Bioconductor Single Package Builder - Build History

Snapshot Date:
URL: https://git.bioconductor.org/packages/StatescopeR
Last Changed Rev: / Revision:
Last Changed Date:
Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)/x86_64	ERROR	skipped	skipped	skipped
nebbiolo2 Summary

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Package: StatescopeR
Version: 0.99.5
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data StatescopeR
BuildTime: 4 minutes 58.07 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: StatescopeR_20250725151821
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: StatescopeR. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.
nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘StatescopeR/DESCRIPTION’ ... OK
* preparing ‘StatescopeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘StatescopeR.Rmd’ using rmarkdown
Collecting pip
  Using cached https://files.pythonhosted.org/packages/a4/6d/6463d49a933f547439d6b5b98b46af8742cc03ae83543e4d7688c2420f8b/pip-21.3.1-py3-none-any.whl
Collecting wheel
  Using cached https://files.pythonhosted.org/packages/27/d6/003e593296a85fd6ed616ed962795b2f87709c3eee2bca4f6d0fe55c6d00/wheel-0.37.1-py2.py3-none-any.whl
Collecting setuptools
  Using cached https://files.pythonhosted.org/packages/b0/3a/88b210db68e56854d0bcf4b38e165e03be377e13907746f825790f3df5bf/setuptools-59.6.0-py3-none-any.whl
Installing collected packages: pip, wheel, setuptools
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
  Found existing installation: setuptools 40.6.2
    Uninstalling setuptools-40.6.2:
      Successfully uninstalled setuptools-40.6.2
Successfully installed pip-21.3.1 setuptools-59.6.0 wheel-0.37.1
Collecting autogenes==1.0.4
  Using cached autogenes-1.0.4-py3-none-any.whl (15 kB)
Collecting pandas==1.1.5
  Using cached pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting anndata==0.7.8
  Using cached anndata-0.7.8-py3-none-any.whl (91 kB)
Collecting numpy==1.19.5
  Using cached numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB)
Collecting dill==0.3.4
  Using cached dill-0.3.4-py2.py3-none-any.whl (86 kB)
Collecting deap==1.4.1
  Using cached deap-1.4.1-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (134 kB)
Collecting scipy==1.5.4
  Using cached scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
Collecting cachetools==4.2.2
  Using cached cachetools-4.2.2-py3-none-any.whl (11 kB)
Collecting scikit-learn==0.24.2
  Using cached scikit_learn-0.24.2-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB)
Collecting matplotlib==3.3.4
  Using cached matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5 MB)
Collecting pytz>=2017.2
  Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Collecting python-dateutil>=2.7.3
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Collecting natsort
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Collecting h5py
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Collecting xlrd<2.0
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Collecting packaging>=20
  Using cached packaging-21.3-py3-none-any.whl (40 kB)
Collecting importlib_metadata>=0.7
  Using cached importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting joblib>=0.11
  Using cached joblib-1.1.1-py2.py3-none-any.whl (309 kB)
Collecting pillow>=6.2.0
  Using cached Pillow-8.4.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Collecting cycler>=0.10
  Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Using cached pyparsing-3.1.4-py3-none-any.whl (104 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB)
Collecting typing-extensions>=3.6.4
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Collecting zipp>=0.5
  Using cached zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting six>=1.5
  Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Collecting cached-property
  Using cached cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Installing collected packages: six, zipp, typing-extensions, pytz, python-dateutil, pyparsing, numpy, cached-property, xlrd, threadpoolctl, scipy, pillow, pandas, packaging, natsort, kiwisolver, joblib, importlib-metadata, h5py, cycler, scikit-learn, matplotlib, dill, deap, cachetools, anndata, autogenes
Successfully installed anndata-0.7.8 autogenes-1.0.4 cached-property-1.5.2 cachetools-4.2.2 cycler-0.11.0 deap-1.4.1 dill-0.3.4 h5py-3.1.0 importlib-metadata-4.8.3 joblib-1.1.1 kiwisolver-1.3.1 matplotlib-3.3.4 natsort-8.2.0 numpy-1.19.5 packaging-21.3 pandas-1.1.5 pillow-8.4.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2025.2 scikit-learn-0.24.2 scipy-1.5.4 six-1.17.0 threadpoolctl-3.1.0 typing-extensions-4.1.1 xlrd-1.2.0 zipp-3.6.0
Requirement already satisfied: pip in /var/cache/basilisk/1.21.5/StatescopeR/0.99.5/deconvolution/lib/python3.11/site-packages (24.0)
Collecting pip
  Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in /var/cache/basilisk/1.21.5/StatescopeR/0.99.5/deconvolution/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Collecting numba==0.59.1
  Using cached numba-0.59.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting pandas==1.5.3
  Using cached pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting joblib==1.4.2
  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting numpy==1.23.5
  Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting scipy==1.14.1
  Using cached scipy-1.14.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting scikit-learn==1.1.3
  Using cached scikit_learn-1.1.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting matplotlib==3.9.3
  Using cached matplotlib-3.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting llvmlite<0.43,>=0.42.0dev0 (from numba==0.59.1)
  Using cached llvmlite-0.42.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.5.3)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.5.3)
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.1.3)
  Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting contourpy>=1.0.1 (from matplotlib==3.9.3)
  Using cached contourpy-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib==3.9.3)
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib==3.9.3)
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Collecting kiwisolver>=1.3.1 (from matplotlib==3.9.3)
  Using cached kiwisolver-1.4.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.2 kB)
Collecting packaging>=20.0 (from matplotlib==3.9.3)
  Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting pillow>=8 (from matplotlib==3.9.3)
  Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
Collecting pyparsing>=2.3.1 (from matplotlib==3.9.3)
  Using cached pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.5.3)
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Using cached numba-0.59.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB)
Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Using cached pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
Using cached joblib-1.4.2-py3-none-any.whl (301 kB)
Using cached scipy-1.14.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (41.2 MB)
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Using cached matplotlib-3.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB)
Using cached llvmlite-0.42.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.8 MB)
Using cached contourpy-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (326 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.59.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.0 MB)
Using cached kiwisolver-1.4.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.4 MB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
Using cached pyparsing-3.2.3-py3-none-any.whl (111 kB)
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Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Installing collected packages: pytz, threadpoolctl, six, pyparsing, pillow, packaging, numpy, llvmlite, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, numba, contourpy, scikit-learn, pandas, matplotlib
ERROR: Could not install packages due to an OSError: [Errno 28] No space left on device: '/var/cache/basilisk/1.21.5/StatescopeR/0.99.5/deconvolution/lib/python3.11/site-packages/pandas/tests/indexing/test_coercion.py'



Quitting from StatescopeR.Rmd:143-153 [Run StatescopeR]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'numba==0.59.1'", "'pandas==1.5.3'", "'joblib==1.4.2'", "'numpy==1.23.5'", "'scipy==1.14.1'", "'scikit-learn==1.1.3'", "'matplotlib==3.9.3'"
---
Backtrace:
    ▆
 1. └─StatescopeR::BLADE_deconvolution(...)
 2.   └─basilisk::basiliskStart(deconvolution)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'StatescopeR.Rmd' failed with diagnostics:
Error installing package(s): "'numba==0.59.1'", "'pandas==1.5.3'", "'joblib==1.4.2'", "'numpy==1.23.5'", "'scipy==1.14.1'", "'scikit-learn==1.1.3'", "'matplotlib==3.9.3'"
--- failed re-building ‘StatescopeR.Rmd’

SUMMARY: processing the following file failed:
  ‘StatescopeR.Rmd’

Error: Vignette re-building failed.
Execution halted
nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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