| Back to Books build report for BioC 3.23 |
This page was generated on 2025-11-19 14:30 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 10/11 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| OSTA 1.1.1 (landing page) Lukas M. Weber
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the OSTA package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OSTA |
| Version: 1.1.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA |
| StartedAt: 2025-11-19 06:49:45 -0500 (Wed, 19 Nov 2025) |
| EndedAt: 2025-11-19 06:51:39 -0500 (Wed, 19 Nov 2025) |
| EllapsedTime: 113.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
##############################################################################
##############################################################################
* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’
quarto render ../inst/
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[39m[31mWarning message:
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[39m[31mWarning message:
In readLines(input) :
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In readLines(input) :
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[31moutput file: bkg-importing-data.knit.md
[39m[31mWarning message:
In readLines(input) :
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[31moutput file: bkg-example-datasets.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 25
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In readLines(input) :
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Channels:
- conda-forge
- bioconda
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
[31m
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
[39m
# All requested packages already installed.
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8/49 [conda-create]
Channels:
- conda-forge
- bioconda
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop
added / updated specs:
- python=3.11
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-hd037594_8
ca-certificates conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0
icu conda-forge/osx-arm64::icu-75.1-hfee45f7_0
libexpat conda-forge/osx-arm64::libexpat-2.7.1-hec049ff_0
libffi conda-forge/osx-arm64::libffi-3.5.2-he5f378a_0
liblzma conda-forge/osx-arm64::liblzma-5.8.1-h39f12f2_2
libsqlite conda-forge/osx-arm64::libsqlite-3.51.0-h8adb53f_0
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3
openssl conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0
pip conda-forge/noarch::pip-25.3-pyh8b19718_0
python conda-forge/osx-arm64::python-3.11.14-h18782d2_2_cpython
readline conda-forge/osx-arm64::readline-8.2-h1d1bf99_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/osx-arm64::tk-8.6.13-h892fb3f_3
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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Channels:
- conda-forge
- nodefaults
- bioconda
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
[31m
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
[39m
## Package Plan ##
environment location: /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop
added / updated specs:
- libcxx
- llvm-openmp
- llvmlite
- numba
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.11.0 |1_h51639a9_openblas 18 KB conda-forge
libcblas-3.11.0 |1_hb0561ab_openblas 18 KB conda-forge
libcxx-21.1.6 | hf598326_0 556 KB conda-forge
liblapack-3.11.0 |1_hd9741b5_openblas 18 KB conda-forge
llvm-openmp-21.1.6 | h4a912ad_0 279 KB conda-forge
------------------------------------------------------------
Total: 891 KB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-arm64::libblas-3.11.0-1_h51639a9_openblas
libcblas conda-forge/osx-arm64::libcblas-3.11.0-1_hb0561ab_openblas
libcxx conda-forge/osx-arm64::libcxx-21.1.6-hf598326_0
libgfortran conda-forge/osx-arm64::libgfortran-15.2.0-hfcf01ff_1
libgfortran5 conda-forge/osx-arm64::libgfortran5-15.2.0-h742603c_1
liblapack conda-forge/osx-arm64::liblapack-3.11.0-1_hd9741b5_openblas
libopenblas conda-forge/osx-arm64::libopenblas-0.3.30-openmp_ha158390_3
llvm-openmp conda-forge/osx-arm64::llvm-openmp-21.1.6-h4a912ad_0
llvmlite conda-forge/osx-arm64::llvmlite-0.45.1-py311h27de090_0
numba conda-forge/osx-arm64::numba-0.62.1-py311h922685c_0
numpy conda-forge/osx-arm64::numpy-2.3.5-py311h8685306_0
python_abi conda-forge/noarch::python_abi-3.11-8_cp311
zstd conda-forge/osx-arm64::zstd-1.5.7-h6491c7d_2
Downloading and Extracting Packages: ...working...
libcxx-21.1.6 | 556 KB | | 0%
llvm-openmp-21.1.6 | 279 KB | | 0% [A
liblapack-3.11.0 | 18 KB | | 0% [A[A
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libcblas-3.11.0 | 18 KB | | 0% [A[A[A[A
llvm-openmp-21.1.6 | 279 KB | 5 | 6% [A
libcxx-21.1.6 | 556 KB | 2 | 3%
libcblas-3.11.0 | 18 KB | ########7 | 88% [A[A[A[A
liblapack-3.11.0 | 18 KB | ########7 | 88% [A[A
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llvm-openmp-21.1.6 | 279 KB | ########## | 100% [A
libcxx-21.1.6 | 556 KB | ########## | 100%
llvm-openmp-21.1.6 | 279 KB | ########## | 100% [A
libcxx-21.1.6 | 556 KB | ########## | 100%
libblas-3.11.0 | 18 KB | ########7 | 88% [A[A[A
libblas-3.11.0 | 18 KB | ########## | 100% [A[A[A
libblas-3.11.0 | 18 KB | ########## | 100% [A[A[A
[A
[A[A
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[A[A[A[A done
Preparing transaction: - done
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14/49 [deps-pypi]
+ . /Users/biocbuild/Library/r-miniconda-arm64/bin/activate
+ conda activate 'py-interop'
+ '/Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/bin/python' -m pip install --upgrade --no-user 'Dask==2024.12.1' 'zarr==2.18.7' 'squidpy==1.6.2'
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INFO: pip is looking at multiple versions of spatialdata to determine which version is compatible with other requirements. This could take a while.
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Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
[31m error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [1 lines of output]
ERROR: Minimum supported PROJ version is 9.4.0, installed version is 9.1.0. For more information see: https://pyproj4.github.io/pyproj/stable/installation.html
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
[39m[31mERROR: Failed to build 'pyproj' when getting requirements to build wheel
[39m[31mError: Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"
[39m[31m
Quitting from bkg-python-interoperability.qmd:108-115 [deps-pypi]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"
---
Backtrace:
▆
1. └─reticulate::conda_install(...)
2. └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted