[Bioc-devel] HiCBricks build error

Mon, Jul 29, 2019 8:45 AM

Hi, 

My package HiCBricks is producing build errors on malbec1 and merida1, but build has passed on tokay1. The corresponding build on travis-ci has also passed. I can also confirm that the last commits on travis is the same as that on the bioconductor build machines. 

Herein, is the build logs from the malbec1. travis-ci vignette building also completes successfully.

* checking for file ?HiCBricks/DESCRIPTION? ... OK
* preparing ?HiCBricks?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ?IntroductionToHiCBricks.rmd? using rmarkdown
Loading required package: curl
Loading required package: rhdf5
Loading required package: R6
Loading required package: grid
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
Quitting from lines 286-289 (IntroductionToHiCBricks.rmd) 
Error: processing vignette 'IntroductionToHiCBricks.rmd' failed with diagnostics:
Unable to read dataset.
Not all required filters available.
Missing filters: deflate
--- failed re-building ?IntroductionToHiCBricks.rmd?

SUMMARY: processing the following file failed:
  ?IntroductionToHiCBricks.rmd?

Error: Vignette re-building failed.
Execution halted

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav.pal at ifom.eu

[Bioc-devel] HiCBricks build error

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