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....@ifom.eu
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