aarch64 cuda13 singlecell gpu notebook ff9cb3dc11f0 - huchlab/sequencing-docker-stacks GitHub Wiki
- Build timestamp: 2026-02-12T15:07:01Z
- Docker image:
quay.io/huchlab/singlecell-gpu-notebook:ff9cb3dc11f0 - Docker image size: 41.5GB
- Git commit SHA: ff9cb3dc11f089136446c65f5863479d03c5b72e
- Git commit message:
Add singlecell GPU notebook support with CUDA variants (#570)
* Add singlecell GPU notebook support with CUDA variants and update workflows
* add scvi-tools with cuda to singlecell-gpu-notebook
* Fix Dockerfile to remove wrong RUN command for pip installation of PyTorch
* Enable aggressive disk cleanup for aarch64 runners
Co-authored-by: fbnrst <[email protected]>
* Add more folders to free disk space in build-upload workflow
Co-authored-by: fbnrst <[email protected]>
* free more disk space
* even more
* Refine disk cleanup process by updating folders to remove in build-upload workflow
* Remove duplicate torch
* Update disk cleanup process by adding additional folders to remove
* Enhance disk cleanup process by adding additional folders to remove
* Refine disk cleanup process by updating folders to remove in build-upload workflow
* Initial plan
* Implement GHCR for intermediate Docker images
Co-authored-by: fbnrst <[email protected]>
* Add documentation for GHCR implementation
Co-authored-by: fbnrst <[email protected]>
* Add packages:read permission to all workflows using load-image
Co-authored-by: fbnrst <[email protected]>
* Use docker/login-action for secure credential handling
Co-authored-by: fbnrst <[email protected]>
* Refine disk cleanup process by updating folders to remove in build-upload workflow
* Add run_id to GHCR tags and implement cleanup workflow
Co-authored-by: fbnrst <[email protected]>
* Fix documentation comments for clarity
Co-authored-by: fbnrst <[email protected]>
* Simplify cleanup workflow by removing regex pattern
Co-authored-by: fbnrst <[email protected]>
* Fix formatting inconsistencies in GHCR cleanup workflow
* Update disk cleanup process by refining folders to remove in build-upload workflow
* Refine disk cleanup process by updating folders to remove in build-upload workflow
* Fix platform mismatch in docker pull command
Co-authored-by: fbnrst <[email protected]>
* Improve platform mapping with explicit conversion logic
Co-authored-by: fbnrst <[email protected]>
* Rename steps in Docker tag push workflow for clarity
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add conditional checks to skip jobs for FAST_BUILD pull requests
* Remove aarch64 CUDA variant builds for singlecell-gpu-notebook (#576)
* Initial plan
* Remove aarch64 CUDA variant builds for singlecell-gpu-notebook
Co-authored-by: fbnrst <[email protected]>
* Skip aarch64 steps in tag-push and tag-merge workflows for CUDA variants
Co-authored-by: fbnrst <[email protected]>
---------
Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: fbnrst <[email protected]>
* Add mypy configuration for torchaudio and torchvision; create unit tests for both
* Update Dockerfiles to install PyTorch without specific version
* Add disk space cleanup step in Docker test workflow
* run ncdu to get disk space overview
* Add disk usage checks before and after cleanup in Docker workflow
* Update ncdu output artifact name to include image, platform, and variant
* Add additional folders to cleanup list in Docker workflow
* Add aarch64 singlecell GPU notebook jobs for cuda12 and cuda13 variants
* Add Docker storage cleanup step to workflow
* Remove Docker storage cleanup step from build workflow and enable image squashing
* Remove image squashing option from Docker build step
* Optimize build-upload workflow, remove cuda12 variant, and optimize apptainer-push workflow (#577)
* Initial plan
* Build and push image directly to GHCR to save disk space
Co-authored-by: fbnrst <[email protected]>
* Avoid pulling image from GHCR by using source-image parameter
Co-authored-by: fbnrst <[email protected]>
* Fix trailing whitespace in config.py
Co-authored-by: fbnrst <[email protected]>
* Revert to 35055df and remove cuda12 variant
Co-authored-by: fbnrst <[email protected]>
* Add comprehensive disk cleanup strategy to apptainer-push workflow
Co-authored-by: fbnrst <[email protected]>
* Remove ncdu analysis from all workflows
Co-authored-by: fbnrst <[email protected]>
* Update apptainer-push to use GHCR image directly in definition file
Co-authored-by: fbnrst <[email protected]>
---------
Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: fbnrst <[email protected]>
* Copy images directly from GHCR to quay.io to save disk space (#585)
* Initial plan
* Add direct image copy from GHCR to quay.io to save disk space
Co-authored-by: fbnrst <[email protected]>
* Fix tag parsing to use rsplit for better robustness
Co-authored-by: fbnrst <[email protected]>
* Remove PUSH_TO_REGISTRY condition from login step for testing
Co-authored-by: fbnrst <[email protected]>
* correct image for SBOM
* Update pull request trigger types for Docker workflow
* Revert "Remove PUSH_TO_REGISTRY condition from login step for testing"
This reverts commit ac6d619eb3818d4811d5aeffe461e5cf811e6b27.
* Comment out SBOM upload step in copy-and-tag-image action
* Re-enable SBOM upload step in copy-and-tag-image action with correct image reference
* Update job conditions for Apptainer push workflow to use self-hosted
* Add condition to Create dev environment step in Apptainer push workflow
* Comment out Dockerfile build steps and tests
* Revert "Comment out Dockerfile build steps and tests"
This reverts commit aef6e68734918af42ae4133881c93200a53f896f.
* Revert "Add condition to Create dev environment step in Apptainer push workflow"
This reverts commit 9a74936a547d435ae96a1c287fcc85971c141e17.
* Revert "Update job conditions for Apptainer push workflow to use self-hosted"
This reverts commit d2e3ce633c24789cc7435a7728d874e6cc2c8423.
* Comment out singlecell-gpu-notebook inclusion in Apptainer push workflow due to disk space issues
---------
Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: fbnrst <[email protected]>
Co-authored-by: rost <[email protected]>
* Disable apptainer-push for singlecell-gpu-notebook:cuda13 due to disk space issues
* remove cuda apptainer from .mergify.yml
* Swap x86_64 and aarch64 image copy steps in docker-tag-push workflow
* Add additional login step for GHCR
* Refactor Docker login steps to use password-stdin for improved security
* Comment out Dockerfile build steps for future reference
* Refactor SBOM generation steps to install Syft and streamline artifact upload process
* Comment out disk space cleanup step for future reference
* Comment out disk space cleanup step for future reference
* Comment out GHCR login steps for future reference
* remove not needed GHCR login
* Revert "Comment out disk space cleanup step for future reference"
This reverts commit 841a27deca31153e75a73de8b7221206ed76d7c0.
* Revert "Comment out disk space cleanup step for future reference"
This reverts commit 5b30027f37c2409713400579f3681b86af8f8947.
* Revert "Comment out Dockerfile build steps for future reference"
This reverts commit b862ffeaf51e55adea20cb526fb7713a08dfe023.
* Revert "Swap x86_64 and aarch64 image copy steps in docker-tag-push workflow"
This reverts commit 803a901d7766289105daa3c71735cd1a978d37e4.
* Increase timeout for singlecell GPU test jobs to 30 minutes
---------
Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: fbnrst <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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tbb 2022.3.0 h0eac15c_1 conda-forge
tbb-devel 2022.3.0 h828ce58_1 conda-forge
tblib 3.2.2 pyhcf101f3_0 conda-forge
tensorboard 2.20.0 pyhe01879c_0 conda-forge
tensorboard-data-server 0.7.0 py313hba2fb49_4 conda-forge
terminado 0.18.1 pyhc90fa1f_1 conda-forge
texttable 1.7.0 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tifffile 2026.1.28 pyhd8ed1ab_0 conda-forge
tinycss2 1.5.1 pyhcf101f3_0 conda-forge
tk 8.6.13 noxft_h0dc03b3_103 conda-forge
tktable 2.10 h89546af_7 conda-forge
toml 0.10.2 pyhcf101f3_3 conda-forge
tomli 2.4.0 pyhcf101f3_0 conda-forge
tomlkit 0.14.0 pyha770c72_0 conda-forge
toolz 1.1.0 pyhd8ed1ab_1 conda-forge
torch 2.10.0 pypi_0 pypi
torchaudio 2.10.0 pypi_0 pypi
torchmetrics 1.8.2 pyhd8ed1ab_0 conda-forge
torchvision 0.25.0 pypi_0 pypi
tornado 6.5.4 py313ha35ba76_0 conda-forge
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
trackhub 1.0 pyh7cba7a3_0 bioconda
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
treelite 4.6.1 py313ha0cc5f1_0 conda-forge
triton 3.5.1 pypi_0 pypi
truststore 0.10.4 pyhcf101f3_0 conda-forge
typeguard 4.4.4 pypi_0 pypi
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
tzlocal 5.3.1 pyh8f84b5b_0 conda-forge
uc-micro-py 1.0.3 pyhd8ed1ab_1 conda-forge
ucx 1.19.1 h7c31d6f_0 conda-forge
ucxx 0.47.00 cuda13_py313_251210_5d6f0af3 rapidsai
ujson 5.11.0 pypi_0 pypi
umap-learn 0.5.11 py313hd81a959_0 conda-forge
unixodbc 2.3.14 h1344786_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
uriparser 0.9.8 h0a1ffab_0 conda-forge
urllib3 2.6.3 pyhd8ed1ab_0 conda-forge
uv 0.10.2 hf7c115b_0 conda-forge
uvicorn 0.40.0 pypi_0 pypi
vitessce 3.8.2 pypi_0 pypi
wcwidth 0.5.3 pyhd8ed1ab_0 conda-forge
webcolors 25.10.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.9.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.5 pyhcf101f3_0 conda-forge
wget 3.2 pypi_0 pypi
widgetsnbextension 4.0.15 pyhd8ed1ab_0 conda-forge
wrapt 2.1.1 py313h6194ac5_0 conda-forge
xarray 2026.1.0 pyhcf101f3_0 conda-forge
xerces-c 3.3.0 h595f43b_0 conda-forge
xgboost 3.1.2 rapidsai_pyh3432f66_1 rapidsai
xlrd 2.0.2 pyhd8ed1ab_0 conda-forge
xlsxwriter 3.2.9 pyhd8ed1ab_0 conda-forge
xmltodict 1.0.2 pyhcf101f3_0 conda-forge
xorg-libice 1.1.2 h86ecc28_0 conda-forge
xorg-libsm 1.2.6 h0808dbd_0 conda-forge
xorg-libx11 1.8.12 hca56bd8_0 conda-forge
xorg-libxau 1.0.12 he30d5cf_1 conda-forge
xorg-libxdmcp 1.1.5 he30d5cf_1 conda-forge
xorg-libxext 1.3.7 he30d5cf_0 conda-forge
xorg-libxrender 0.9.12 h86ecc28_0 conda-forge
xorg-libxt 1.3.1 h57736b2_0 conda-forge
xorg-xextproto 7.3.0 h57736b2_1004 conda-forge
xyzservices 2025.11.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h80f16a2_3 conda-forge
yaml-cpp 0.8.0 h5ad3122_0 conda-forge
yarl 1.22.0 py313hd3a54cf_0 conda-forge
yq 3.4.3 pyhe01879c_2 conda-forge
zarr 3.1.5 pyhcf101f3_0 conda-forge
zeromq 4.3.5 hefbcea8_9 conda-forge
zfp 1.0.1 h05c1e92_5 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.23.0 pyhcf101f3_1 conda-forge
zlib 1.3.1 h86ecc28_2 conda-forge
zlib-ng 2.3.3 ha7cb516_1 conda-forge
zstandard 0.25.0 py313h62ef0ea_1 conda-forge
zstd 1.5.7 h85ac4a6_6 conda-forge
apt list --installed:
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Listing...
adduser/now 3.137ubuntu1 all [installed,local]
apt/now 2.8.3 arm64 [installed,local]
base-files/now 13ubuntu10.3 arm64 [installed,local]
base-passwd/now 3.6.3build1 arm64 [installed,local]
bash/now 5.2.21-2ubuntu4 arm64 [installed,local]
binutils-aarch64-linux-gnu/now 2.42-4ubuntu2.8 arm64 [installed,local]
binutils-common/now 2.42-4ubuntu2.8 arm64 [installed,local]
binutils/now 2.42-4ubuntu2.8 arm64 [installed,local]
bsdutils/now 1:2.39.3-9ubuntu6.4 arm64 [installed,local]
build-essential/now 12.10ubuntu1 arm64 [installed,local]
bzip2/now 1.0.8-5.1build0.1 arm64 [installed,local]
ca-certificates/now 20240203 all [installed,local]
cm-super-minimal/now 0.3.4-17 all [installed,local]
cm-super/now 0.3.4-17 all [installed,local]
coreutils/now 9.4-3ubuntu6.1 arm64 [installed,local]
cpp-13-aarch64-linux-gnu/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
cpp-13/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
cpp-aarch64-linux-gnu/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
cpp/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
curl/now 8.5.0-2ubuntu10.6 arm64 [installed,local]
dash/now 0.5.12-6ubuntu5 arm64 [installed,local]
debconf/now 1.5.86ubuntu1 all [installed,local]
debianutils/now 5.17build1 arm64 [installed,local]
diffutils/now 1:3.10-1build1 arm64 [installed,local]
dpkg-dev/now 1.22.6ubuntu6.5 all [installed,local]
dpkg/now 1.22.6ubuntu6.5 arm64 [installed,local]
dvipng/now 1.15-1.1 arm64 [installed,local]
e2fsprogs/now 1.47.0-2.4~exp1ubuntu4.1 arm64 [installed,local]
ffmpeg/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
findutils/now 4.9.0-5build1 arm64 [installed,local]
fontconfig-config/now 2.15.0-1.1ubuntu2 arm64 [installed,local]
fontconfig/now 2.15.0-1.1ubuntu2 arm64 [installed,local]
fonts-dejavu-core/now 2.37-8 all [installed,local]
fonts-dejavu-extra/now 2.37-8 all [installed,local]
fonts-dejavu-mono/now 2.37-8 all [installed,local]
fonts-dejavu/now 2.37-8 all [installed,local]
fonts-liberation/now 1:2.1.5-3 all [installed,local]
fonts-lmodern/now 2.005-1 all [installed,local]
fonts-urw-base35/now 20200910-8 all [installed,local]
g++-13-aarch64-linux-gnu/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
g++-13/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
g++-aarch64-linux-gnu/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
g++/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
gcc-13-aarch64-linux-gnu/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
gcc-13-base/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
gcc-13/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
gcc-14-base/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
gcc-aarch64-linux-gnu/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
gcc/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
gfortran-13-aarch64-linux-gnu/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
gfortran-13/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
gfortran-aarch64-linux-gnu/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
gfortran/now 4:13.2.0-7ubuntu1 arm64 [installed,local]
ghostscript/now 10.02.1~dfsg1-0ubuntu7.8 arm64 [installed,local]
git-lfs/now 3.4.1-1ubuntu0.3 arm64 [installed,local]
git-man/now 1:2.43.0-1ubuntu7.3 all [installed,local]
git/now 1:2.43.0-1ubuntu7.3 arm64 [installed,local]
gpgv/now 2.4.4-2ubuntu17.4 arm64 [installed,local]
grep/now 3.11-4build1 arm64 [installed,local]
gzip/now 1.12-1ubuntu3.1 arm64 [installed,local]
hostname/now 3.23+nmu2ubuntu2 arm64 [installed,local]
init-system-helpers/now 1.66ubuntu1 all [installed,local]
less/now 590-2ubuntu2.1 arm64 [installed,local]
libacl1/now 2.3.2-1build1.1 arm64 [installed,local]
libaom3/now 3.8.2-2ubuntu0.1 arm64 [installed,local]
libapache-pom-java/now 29-2 all [installed,local]
libapparmor1/now 4.0.1really4.0.1-0ubuntu0.24.04.5 arm64 [installed,local]
libapt-pkg6.0t64/now 2.8.3 arm64 [installed,local]
libasan8/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libasound2-data/now 1.2.11-1ubuntu0.1 all [installed,local]
libasound2t64/now 1.2.11-1ubuntu0.1 arm64 [installed,local]
libass9/now 1:0.17.1-2build1 arm64 [installed,local]
libassuan0/now 2.5.6-1build1 arm64 [installed,local]
libasyncns0/now 0.8-6build4 arm64 [installed,local]
libatomic1/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libattr1/now 1:2.5.2-1build1.1 arm64 [installed,local]
libaudit-common/now 1:3.1.2-2.1build1.1 all [installed,local]
libaudit1/now 1:3.1.2-2.1build1.1 arm64 [installed,local]
libavahi-client3/now 0.8-13ubuntu6.1 arm64 [installed,local]
libavahi-common-data/now 0.8-13ubuntu6.1 arm64 [installed,local]
libavahi-common3/now 0.8-13ubuntu6.1 arm64 [installed,local]
libavc1394-0/now 0.5.4-5build3 arm64 [installed,local]
libavcodec60/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
libavdevice60/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
libavfilter9/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
libavformat60/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
libavutil58/now 7:6.1.1-3ubuntu5 arm64 [installed,local]
libbinutils/now 2.42-4ubuntu2.8 arm64 [installed,local]
libblas3/now 3.12.0-3build1.1 arm64 [installed,local]
libblkid1/now 2.39.3-9ubuntu6.4 arm64 [installed,local]
libbluray2/now 1:1.3.4-1build1 arm64 [installed,local]
libbrotli1/now 1.1.0-2build2 arm64 [installed,local]
libbs2b0/now 3.1.0+dfsg-7build1 arm64 [installed,local]
libbsd0/now 0.12.1-1build1.1 arm64 [installed,local]
libbz2-1.0/now 1.0.8-5.1build0.1 arm64 [installed,local]
libc-bin/now 2.39-0ubuntu8.7 arm64 [installed,local]
libc-dev-bin/now 2.39-0ubuntu8.7 arm64 [installed,local]
libc6-dev/now 2.39-0ubuntu8.7 arm64 [installed,local]
libc6/now 2.39-0ubuntu8.7 arm64 [installed,local]
libcaca0/now 0.99.beta20-4ubuntu0.1 arm64 [installed,local]
libcairo-gobject2/now 1.18.0-3build1 arm64 [installed,local]
libcairo2/now 1.18.0-3build1 arm64 [installed,local]
libcap-ng0/now 0.8.4-2build2 arm64 [installed,local]
libcap2/now 1:2.66-5ubuntu2.2 arm64 [installed,local]
libcbor0.10/now 0.10.2-1.2ubuntu2 arm64 [installed,local]
libcc1-0/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libcdio-cdda2t64/now 10.2+2.0.1-1.1build2 arm64 [installed,local]
libcdio-paranoia2t64/now 10.2+2.0.1-1.1build2 arm64 [installed,local]
libcdio19t64/now 2.1.0-4.1ubuntu1.2 arm64 [installed,local]
libchromaprint1/now 1.5.1-5 arm64 [installed,local]
libcjson1/now 1.7.17-1 arm64 [installed,local]
libcodec2-1.2/now 1.2.0-2build1 arm64 [installed,local]
libcom-err2/now 1.47.0-2.4~exp1ubuntu4.1 arm64 [installed,local]
libcommons-logging-java/now 1.3.0-1ubuntu1 all [installed,local]
libcommons-parent-java/now 56-1 all [installed,local]
libcrypt-dev/now 1:4.4.36-4build1 arm64 [installed,local]
libcrypt1/now 1:4.4.36-4build1 arm64 [installed,local]
libctf-nobfd0/now 2.42-4ubuntu2.8 arm64 [installed,local]
libctf0/now 2.42-4ubuntu2.8 arm64 [installed,local]
libcups2t64/now 2.4.7-1.2ubuntu7.9 arm64 [installed,local]
libcurl3t64-gnutls/now 8.5.0-2ubuntu10.6 arm64 [installed,local]
libcurl4t64/now 8.5.0-2ubuntu10.6 arm64 [installed,local]
libdatrie1/now 0.2.13-3build1 arm64 [installed,local]
libdav1d7/now 1.4.1-1build1 arm64 [installed,local]
libdb5.3t64/now 5.3.28+dfsg2-7 arm64 [installed,local]
libdbus-1-3/now 1.14.10-4ubuntu4.1 arm64 [installed,local]
libdc1394-25/now 2.2.6-4build1 arm64 [installed,local]
libde265-0/now 1.0.15-1build3 arm64 [installed,local]
libdebconfclient0/now 0.271ubuntu3 arm64 [installed,local]
libdecor-0-0/now 0.2.2-1build2 arm64 [installed,local]
libdeflate0/now 1.19-1build1.1 arm64 [installed,local]
libdpkg-perl/now 1.22.6ubuntu6.5 all [installed,local]
libdrm-amdgpu1/now 2.4.125-1ubuntu0.1~24.04.1 arm64 [installed,local]
libdrm-common/now 2.4.125-1ubuntu0.1~24.04.1 all [installed,local]
libdrm2/now 2.4.125-1ubuntu0.1~24.04.1 arm64 [installed,local]
libedit2/now 3.1-20230828-1build1 arm64 [installed,local]
libelf1t64/now 0.190-1.1ubuntu0.1 arm64 [installed,local]
liberror-perl/now 0.17029-2 all [installed,local]
libexpat1/now 2.6.1-2ubuntu0.3 arm64 [installed,local]
libext2fs2t64/now 1.47.0-2.4~exp1ubuntu4.1 arm64 [installed,local]
libffi8/now 3.4.6-1build1 arm64 [installed,local]
libfftw3-double3/now 3.3.10-1ubuntu3 arm64 [installed,local]
libfido2-1/now 1.14.0-1build3 arm64 [installed,local]
libflac12t64/now 1.4.3+ds-2.1ubuntu2 arm64 [installed,local]
libflite1/now 2.2-6build3 arm64 [installed,local]
libfontbox-java/now 1:1.8.16-5 all [installed,local]
libfontconfig1/now 2.15.0-1.1ubuntu2 arm64 [installed,local]
libfontenc1/now 1:1.1.8-1build1 arm64 [installed,local]
libfreetype6/now 2.13.2+dfsg-1build3 arm64 [installed,local]
libfribidi0/now 1.0.13-3build1 arm64 [installed,local]
libgbm1/now 25.2.8-0ubuntu0.24.04.1 arm64 [installed,local]
libgcc-13-dev/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
libgcc-s1/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libgcrypt20/now 1.10.3-2build1 arm64 [installed,local]
libgd3/now 2.3.3-9ubuntu5 arm64 [installed,local]
libgdbm-compat4t64/now 1.23-5.1build1 arm64 [installed,local]
libgdbm6t64/now 1.23-5.1build1 arm64 [installed,local]
libgdk-pixbuf-2.0-0/now 2.42.10+dfsg-3ubuntu3.2 arm64 [installed,local]
libgdk-pixbuf2.0-common/now 2.42.10+dfsg-3ubuntu3.2 all [installed,local]
libgfortran-13-dev/now 13.3.0-6ubuntu2~24.04 arm64 [installed,local]
libgfortran5/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libgl1-mesa-dri/now 25.2.8-0ubuntu0.24.04.1 arm64 [installed,local]
libgl1/now 1.7.0-1build1 arm64 [installed,local]
libglib2.0-0t64/now 2.80.0-6ubuntu3.8 arm64 [installed,local]
libglvnd0/now 1.7.0-1build1 arm64 [installed,local]
libglx-mesa0/now 25.2.8-0ubuntu0.24.04.1 arm64 [installed,local]
libglx0/now 1.7.0-1build1 arm64 [installed,local]
libgme0/now 0.6.3-7build1 arm64 [installed,local]
libgmp10/now 2:6.3.0+dfsg-2ubuntu6.1 arm64 [installed,local]
libgnutls30t64/now 3.8.3-1.1ubuntu3.4 arm64 [installed,local]
libgomp1/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libgpg-error0/now 1.47-3build2.1 arm64 [installed,local]
libgprofng0/now 2.42-4ubuntu2.8 arm64 [installed,local]
libgraphite2-3/now 1.3.14-2build1 arm64 [installed,local]
libgs-common/now 10.02.1~dfsg1-0ubuntu7.8 all [installed,local]
libgs10-common/now 10.02.1~dfsg1-0ubuntu7.8 all [installed,local]
libgs10/now 10.02.1~dfsg1-0ubuntu7.8 arm64 [installed,local]
libgsm1/now 1.0.22-1build1 arm64 [installed,local]
libgssapi-krb5-2/now 1.20.1-6ubuntu2.6 arm64 [installed,local]
libharfbuzz0b/now 8.3.0-2build2 arm64 [installed,local]
libheif-plugin-aomdec/now 1.17.6-1ubuntu4.2 arm64 [installed,local]
libheif-plugin-libde265/now 1.17.6-1ubuntu4.2 arm64 [installed,local]
libheif1/now 1.17.6-1ubuntu4.2 arm64 [installed,local]
libhogweed6t64/now 3.9.1-2.2build1.1 arm64 [installed,local]
libhwasan0/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libhwy1t64/now 1.0.7-8.1build1 arm64 [installed,local]
libice6/now 2:1.0.10-1build3 arm64 [installed,local]
libicu74/now 74.2-1ubuntu3.1 arm64 [installed,local]
libidn12/now 1.42-1build1 arm64 [installed,local]
libidn2-0/now 2.3.7-2build1.1 arm64 [installed,local]
libiec61883-0/now 1.2.0-6build1 arm64 [installed,local]
libijs-0.35/now 0.35-15.1build1 arm64 [installed,local]
libisl23/now 0.26-3build1.1 arm64 [installed,local]
libitm1/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libjack-jackd2-0/now 1.9.21~dfsg-3ubuntu3 arm64 [installed,local]
libjansson4/now 2.14-2build2 arm64 [installed,local]
libjbig0/now 2.1-6.1ubuntu2 arm64 [installed,local]
libjbig2dec0/now 0.20-1build3 arm64 [installed,local]
libjpeg-turbo8/now 2.1.5-2ubuntu2 arm64 [installed,local]
libjpeg8/now 8c-2ubuntu11 arm64 [installed,local]
libjxl0.7/now 0.7.0-10.2ubuntu6.1 arm64 [installed,local]
libk5crypto3/now 1.20.1-6ubuntu2.6 arm64 [installed,local]
libkeyutils1/now 1.6.3-3build1 arm64 [installed,local]
libkpathsea6/now 2023.20230311.66589-9build3 arm64 [installed,local]
libkrb5-3/now 1.20.1-6ubuntu2.6 arm64 [installed,local]
libkrb5support0/now 1.20.1-6ubuntu2.6 arm64 [installed,local]
liblapack3/now 3.12.0-3build1.1 arm64 [installed,local]
liblcms2-2/now 2.14-2build1 arm64 [installed,local]
libldap2/now 2.6.10+dfsg-0ubuntu0.24.04.1 arm64 [installed,local]
liblerc4/now 4.0.0+ds-4ubuntu2 arm64 [installed,local]
liblilv-0-0/now 0.24.22-1build1 arm64 [installed,local]
libllvm20/now 1:20.1.2-0ubuntu1~24.04.2 arm64 [installed,local]
liblsan0/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
liblua5.4-0/now 5.4.6-3build2 arm64 [installed,local]
liblz4-1/now 1.9.4-1build1.1 arm64 [installed,local]
liblzma5/now 5.6.1+really5.4.5-1ubuntu0.2 arm64 [installed,local]
libmbedcrypto7t64/now 2.28.8-1 arm64 [installed,local]
libmd0/now 1.1.0-2build1.1 arm64 [installed,local]
libmount1/now 2.39.3-9ubuntu6.4 arm64 [installed,local]
libmp3lame0/now 3.100-6build1 arm64 [installed,local]
libmpc3/now 1.3.1-1build1.1 arm64 [installed,local]
libmpfr6/now 4.2.1-1build1.1 arm64 [installed,local]
libmpg123-0t64/now 1.32.5-1ubuntu1.1 arm64 [installed,local]
libmysofa1/now 1.3.2+dfsg-2ubuntu2 arm64 [installed,local]
libncursesw6/now 6.4+20240113-1ubuntu2 arm64 [installed,local]
libnettle8t64/now 3.9.1-2.2build1.1 arm64 [installed,local]
libnghttp2-14/now 1.59.0-1ubuntu0.2 arm64 [installed,local]
libnorm1t64/now 1.5.9+dfsg-3.1build1 arm64 [installed,local]
libnpth0t64/now 1.6-3.1build1 arm64 [installed,local]
libnuma1/now 2.0.18-1ubuntu0.24.04.1 arm64 [installed,local]
libogg0/now 1.3.5-3build1 arm64 [installed,local]
libopenal-data/now 1:1.23.1-4build1 all [installed,local]
libopenal1/now 1:1.23.1-4build1 arm64 [installed,local]
libopenjp2-7/now 2.5.0-2ubuntu0.4 arm64 [installed,local]
libopenmpt0t64/now 0.7.3-1.1build3 arm64 [installed,local]
libopus0/now 1.4-1build1 arm64 [installed,local]
libp11-kit0/now 0.25.3-4ubuntu2.1 arm64 [installed,local]
libpam-modules-bin/now 1.5.3-5ubuntu5.5 arm64 [installed,local]
libpam-modules/now 1.5.3-5ubuntu5.5 arm64 [installed,local]
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libpgm-5.3-0t64/now 5.3.128~dfsg-2.1build1 arm64 [installed,local]
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libpng16-16t64/now 1.6.43-5ubuntu0.4 arm64 [installed,local]
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libproc2-0/now 2:4.0.4-4ubuntu3.2 arm64 [installed,local]
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libptexenc1/now 2023.20230311.66589-9build3 arm64 [installed,local]
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librav1e0/now 0.7.1-2 arm64 [installed,local]
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libsndfile1/now 1.2.2-1ubuntu5.24.04.1 arm64 [installed,local]
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libsodium23/now 1.0.18-1ubuntu0.24.04.1 arm64 [installed,local]
libsord-0-0/now 0.16.16-2build1 arm64 [installed,local]
libsoxr0/now 0.1.3-4build3 arm64 [installed,local]
libspeex1/now 1.2.1-2ubuntu2.24.04.1 arm64 [installed,local]
libsphinxbase3t64/now 0.8+5prealpha+1-17build2 arm64 [installed,local]
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libsratom-0-0/now 0.6.16-1build1 arm64 [installed,local]
libsrt1.5-gnutls/now 1.5.3-1build2 arm64 [installed,local]
libss2/now 1.47.0-2.4~exp1ubuntu4.1 arm64 [installed,local]
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libssh-gcrypt-4/now 0.10.6-2ubuntu0.2 arm64 [installed,local]
libssl3t64/now 3.0.13-0ubuntu3.7 arm64 [installed,local]
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libstdc++6/now 14.2.0-4ubuntu2~24.04 arm64 [installed,local]
libsvtav1enc1d1/now 1.7.0+dfsg-2build1 arm64 [installed,local]
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libsynctex2/now 2023.20230311.66589-9build3 arm64 [installed,local]
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media-types/now 10.1.0 all [installed,local]
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mount/now 2.39.3-9ubuntu6.4 arm64 [installed,local]
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netbase/now 6.4 all [installed,local]
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openssh-client/now 1:9.6p1-3ubuntu13.14 arm64 [installed,local]
openssl/now 3.0.13-0ubuntu3.7 arm64 [installed,local]
pandoc-data/now 3.1.3-1 all [installed,local]
pandoc/now 3.1.3+ds-2 arm64 [installed,local]
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sudo/now 1.9.15p5-3ubuntu5.24.04.1 arm64 [installed,local]
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tar/now 1.35+dfsg-3build1 arm64 [installed,local]
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tzdata/now 2025b-0ubuntu0.24.04.1 all [installed,local]
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R --version:
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-conda-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
R --silent -e 'installed.packages(.Library)[, c(1,3)]':
> installed.packages(.Library)[, c(1,3)]
Package Version
abind "abind" "1.4-8"
anndata "anndata" "0.7.5.6"
AnnotationDbi "AnnotationDbi" "1.68.0"
AnnotationFilter "AnnotationFilter" "1.30.0"
ape "ape" "5.8-1"
aplot "aplot" "0.2.9"
arrow "arrow" "21.0.0"
askpass "askpass" "1.2.1"
assertthat "assertthat" "0.2.1"
assorthead "assorthead" "1.0.0"
backports "backports" "1.5.0"
base "base" "4.4.3"
base64enc "base64enc" "0.1-6"
basilisk "basilisk" "1.18.0"
basilisk.utils "basilisk.utils" "1.18.0"
batchelor "batchelor" "1.22.0"
beachmat "beachmat" "2.22.0"
beeswarm "beeswarm" "0.4.0"
BH "BH" "1.87.0-1"
Biobase "Biobase" "2.66.0"
BiocFileCache "BiocFileCache" "2.14.0"
BiocGenerics "BiocGenerics" "0.52.0"
BiocIO "BiocIO" "1.16.0"
BiocManager "BiocManager" "1.30.27"
BiocNeighbors "BiocNeighbors" "2.0.0"
BiocParallel "BiocParallel" "1.40.0"
BiocSingular "BiocSingular" "1.22.0"
biomaRt "biomaRt" "2.62.0"
Biostrings "Biostrings" "2.74.0"
biovizBase "biovizBase" "1.54.0"
bit "bit" "4.6.0"
bit64 "bit64" "4.6.0-1"
bitops "bitops" "1.0-9"
blob "blob" "1.3.0"
bluster "bluster" "1.16.0"
boot "boot" "1.3-32"
brew "brew" "1.0-10"
brio "brio" "1.1.5"
broom "broom" "1.0.12"
broom.helpers "broom.helpers" "1.22.0"
BSgenome "BSgenome" "1.74.0"
bslib "bslib" "0.10.0"
cachem "cachem" "1.1.0"
Cairo "Cairo" "1.7-0"
callr "callr" "3.7.6"
car "car" "3.1-5"
carData "carData" "3.0-6"
cards "cards" "0.7.1"
caret "caret" "7.0-1"
caTools "caTools" "1.18.3"
CCPlotR "CCPlotR" "1.4.0"
cellranger "cellranger" "1.1.0"
checkmate "checkmate" "2.3.3"
circlize "circlize" "0.4.17"
class "class" "7.3-23"
cli "cli" "3.6.5"
clipr "clipr" "0.8.0"
clock "clock" "0.7.4"
clue "clue" "0.3-66"
cluster "cluster" "2.1.8.2"
clusterProfiler "clusterProfiler" "4.14.0"
clustree "clustree" "0.5.1"
codetools "codetools" "0.2-20"
collections "collections" "0.3.11"
colorspace "colorspace" "2.1-2"
commonmark "commonmark" "2.0.0"
compiler "compiler" "4.4.3"
ComplexHeatmap "ComplexHeatmap" "2.22.0"
conflicted "conflicted" "1.2.0"
conquer "conquer" "1.3.3"
corrplot "corrplot" "0.95"
cowplot "cowplot" "1.2.0"
cpp11 "cpp11" "0.5.3"
crayon "crayon" "1.5.3"
credentials "credentials" "2.0.3"
crosstalk "crosstalk" "1.2.2"
crul "crul" "1.6.0"
curl "curl" "7.0.0"
cyclocomp "cyclocomp" "1.1.1"
data.table "data.table" "1.17.8"
datasets "datasets" "4.4.3"
DBI "DBI" "1.2.3"
dbplyr "dbplyr" "2.5.1"
decoupleR "decoupleR" "2.12.0"
DelayedArray "DelayedArray" "0.32.0"
DelayedMatrixStats "DelayedMatrixStats" "1.28.0"
deldir "deldir" "2.0-4"
Deriv "Deriv" "4.2.0"
desc "desc" "1.4.3"
DESeq2 "DESeq2" "1.46.0"
devtools "devtools" "2.4.6"
diagram "diagram" "1.6.5"
dials "dials" "1.4.2"
DiceDesign "DiceDesign" "1.10"
dichromat "dichromat" "2.0-0.1"
diffobj "diffobj" "0.3.6"
digest "digest" "0.6.39"
dir.expiry "dir.expiry" "1.14.0"
doBy "doBy" "4.7.1"
doParallel "doParallel" "1.0.17"
DOSE "DOSE" "4.0.0"
dotCall64 "dotCall64" "1.2"
downlit "downlit" "0.4.5"
dplyr "dplyr" "1.2.0"
dqrng "dqrng" "0.3.2"
dtplyr "dtplyr" "1.3.3"
e1071 "e1071" "1.7-17"
edgeR "edgeR" "4.4.0"
ellipsis "ellipsis" "0.3.2"
enrichplot "enrichplot" "1.26.1"
ensembldb "ensembldb" "2.30.0"
evaluate "evaluate" "1.0.5"
fansi "fansi" "1.0.7"
farver "farver" "2.1.2"
fastcluster "fastcluster" "1.3.0"
fastDummies "fastDummies" "1.7.5"
fastmap "fastmap" "1.2.0"
fastmatch "fastmatch" "1.1-8"
feather "feather" "0.4.0"
fgsea "fgsea" "1.32.2"
filelock "filelock" "1.0.3"
fitdistrplus "fitdistrplus" "1.2-6"
FNN "FNN" "1.1.4.1"
fontawesome "fontawesome" "0.5.3"
fontBitstreamVera "fontBitstreamVera" "0.1.1"
fontLiberation "fontLiberation" "0.1.0"
fontquiver "fontquiver" "0.2.1"
forcats "forcats" "1.0.1"
foreach "foreach" "1.5.2"
forecast "forecast" "9.0.0"
foreign "foreign" "0.8-91"
formatR "formatR" "1.14"
Formula "Formula" "1.2-5"
fracdiff "fracdiff" "1.5-3"
fs "fs" "1.6.6"
furrr "furrr" "0.3.1"
futile.logger "futile.logger" "1.4.9"
futile.options "futile.options" "1.0.1"
future "future" "1.69.0"
future.apply "future.apply" "1.20.1"
gargle "gargle" "1.6.1"
gbRd "gbRd" "0.4.12"
gdtools "gdtools" "0.5.0"
generics "generics" "0.1.4"
GenomeInfoDb "GenomeInfoDb" "1.42.0"
GenomeInfoDbData "GenomeInfoDbData" "1.2.13"
GenomicAlignments "GenomicAlignments" "1.42.0"
GenomicFeatures "GenomicFeatures" "1.58.0"
GenomicRanges "GenomicRanges" "1.58.0"
gert "gert" "2.3.1"
GetoptLong "GetoptLong" "1.1.0"
gfonts "gfonts" "0.2.0"
GGally "GGally" "2.4.0"
ggbeeswarm "ggbeeswarm" "0.7.3"
ggbump "ggbump" "0.1.0"
ggforce "ggforce" "0.5.0"
ggfun "ggfun" "0.2.0"
ggh4x "ggh4x" "0.3.1"
ggiraph "ggiraph" "0.9.4"
ggnewscale "ggnewscale" "0.5.2"
ggplot2 "ggplot2" "4.0.2"
ggplotify "ggplotify" "0.1.3"
ggpubr "ggpubr" "0.6.2"
ggraph "ggraph" "2.2.2"
ggrastr "ggrastr" "1.0.2"
ggrepel "ggrepel" "0.9.6"
ggridges "ggridges" "0.5.7"
ggsci "ggsci" "4.2.0"
ggsignif "ggsignif" "0.6.4"
ggstats "ggstats" "0.12.0"
ggtangle "ggtangle" "0.1.1"
ggtext "ggtext" "0.1.2"
ggthemes "ggthemes" "5.2.0"
ggtree "ggtree" "3.14.0"
ggupset "ggupset" "0.4.1"
ggvenn "ggvenn" "0.1.19"
gh "gh" "1.5.0"
gitcreds "gitcreds" "0.1.2"
GlobalOptions "GlobalOptions" "0.1.3"
globals "globals" "0.19.0"
glue "glue" "1.8.0"
GO.db "GO.db" "3.20.0"
goftest "goftest" "1.2-3"
googledrive "googledrive" "2.1.2"
googlesheets4 "googlesheets4" "1.1.2"
GOSemSim "GOSemSim" "2.32.0"
gower "gower" "1.0.2"
GPfit "GPfit" "1.0-9"
gplots "gplots" "3.3.0"
graph "graph" "1.84.0"
graphics "graphics" "4.4.3"
graphlayouts "graphlayouts" "1.2.2"
grDevices "grDevices" "4.4.3"
grid "grid" "4.4.3"
gridExtra "gridExtra" "2.3"
gridGraphics "gridGraphics" "0.5-1"
gridtext "gridtext" "0.1.5"
grImport "grImport" "0.9-7"
gson "gson" "0.1.0"
gtable "gtable" "0.3.6"
gtools "gtools" "3.9.5"
Gviz "Gviz" "1.50.0"
hardhat "hardhat" "1.4.2"
harmony "harmony" "1.2.4"
haven "haven" "2.5.5"
HDF5Array "HDF5Array" "1.34.0"
here "here" "1.0.2"
hexbin "hexbin" "1.28.5"
highr "highr" "0.11"
Hmisc "Hmisc" "5.2-5"
hms "hms" "1.1.4"
htmlTable "htmlTable" "2.4.3"
htmltools "htmltools" "0.5.9"
htmlwidgets "htmlwidgets" "1.6.4"
httpcode "httpcode" "0.3.0"
httpuv "httpuv" "1.6.16"
httr "httr" "1.4.7"
httr2 "httr2" "1.2.2"
ica "ica" "1.0-3"
ids "ids" "1.0.1"
igraph "igraph" "2.1.4"
infer "infer" "1.1.0"
ini "ini" "0.3.1"
InteractionSet "InteractionSet" "1.34.0"
interp "interp" "1.1-6"
ipred "ipred" "0.9-15"
IRanges "IRanges" "2.40.0"
IRdisplay "IRdisplay" "1.1"
IRkernel "IRkernel" "1.3.2"
irlba "irlba" "2.3.7"
isoband "isoband" "0.3.0"
iterators "iterators" "1.0.14"
janitor "janitor" "2.2.1"
jpeg "jpeg" "0.1-11"
jquerylib "jquerylib" "0.1.4"
jsonlite "jsonlite" "2.0.0"
KEGGREST "KEGGREST" "1.46.0"
kernlab "kernlab" "0.9-33"
KernSmooth "KernSmooth" "2.23-26"
knitr "knitr" "1.51"
ks "ks" "1.15.1"
labeling "labeling" "0.4.3"
labelled "labelled" "2.16.0"
lambda.r "lambda.r" "1.2.4"
languageserver "languageserver" "0.3.16"
later "later" "1.4.5"
lattice "lattice" "0.22-9"
latticeExtra "latticeExtra" "0.6-31"
lava "lava" "1.8.2"
lazyeval "lazyeval" "0.2.2"
leidenbase "leidenbase" "0.1.36"
lhs "lhs" "1.2.0"
lifecycle "lifecycle" "1.0.5"
limma "limma" "3.62.1"
lintr "lintr" "3.3.0-1"
listenv "listenv" "0.10.0"
litedown "litedown" "0.9"
lme4 "lme4" "1.1-38"
lmtest "lmtest" "0.9-40"
locfit "locfit" "1.5-9.12"
LoomExperiment "LoomExperiment" "1.24.0"
lubridate "lubridate" "1.9.5"
magrittr "magrittr" "2.0.4"
markdown "markdown" "2.0"
MASS "MASS" "7.3-65"
MAST "MAST" "1.32.0"
Matrix "Matrix" "1.7-4"
MatrixGenerics "MatrixGenerics" "1.18.0"
MatrixModels "MatrixModels" "0.5-4"
matrixStats "matrixStats" "1.5.0"
mclust "mclust" "6.1.2"
memoise "memoise" "2.0.1"
metapod "metapod" "1.14.0"
methods "methods" "4.4.3"
mgcv "mgcv" "1.9-4"
microbenchmark "microbenchmark" "1.5.0"
mime "mime" "0.13"
miniUI "miniUI" "0.1.2"
minqa "minqa" "1.2.8"
misc3d "misc3d" "0.9-2"
modeldata "modeldata" "1.5.1"
modelenv "modelenv" "0.2.0"
ModelMetrics "ModelMetrics" "1.2.2.2"
modelr "modelr" "0.1.11"
multicool "multicool" "1.0.1"
munsell "munsell" "0.5.1"
mvtnorm "mvtnorm" "1.3-3"
Nebulosa "Nebulosa" "1.16.0"
nlme "nlme" "3.1-168"
nloptr "nloptr" "2.2.1"
nnet "nnet" "7.3-20"
numDeriv "numDeriv" "2016.8-1.1"
nycflights13 "nycflights13" "1.0.2"
openssl "openssl" "2.3.4"
openxlsx "openxlsx" "4.2.8.1"
org.Hs.eg.db "org.Hs.eg.db" "3.20.0"
org.Mm.eg.db "org.Mm.eg.db" "3.20.0"
otel "otel" "0.2.0"
paletteer "paletteer" "1.7.0"
parallel "parallel" "4.4.3"
parallelDist "parallelDist" "0.2.7"
parallelly "parallelly" "1.46.1"
parsnip "parsnip" "1.4.1"
patchwork "patchwork" "1.3.2"
pbapply "pbapply" "1.7-4"
pbdZMQ "pbdZMQ" "0.3-14"
pbkrtest "pbkrtest" "0.5.5"
pheatmap "pheatmap" "1.0.13"
pillar "pillar" "1.11.1"
pkgbuild "pkgbuild" "1.4.8"
pkgconfig "pkgconfig" "2.0.3"
pkgdown "pkgdown" "2.2.0"
pkgload "pkgload" "1.5.0"
plogr "plogr" "0.2.0"
plot3D "plot3D" "1.4.2"
plotly "plotly" "4.12.0"
plyr "plyr" "1.8.9"
png "png" "0.1-8"
polyclip "polyclip" "1.10-7"
polynom "polynom" "1.4-1"
pracma "pracma" "2.4.6"
praise "praise" "1.0.0"
presto "presto" "1.0.0"
prettyunits "prettyunits" "1.2.0"
prismatic "prismatic" "1.1.2"
pROC "pROC" "1.19.0.1"
processx "processx" "3.8.6"
prodlim "prodlim" "2025.04.28"
profvis "profvis" "0.4.0"
progress "progress" "1.2.3"
progressr "progressr" "0.18.0"
promises "promises" "1.5.0"
ProtGenerics "ProtGenerics" "1.38.0"
proxy "proxy" "0.4-29"
ps "ps" "1.9.1"
purrr "purrr" "1.2.1"
quadprog "quadprog" "1.5-8"
quantmod "quantmod" "0.4.28"
quantreg "quantreg" "6.1"
qvalue "qvalue" "2.38.0"
R.cache "R.cache" "0.17.0"
R.methodsS3 "R.methodsS3" "1.8.2"
R.oo "R.oo" "1.27.1"
R.utils "R.utils" "2.13.0"
R6 "R6" "2.6.1"
ragg "ragg" "1.5.0"
randomForest "randomForest" "4.7-1.2"
RANN "RANN" "2.6.2"
rappdirs "rappdirs" "0.3.4"
rbibutils "rbibutils" "2.4.1"
rcmdcheck "rcmdcheck" "1.4.0"
RColorBrewer "RColorBrewer" "1.1-3"
Rcpp "Rcpp" "1.1.1"
RcppAnnoy "RcppAnnoy" "0.0.23"
RcppArmadillo "RcppArmadillo" "15.2.3-1"
RcppEigen "RcppEigen" "0.3.4.0.2"
RcppHNSW "RcppHNSW" "0.6.0"
RcppML "RcppML" "0.3.7"
RcppParallel "RcppParallel" "5.1.11-1"
RcppProgress "RcppProgress" "0.4.2"
RcppTOML "RcppTOML" "0.2.3"
RCurl "RCurl" "1.98-1.17"
Rdpack "Rdpack" "2.6.6"
readr "readr" "2.1.6"
readxl "readxl" "1.4.5"
recipes "recipes" "1.3.1"
reformulas "reformulas" "0.4.4"
rematch "rematch" "2.0.0"
rematch2 "rematch2" "2.1.2"
remotes "remotes" "2.5.0"
repr "repr" "1.1.7"
reprex "reprex" "2.1.1"
reshape2 "reshape2" "1.4.5"
ResidualMatrix "ResidualMatrix" "1.16.0"
restfulr "restfulr" "0.0.16"
reticulate "reticulate" "1.44.1"
rex "rex" "1.2.1"
Rgraphviz "Rgraphviz" "2.50.0"
rhdf5 "rhdf5" "2.50.0"
rhdf5filters "rhdf5filters" "1.18.0"
Rhdf5lib "Rhdf5lib" "1.28.0"
RhpcBLASctl "RhpcBLASctl" "0.23-42"
Rhtslib "Rhtslib" "3.2.0"
rjson "rjson" "0.2.23"
rlang "rlang" "1.1.7"
rmarkdown "rmarkdown" "2.30"
ROCR "ROCR" "1.0-12"
RODBC "RODBC" "1.3-26.1"
roxygen2 "roxygen2" "7.3.3"
rpart "rpart" "4.1.24"
rprojroot "rprojroot" "2.1.1"
rsample "rsample" "1.3.2"
Rsamtools "Rsamtools" "2.22.0"
RSpectra "RSpectra" "0.16-2"
RSQLite "RSQLite" "2.4.6"
rstatix "rstatix" "0.7.3"
rstudioapi "rstudioapi" "0.18.0"
rsvd "rsvd" "1.0.5"
rtracklayer "rtracklayer" "1.66.0"
Rtsne "Rtsne" "0.17"
rversions "rversions" "3.0.0"
rvest "rvest" "1.0.5"
S4Arrays "S4Arrays" "1.6.0"
S4Vectors "S4Vectors" "0.44.0"
S7 "S7" "0.2.1"
sass "sass" "0.4.10"
ScaledMatrix "ScaledMatrix" "1.14.0"
scales "scales" "1.4.0"
scater "scater" "1.34.1"
scattermore "scattermore" "1.2"
scatterpie "scatterpie" "0.2.6"
scran "scran" "1.34.0"
sctransform "sctransform" "0.4.3"
scuttle "scuttle" "1.16.0"
selectr "selectr" "0.5-1"
sessioninfo "sessioninfo" "1.2.3"
Seurat "Seurat" "5.4.0"
SeuratObject "SeuratObject" "5.3.0"
sfd "sfd" "0.1.0"
shadowtext "shadowtext" "0.1.6"
shape "shape" "1.4.6.1"
shiny "shiny" "1.12.1"
SingleCellExperiment "SingleCellExperiment" "1.28.0"
sitmo "sitmo" "2.0.2"
slam "slam" "0.1-55"
slider "slider" "0.3.3"
snakecase "snakecase" "0.11.1"
snow "snow" "0.4-4"
sourcetools "sourcetools" "0.1.7-1"
sp "sp" "2.2-0"
spam "spam" "2.11-3"
SparseArray "SparseArray" "1.6.0"
SparseM "SparseM" "1.84-2"
sparseMatrixStats "sparseMatrixStats" "1.18.0"
sparsevctrs "sparsevctrs" "0.3.5"
spatstat.data "spatstat.data" "3.1-9"
spatstat.explore "spatstat.explore" "3.7-0"
spatstat.geom "spatstat.geom" "3.7-0"
spatstat.random "spatstat.random" "3.4-4"
spatstat.sparse "spatstat.sparse" "3.1-0"
spatstat.univar "spatstat.univar" "3.1-6"
spatstat.utils "spatstat.utils" "3.2-1"
splines "splines" "4.4.3"
SQUAREM "SQUAREM" "2021.1"
statmod "statmod" "1.5.1"
stats "stats" "4.4.3"
stats4 "stats4" "4.4.3"
strawr "strawr" "0.0.92"
stringi "stringi" "1.8.7"
stringr "stringr" "1.6.0"
styler "styler" "1.11.0"
SummarizedExperiment "SummarizedExperiment" "1.36.0"
survival "survival" "3.8-6"
svglite "svglite" "2.2.2"
sys "sys" "3.4.3"
systemfonts "systemfonts" "1.3.1"
tailor "tailor" "0.1.0"
tcltk "tcltk" "4.4.3"
tensor "tensor" "1.5.1"
testthat "testthat" "3.3.2"
textshape "textshape" "1.7.5"
textshaping "textshaping" "1.0.4"
tibble "tibble" "3.3.1"
tidygraph "tidygraph" "1.3.0"
tidymodels "tidymodels" "1.4.1"
tidyr "tidyr" "1.3.2"
tidyselect "tidyselect" "1.2.1"
tidytree "tidytree" "0.4.7"
tidyverse "tidyverse" "2.0.0"
timechange "timechange" "0.4.0"
timeDate "timeDate" "4052.112"
tinytex "tinytex" "0.58"
tools "tools" "4.4.3"
topGO "topGO" "2.58.0"
trackViewer "trackViewer" "1.42.0"
treeio "treeio" "1.30.0"
triebeard "triebeard" "0.4.1"
tseries "tseries" "0.10-59"
TTR "TTR" "0.24.4"
tune "tune" "2.0.1"
tweenr "tweenr" "2.0.3"
txdbmaker "txdbmaker" "1.2.0"
tzdb "tzdb" "0.5.0"
UCSC.utils "UCSC.utils" "1.2.0"
urca "urca" "1.3-4"
urlchecker "urlchecker" "1.0.1"
urltools "urltools" "1.7.3.1"
usethis "usethis" "3.2.1"
utf8 "utf8" "1.2.6"
utils "utils" "4.4.3"
uuid "uuid" "1.2-2"
uwot "uwot" "0.2.4"
VariantAnnotation "VariantAnnotation" "1.52.0"
vctrs "vctrs" "0.7.1"
vipor "vipor" "0.4.7"
viridis "viridis" "0.6.5"
viridisLite "viridisLite" "0.4.3"
vroom "vroom" "1.6.7"
waldo "waldo" "0.6.2"
warp "warp" "0.2.3"
wesanderson "wesanderson" "0.3.7"
whisker "whisker" "0.4.1"
withr "withr" "3.0.2"
workflows "workflows" "1.3.0"
workflowsets "workflowsets" "1.1.1"
writexl "writexl" "1.5.4"
xfun "xfun" "0.56"
XML "XML" "3.99-0.22"
xml2 "xml2" "1.5.2"
xmlparsedata "xmlparsedata" "1.0.5"
xopen "xopen" "1.0.1"
xtable "xtable" "1.8-4"
xts "xts" "0.14.1"
XVector "XVector" "0.46.0"
yaml "yaml" "2.3.12"
yardstick "yardstick" "1.3.2"
yulab.utils "yulab.utils" "0.2.4"
zellkonverter "zellkonverter" "1.16.0"
zip "zip" "2.3.3"
zlibbioc "zlibbioc" "1.52.0"
zoo "zoo" "1.8-14"
>
>
julia -E 'using InteractiveUtils; versioninfo()':
Julia Version 1.12.4
Commit 01a2eadb047 (2026-01-06 16:56 UTC)
Build Info:
Official https://julialang.org release
Platform Info:
OS: Linux (aarch64-linux-gnu)
CPU: 4 × unknown
WORD_SIZE: 64
LLVM: libLLVM-18.1.7 (ORCJIT, neoverse-n2)
GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 4 virtual cores)
Environment:
JULIA_DEPOT_PATH = /opt/julia
JULIA_PKGDIR = /opt/julia
LD_LIBRARY_PATH = :/usr/local/nvidia/lib64
nothing
julia -E 'import Pkg; Pkg.status()':
Status `/opt/julia/environments/v1.12/Project.toml`
[f67ccb44] HDF5 v0.17.2
[7073ff75] IJulia v1.34.2
[c3e4b0f8] Pluto v0.20.21
nothing