[Bioc-devel] HiCBricks build error

[Mike Smith]

There are many other packages affected by this
e.g. biomformat, BiocSklearn, CoGAPS, ...  It looks like Rhdf5lib is being
built without linking to zlib, and so files written with zlib compression
can't be read.  I've been trying to get Rhdf5lib to play more smoothly for
systems that use conda as a package manager, but it seems I've introduced a
regression.  I'll look into why this is the case, I'm a bit confused as to
why rhdf5 is not failing in a similar way.

Mike

On Mon, 29 Jul 2019 at 17:53, 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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