[Bioc-devel] HiCBricks build error

[Koustav Pal]

Hi Bioconductor team, can you please help with this issue? 


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



> On 29 Jul 2019, at 17:45, Koustav Pal <koustav.pal using ifom.eu> wrote:
> 
> 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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> 
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