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error
    major: Plugin for dynamically loaded library
    minor: Can't get value
  #007: H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin
    major: Plugin for dynamically loaded library
    minor: Can't open directory or file
Error in h5mread(filepath, name, starts = index) :
  H5Dread() returned an error

Anytime I load the dataset from the cache, I get the same error. A quick google search didn't really help either. Any thoughts?

PeteHaitch commented 4 years ago

This isn't on JHPCE is it @stephaniehicks? I don't think HDF5 is properly working on there currently.

stephaniehicks commented 4 years ago

@PeteHaitch -- 😱 😱 😱 It is on JHPCE. Do you have any links to what's going on or who I need to bug to get this fixed? I guess I could try install everything locally in the mean time. 🤔

@LTLA -- sorry for the confusion. I'll keep you posted on my progressing getting this sorted out.

PeteHaitch commented 4 years ago

@stephaniehicks I think you'll need to go the usual Kasper + bit support route. From memory there was some discussion on Slack (but I don't remember if Biostats or JHU Genomics group) and on the bit support mailing list. I know it's also a roadblock for one of Kasper's projects, so that might bump it up the priority list :)