[Bioc-devel] HiCBricks build error

[Koustav Pal]

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 using ifom.eu




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