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 at 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
major: Low-level I/O
minor: Read failed
#003: H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read
major: Dataset
minor: Filter operation failed
#004: H5Z.c line 1301 in H5Z_pipeline(): required filter 'deflate' is
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
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
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