Vincent Carey
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/scviR |
| git_branch: devel |
| git_last_commit: 8734133 |
| git_last_commit_date: 2024-03-20 08:01:40 -0400 (Wed, 20 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:18 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1905/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scviR 1.3.3 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the scviR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scviR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: scviR |
| Version: 1.3.3 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data scviR |
| StartedAt: 2024-03-28 01:33:54 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 01:36:55 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 181.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
###
##############################################################################
##############################################################################
* 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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
wheel-0.43.0 | pyhd8ed1ab_1 57 KB conda-forge
------------------------------------------------------------
Total: 57 KB
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.10.14-hbbe8eec_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- python=3.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- numpy=1.24.4
- pandas=1.5.3
- python[version='3.10.*,3.10.*']
The following NEW packages will be INSTALLED:
bottleneck conda-forge/linux-aarch64::bottleneck-1.3.8-py310h8b6b5fc_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numexpr conda-forge/linux-aarch64::numexpr-2.9.0-py310had05d37_0
numpy conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0
pandas pkgs/main/linux-aarch64::pandas-1.5.3-py310hfb1e5ee_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::python_abi-3.10-4_cp310
pytz conda-forge/noarch::pytz-2024.1-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-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting anndata==0.10.1
Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB)
Collecting docrep==0.3.2
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting flax==0.8.1
Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB)
Collecting jax==0.4.23
Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB)
Collecting jaxlib==0.4.23
Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB)
Collecting optax==0.1.9
Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB)
Collecting scipy==1.12.0
Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB)
Collecting scikit-learn==1.4.0
Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting rich==13.7.1
Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting h5py==3.9.0
Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting torch==1.13.1
Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB)
Collecting lightning==2.1.4
Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB)
Collecting torchmetrics==0.11.0
Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB)
Collecting tqdm==4.66.2
Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting ml-collections==0.1.1
Using cached ml_collections-0.1.1.tar.gz (77 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting mudata==0.2.3
Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB)
Collecting scvi-tools==1.1.2
Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB)
Collecting scanpy==1.9.5
Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB)
Collecting matplotlib==3.7.3
Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB)
Collecting scikit-misc==0.3.1
Using cached scikit_misc-0.3.1.tar.gz (302 kB)
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 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [59 lines of output]
+ meson setup /home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7 /home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7/.mesonpy-3u7iz3p3 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7/.mesonpy-3u7iz3p3/meson-python-native-file.ini
The Meson build system
Version: 1.4.0
Source dir: /home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7
Build dir: /home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7/.mesonpy-3u7iz3p3
Build type: native build
Project name: scikit-misc
Project version: 0.3.1
C compiler for the host machine: cc (gcc 10.3.1 "cc (GCC) 10.3.1")
C linker for the host machine: cc ld.bfd 2.37
Cython compiler for the host machine: cython (cython 3.0.9)
Host machine cpu family: aarch64
Host machine cpu: aarch64
Fortran compiler for the host machine: gfortran (gcc 10.3.1 "GNU Fortran (GCC) 10.3.1")
Fortran linker for the host machine: gfortran ld.bfd 2.37
Program python found: YES (/home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv/bin/python)
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.0
Run-time dependency python found: YES 3.10
Program cython found: YES (/home/biocbuild/tmp/pip-build-env-1u4pd6y4/overlay/bin/cython)
Library m found: YES
Compiler for Fortran supports arguments -Wno-conversion: YES
Library npymath found: YES
Library npyrandom found: YES
Compiler for C supports arguments -Wno-maybe-uninitialized: YES
Compiler for C supports arguments -Wno-discarded-qualifiers: YES
Compiler for C supports arguments -Wno-empty-body: YES
Compiler for C supports arguments -Wno-implicit-function-declaration: YES
Compiler for C supports arguments -Wno-parentheses: YES
Compiler for C supports arguments -Wno-switch: YES
Compiler for C supports arguments -Wno-unused-result: YES
Compiler for C supports arguments -Wno-unused-label: YES
Compiler for C supports arguments -Wno-unused-variable: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES
Compiler for Fortran supports arguments -Wno-surprising: YES
Compiler for Fortran supports arguments -Wno-uninitialized: YES
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES
Compiler for Fortran supports arguments -Wno-unused-label: YES
Compiler for Fortran supports arguments -Wno-unused-variable: YES
Compiler for Fortran supports arguments -Wno-tabs: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
Compiler for C supports link arguments -Wl,-no_compact_unwind: NO
Compiler for C supports link arguments -Wl,-no_fixup_chains: NO
Found CMake: /usr/bin/cmake (3.22.0)
WARNING: CMake Toolchain: Failed to determine CMake compilers state
Run-time dependency openblas found: NO (tried pkgconfig and cmake)
Run-time dependency openblas found: NO (tried pkgconfig and cmake)
../skmisc/meson.build:173:9: ERROR: Dependency "OpenBLAS" not found, tried pkgconfig and cmake
A full log can be found at /home/biocbuild/tmp/pip-install-3u52zki9/scikit-misc_36726798ad40427b932461d6bf9b7ca7/.mesonpy-3u7iz3p3/meson-logs/meson-log.txt
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Quitting from lines 43-48 [doinit] (citeseq_tut.Rmd)
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- failed re-building ‘citeseq_tut.Rmd’
--- re-building ‘compch12.Rmd’ using rmarkdown
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- python=3.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.10.14-hbbe8eec_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- python=3.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv
added / updated specs:
- numpy=1.24.4
- pandas=1.5.3
- python[version='3.10.*,3.10.*']
The following NEW packages will be INSTALLED:
bottleneck conda-forge/linux-aarch64::bottleneck-1.3.8-py310h8b6b5fc_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numexpr conda-forge/linux-aarch64::numexpr-2.9.0-py310had05d37_0
numpy conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0
pandas pkgs/main/linux-aarch64::pandas-1.5.3-py310hfb1e5ee_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::python_abi-3.10-4_cp310
pytz conda-forge/noarch::pytz-2024.1-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-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting anndata==0.10.1
Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB)
Collecting docrep==0.3.2
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting flax==0.8.1
Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB)
Collecting jax==0.4.23
Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB)
Collecting jaxlib==0.4.23
Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB)
Collecting optax==0.1.9
Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB)
Collecting scipy==1.12.0
Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB)
Collecting scikit-learn==1.4.0
Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting rich==13.7.1
Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting h5py==3.9.0
Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting torch==1.13.1
Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB)
Collecting lightning==2.1.4
Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB)
Collecting torchmetrics==0.11.0
Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB)
Collecting tqdm==4.66.2
Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting ml-collections==0.1.1
Using cached ml_collections-0.1.1.tar.gz (77 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting mudata==0.2.3
Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB)
Collecting scvi-tools==1.1.2
Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB)
Collecting scanpy==1.9.5
Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB)
Collecting matplotlib==3.7.3
Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB)
Collecting scikit-misc==0.3.1
Using cached scikit_misc-0.3.1.tar.gz (302 kB)
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 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [59 lines of output]
+ meson setup /home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea /home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea/.mesonpy-eldq31f6 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea/.mesonpy-eldq31f6/meson-python-native-file.ini
The Meson build system
Version: 1.4.0
Source dir: /home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea
Build dir: /home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea/.mesonpy-eldq31f6
Build type: native build
Project name: scikit-misc
Project version: 0.3.1
C compiler for the host machine: cc (gcc 10.3.1 "cc (GCC) 10.3.1")
C linker for the host machine: cc ld.bfd 2.37
Cython compiler for the host machine: cython (cython 3.0.9)
Host machine cpu family: aarch64
Host machine cpu: aarch64
Fortran compiler for the host machine: gfortran (gcc 10.3.1 "GNU Fortran (GCC) 10.3.1")
Fortran linker for the host machine: gfortran ld.bfd 2.37
Program python found: YES (/home/biocbuild/.cache/R/basilisk/1.15.5/scviR/1.3.3/bsklenv/bin/python)
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.0
Run-time dependency python found: YES 3.10
Program cython found: YES (/home/biocbuild/tmp/pip-build-env-c6irhmzc/overlay/bin/cython)
Library m found: YES
Compiler for Fortran supports arguments -Wno-conversion: YES
Library npymath found: YES
Library npyrandom found: YES
Compiler for C supports arguments -Wno-maybe-uninitialized: YES
Compiler for C supports arguments -Wno-discarded-qualifiers: YES
Compiler for C supports arguments -Wno-empty-body: YES
Compiler for C supports arguments -Wno-implicit-function-declaration: YES
Compiler for C supports arguments -Wno-parentheses: YES
Compiler for C supports arguments -Wno-switch: YES
Compiler for C supports arguments -Wno-unused-result: YES
Compiler for C supports arguments -Wno-unused-label: YES
Compiler for C supports arguments -Wno-unused-variable: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES
Compiler for Fortran supports arguments -Wno-surprising: YES
Compiler for Fortran supports arguments -Wno-uninitialized: YES
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES
Compiler for Fortran supports arguments -Wno-unused-label: YES
Compiler for Fortran supports arguments -Wno-unused-variable: YES
Compiler for Fortran supports arguments -Wno-tabs: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
Compiler for C supports link arguments -Wl,-no_compact_unwind: NO
Compiler for C supports link arguments -Wl,-no_fixup_chains: NO
Found CMake: /usr/bin/cmake (3.22.0)
WARNING: CMake Toolchain: Failed to determine CMake compilers state
Run-time dependency openblas found: NO (tried pkgconfig and cmake)
Run-time dependency openblas found: NO (tried pkgconfig and cmake)
../skmisc/meson.build:173:9: ERROR: Dependency "OpenBLAS" not found, tried pkgconfig and cmake
A full log can be found at /home/biocbuild/tmp/pip-install-0yc0oj8r/scikit-misc_ae49bfa24144412694b30d1896d9f5ea/.mesonpy-eldq31f6/meson-logs/meson-log.txt
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Quitting from lines 50-53 [getdat2] (compch12.Rmd)
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- 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