############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data velociraptor ### ############################################################################## ############################################################################## * checking for file ‘velociraptor/DESCRIPTION’ ... OK * preparing ‘velociraptor’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘velociraptor.Rmd’ using rmarkdown /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_excel from `anndata` is deprecated. Import anndata.io.read_excel instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_hdf from `anndata` is deprecated. Import anndata.io.read_hdf instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_mtx from `anndata` is deprecated. Import anndata.io.read_mtx instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead. warnings.warn(msg, FutureWarning) /home/biocbuild/.cache/R/basilisk/1.19.0/velociraptor/1.17.0/env/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_umi_tools from `anndata` is deprecated. Import anndata.io.read_umi_tools instead. warnings.warn(msg, FutureWarning) Quitting from lines 76-82 [unnamed-chunk-5] (velociraptor.Rmd) Error: processing vignette 'velociraptor.Rmd' failed with diagnostics: AttributeError: module 'scipy.linalg' has no attribute 'tril' Run `reticulate::py_last_error()` for details. --- failed re-building ‘velociraptor.Rmd’ SUMMARY: processing the following file failed: ‘velociraptor.Rmd’ Error: Vignette re-building failed. Execution halted