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R CMD BUILD
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* checking for file ‘scviR/DESCRIPTION’ ... OK
* preparing ‘scviR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘citeseq_tut.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/demo2.h5ad.gz'
Content type 'application/octet-stream' length 51844915 bytes (49.4 MB)
==================================================
downloaded 49.4 MB
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.0/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
pip-23.0.1 | pyhd8ed1ab_0 1.3 MB conda-forge
setuptools-67.4.0 | pyhd8ed1ab_0 567 KB conda-forge
------------------------------------------------------------
Total: 1.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.3-h58526e2_2
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libsqlite conda-forge/linux-64::libsqlite-3.40.0-h753d276_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-1.1.1t-h0b41bf4_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python pkgs/main/linux-64::python-3.8.13-haa1d7c7_1
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.40.0-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
zlib conda-forge/linux-64::zlib-1.2.13-h166bdaf_4
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.0/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
openssl-1.1.1t | h7f8727e_0 3.7 MB
------------------------------------------------------------
Total: 3.7 MB
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-h06a4308_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-1.1.1t-h0b41bf4_0 --> pkgs/main::openssl-1.1.1t-h7f8727e_0
Downloading and Extracting Packages
openssl-1.1.1t | 3.7 MB | | 0%
openssl-1.1.1t | 3.7 MB | #####7 | 58%
openssl-1.1.1t | 3.7 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.0/bsklenv
added / updated specs:
- numpy=1.23.1
- pandas=1.4.4
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
numpy-1.23.1 | py38h3a7f9d9_0 7.1 MB conda-forge
pandas-1.4.4 | py38h47df419_0 12.7 MB conda-forge
------------------------------------------------------------
Total: 19.8 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19
libgfortran5 conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19
liblapack conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3
numpy conda-forge/linux-64::numpy-1.23.1-py38h3a7f9d9_0
pandas conda-forge/linux-64::pandas-1.4.4-py38h47df419_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.8-2_cp38
pytz conda-forge/noarch::pytz-2022.7.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-ha878542_0
openssl pkgs/main::openssl-1.1.1t-h7f8727e_0 --> conda-forge::openssl-1.1.1t-h0b41bf4_0
Downloading and Extracting Packages
numpy-1.23.1 | 7.1 MB | | 0%
numpy-1.23.1 | 7.1 MB | #2 | 13%
numpy-1.23.1 | 7.1 MB | ########4 | 85%
numpy-1.23.1 | 7.1 MB | ########## | 100%
pandas-1.4.4 | 12.7 MB | | 0%
pandas-1.4.4 | 12.7 MB | ##2 | 23%
pandas-1.4.4 | 12.7 MB | ######7 | 67%
pandas-1.4.4 | 12.7 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting scvi-tools==0.20.0
Downloading scvi_tools-0.20.0-py3-none-any.whl (330 kB)
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Collecting scanpy==1.9.1
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Collecting scikit-learn>=0.21.2
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Collecting tqdm>=4.56.0
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Collecting docrep>=0.3.2
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Collecting optax
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Requirement already satisfied: numpy>=1.17.0 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.0/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.23.1)
Requirement already satisfied: pandas>=1.0 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.0/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.4.4)
Collecting numpyro
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Collecting flax
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Collecting scipy
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Collecting rich>=12.0.0
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Collecting h5py>=2.9.0
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Collecting mudata>=0.1.2
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Collecting torchmetrics>=0.11.0
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Collecting jaxlib
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Collecting seaborn
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Collecting statsmodels>=0.10.0rc2
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Collecting patsy
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Collecting umap-learn>=0.3.10
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Collecting joblib
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Collecting numba>=0.41.0
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Collecting session-info
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Collecting packaging
Using cached packaging-23.0-py3-none-any.whl (42 kB)
Collecting fonttools>=4.22.0
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Collecting contourpy>=1.0.1
Downloading contourpy-1.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
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Collecting pyparsing>=2.2.1
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Collecting cycler>=0.10
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Collecting opt_einsum
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Collecting PyYAML
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Collecting llvmlite<0.40,>=0.39.0dev0
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Building wheels for collected packages: docrep, jax, ml-collections, umap-learn, session-info, pynndescent
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Successfully built docrep jax ml-collections umap-learn session-info pynndescent
Installing collected packages: stdlib_list, pyro-api, msgpack, dm-tree, charset-normalizer, cached_property, zipp, urllib3, typing-extensions, tqdm, toolz, threadpoolctl, tensorstore, session-info, scipy, PyYAML, pyparsing, pygments, pillow, patsy, packaging, opt_einsum, nvidia-cuda-runtime-cu11, nvidia-cuda-nvrtc-cu11, nvidia-cublas-cu11, networkx, natsort, multipledispatch, multidict, mdurl, llvmlite, kiwisolver, joblib, idna, h5py, fsspec, frozenlist, fonttools, etils, et-xmlfile, docrep, cycler, contourpy, contextlib2, certifi, attrs, async-timeout, absl-py, yarl, scikit-learn, requests, openpyxl, nvidia-cudnn-cu11, ml-collections, matplotlib, markdown-it-py, lightning-utilities, jaxlib, jax, importlib_resources, importlib-metadata, aiosignal, torch, statsmodels, seaborn, rich, numpyro, numba, chex, anndata, aiohttp, torchmetrics, pyro-ppl, pynndescent, optax, mudata, umap-learn, pytorch-lightning, scanpy, orbax, flax, scvi-tools
Successfully installed PyYAML-6.0 absl-py-1.4.0 aiohttp-3.8.4 aiosignal-1.3.1 anndata-0.8.0 async-timeout-4.0.2 attrs-22.2.0 cached_property-1.5.2 certifi-2022.12.7 charset-normalizer-3.0.1 chex-0.1.6 contextlib2-21.6.0 contourpy-1.0.7 cycler-0.11.0 dm-tree-0.1.8 docrep-0.3.2 et-xmlfile-1.1.0 etils-1.0.0 flax-0.6.4 fonttools-4.38.0 frozenlist-1.3.3 fsspec-2023.1.0 h5py-3.8.0 idna-3.4 importlib-metadata-6.0.0 importlib_resources-5.12.0 jax-0.4.4 jaxlib-0.4.4 joblib-1.2.0 kiwisolver-1.4.4 lightning-utilities-0.7.1 llvmlite-0.39.1 markdown-it-py-2.2.0 matplotlib-3.6.3 mdurl-0.1.2 ml-collections-0.1.1 msgpack-1.0.4 mudata-0.2.1 multidict-6.0.4 multipledispatch-0.6.0 natsort-8.2.0 networkx-3.0 numba-0.56.4 numpyro-0.11.0 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 openpyxl-3.1.1 opt_einsum-3.3.0 optax-0.1.4 orbax-0.1.2 packaging-23.0 patsy-0.5.3 pillow-9.4.0 pygments-2.14.0 pynndescent-0.5.8 pyparsing-3.0.9 pyro-api-0.1.2 pyro-ppl-1.8.4 pytorch-lightning-1.9.3 requests-2.28.2 rich-13.3.1 scanpy-1.9.1 scikit-learn-1.2.1 scipy-1.10.1 scvi-tools-0.20.0 seaborn-0.12.2 session-info-1.0.0 statsmodels-0.13.5 stdlib_list-0.8.0 tensorstore-0.1.32 threadpoolctl-3.1.0 toolz-0.12.0 torch-1.13.1 torchmetrics-0.11.1 tqdm-4.64.1 typing-extensions-4.5.0 umap-learn-0.5.3 urllib3-1.26.14 yarl-1.8.2 zipp-3.14.0
Quitting from lines 26-31 (citeseq_tut.Rmd)
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/home/pkgbuild/.cache/R/BiocFileCache/56ffb361275cb_demo2.h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
--- failed re-building ‘citeseq_tut.Rmd’
--- re-building ‘compch12.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/ch12sce.rda'
Content type 'application/octet-stream' length 58079368 bytes (55.4 MB)
==================================================
downloaded 55.4 MB
Quitting from lines 40-42 (compch12.Rmd)
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘compch12.Rmd’
--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’
SUMMARY: processing the following files failed:
‘citeseq_tut.Rmd’ ‘compch12.Rmd’
Error: Vignette re-building failed.
Execution halted