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....@ifom.eu > On 29 Jul 2019, at 17:45, Koustav Pal <koustav....@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....@ifom.eu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
