Luke Zappia
| Snapshot Date: 2024-10-02 13:40 -0400 (Wed, 02 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/zellkonverter |
| git_branch: devel |
| git_last_commit: f348c5d |
| git_last_commit_date: 2024-10-02 07:55:00 -0400 (Wed, 02 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-03 11:50 -0400 (Thu, 03 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 2260/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.15.2 (landing page) Luke Zappia
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the zellkonverter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zellkonverter.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: zellkonverter |
| Version: 1.15.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings zellkonverter_1.15.2.tar.gz |
| StartedAt: 2024-10-03 10:40:20 -0000 (Thu, 03 Oct 2024) |
| EndedAt: 2024-10-03 10:54:35 -0000 (Thu, 03 Oct 2024) |
| EllapsedTime: 854.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings zellkonverter_1.15.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.15.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnData-Conversion 28.257 1.743 30.737
writeH5AD 5.987 0.532 6.536
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Error ('test-write.R:136:5'): writeH5AD works as expected with version 0.7.6 ──
Error: one or more Python packages failed to install [error code 1]
Backtrace:
▆
1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:136:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
[ FAIL 2 | WARN 30 | SKIP 4 | PASS 143 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘zellkonverter’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (zellkonverter)
zellkonverter.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (requireNamespace("spelling", quietly = TRUE)) {
+ spelling::spell_check_test(
+ vignettes = TRUE,
+ error = FALSE,
+ skip_on_cran = TRUE
+ )
+ }
NULL
>
> proc.time()
user system elapsed
0.185 0.037 0.206
zellkonverter.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
>
> test_check("zellkonverter")
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.2
added / updated specs:
- python=3.11.5
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-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.8.30-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_1
libexpat conda-forge/linux-aarch64::libexpat-2.6.3-h5ad3122_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc conda-forge/linux-aarch64::libgcc-14.1.0-he277a41_1
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.1.0-he9431aa_1
libgomp conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_1
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.46.1-hc4a20ef_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1
ncurses conda-forge/linux-aarch64::ncurses-6.5-hcccb83c_1
openssl conda-forge/linux-aarch64::openssl-3.3.2-h86ecc28_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-aarch64::python-3.11.5-h43d1f9e_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h8827d51_1
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.2
added / updated specs:
- anndata=0.10.2
- h5py=3.10.0
- hdf5=1.14.2
- natsort=8.4.0
- numpy=1.26.0
- packaging=23.2
- pandas=2.1.1
- python[version='3.11.5.*,3.11.5.*']
- scipy=1.11.3
The following packages will be downloaded:
package | build
---------------------------|-----------------
array-api-compat-1.9 | pyhd8ed1ab_0 37 KB conda-forge
------------------------------------------------------------
Total: 37 KB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.10.2-pyhd8ed1ab_0
array-api-compat conda-forge/noarch::array-api-compat-1.9-pyhd8ed1ab_0
c-ares conda-forge/linux-aarch64::c-ares-1.33.1-ha64f414_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
exceptiongroup conda-forge/noarch::exceptiongroup-1.2.2-pyhd8ed1ab_0
h5py conda-forge/linux-aarch64::h5py-3.10.0-nompi_py311haaf5ff5_100
hdf5 conda-forge/linux-aarch64::hdf5-1.14.2-nompi_ha486f32_100
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_0
krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0
libaec conda-forge/linux-aarch64::libaec-1.1.3-h2f0025b_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas
libcurl conda-forge/linux-aarch64::libcurl-8.10.1-h3ec0cbf_0
libedit conda-forge/linux-aarch64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2
libgfortran conda-forge/linux-aarch64::libgfortran-14.1.0-he9431aa_1
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.1.0-he9431aa_1
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.1.0-h9420597_1
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.58.0-hb0e430d_1
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.0-h492db2e_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.1.0-h3f4de04_1
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-hf1166c9_1
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/linux-aarch64::numpy-1.26.0-py311h69ead2a_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/linux-aarch64::pandas-2.1.1-py311h2dc6514_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::python_abi-3.11-5_cp311
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/linux-aarch64::scipy-1.11.3-py311h69ead2a_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/linux-aarch64::zstd-1.5.6-h02f22dd_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.9.2
added / updated specs:
- python=3.11.5
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-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.8.30-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_1
libexpat conda-forge/linux-aarch64::libexpat-2.6.3-h5ad3122_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc conda-forge/linux-aarch64::libgcc-14.1.0-he277a41_1
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.1.0-he9431aa_1
libgomp conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_1
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.46.1-hc4a20ef_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1
ncurses conda-forge/linux-aarch64::ncurses-6.5-hcccb83c_1
openssl conda-forge/linux-aarch64::openssl-3.3.2-h86ecc28_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-aarch64::python-3.11.5-h43d1f9e_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h8827d51_1
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.9.2
added / updated specs:
- anndata=0.9.2
- h5py=3.9.0
- hdf5=1.14.2
- natsort=8.4.0
- numpy=1.26.0
- packaging=23.2
- pandas=2.1.1
- python[version='3.11.5.*,3.11.5.*']
- scipy=1.11.3
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.9.2-pyhd8ed1ab_0
c-ares conda-forge/linux-aarch64::c-ares-1.33.1-ha64f414_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
h5py conda-forge/linux-aarch64::h5py-3.9.0-nompi_py311haaf5ff5_103
hdf5 conda-forge/linux-aarch64::hdf5-1.14.2-nompi_ha486f32_100
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_0
krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0
libaec conda-forge/linux-aarch64::libaec-1.1.3-h2f0025b_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas
libcurl conda-forge/linux-aarch64::libcurl-8.10.1-h3ec0cbf_0
libedit conda-forge/linux-aarch64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2
libgfortran conda-forge/linux-aarch64::libgfortran-14.1.0-he9431aa_1
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.1.0-he9431aa_1
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.1.0-h9420597_1
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.58.0-hb0e430d_1
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.0-h492db2e_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.1.0-h3f4de04_1
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-hf1166c9_1
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/linux-aarch64::numpy-1.26.0-py311h69ead2a_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/linux-aarch64::pandas-2.1.1-py311h2dc6514_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::python_abi-3.11-5_cp311
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/linux-aarch64::scipy-1.11.3-py311h69ead2a_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/linux-aarch64::zstd-1.5.6-h02f22dd_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.8.0
added / updated specs:
- python=3.8.13
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-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.8.30-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_1
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc conda-forge/linux-aarch64::libgcc-14.1.0-he277a41_1
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.1.0-he9431aa_1
libgomp conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_1
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.46.1-hc4a20ef_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1
ncurses conda-forge/linux-aarch64::ncurses-6.5-hcccb83c_1
openssl conda-forge/linux-aarch64::openssl-3.3.2-h86ecc28_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-aarch64::python-3.8.13-h92ab765_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.46.1-h578a6b9_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.8.0
added / updated specs:
- anndata=0.8.0
- h5py=3.6.0
- hdf5=1.12.1
- natsort=8.1.0
- numpy=1.22.3
- packaging=21.3
- pandas=1.4.2
- python[version='3.8.13.*,3.8.13.*']
- scipy=1.7.3
- sqlite=3.38.2
The following packages will be downloaded:
package | build
---------------------------|-----------------
importlib-metadata-8.5.0 | pyha770c72_0 28 KB conda-forge
importlib_metadata-8.5.0 | hd8ed1ab_0 9 KB conda-forge
pyparsing-3.1.4 | pyhd8ed1ab_0 88 KB conda-forge
zipp-3.20.2 | pyhd8ed1ab_0 21 KB conda-forge
------------------------------------------------------------
Total: 146 KB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1
c-ares conda-forge/linux-aarch64::c-ares-1.33.1-ha64f414_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
h5py conda-forge/linux-aarch64::h5py-3.6.0-nompi_py38hb2a0d32_100
hdf5 conda-forge/linux-aarch64::hdf5-1.12.1-nompi_h3900512_104
importlib-metadata conda-forge/noarch::importlib-metadata-8.5.0-pyha770c72_0
importlib_metadata conda-forge/noarch::importlib_metadata-8.5.0-hd8ed1ab_0
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_0
krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas
libcurl conda-forge/linux-aarch64::libcurl-8.8.0-h4e8248e_1
libedit conda-forge/linux-aarch64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2
libgfortran conda-forge/linux-aarch64::libgfortran-14.1.0-he9431aa_1
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.1.0-he9431aa_1
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.1.0-h9420597_1
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.58.0-hb0e430d_1
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.0-h492db2e_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.1.0-h3f4de04_1
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-hf1166c9_1
natsort conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0
numpy conda-forge/linux-aarch64::numpy-1.22.3-py38h9138613_2
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pandas conda-forge/linux-aarch64::pandas-1.4.2-py38h2fe58aa_2
pyparsing conda-forge/noarch::pyparsing-3.1.4-pyhd8ed1ab_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::python_abi-3.8-5_cp38
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/linux-aarch64::scipy-1.7.3-py38ha629af0_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0
zipp conda-forge/noarch::zipp-3.20.2-pyhd8ed1ab_0
zlib conda-forge/linux-aarch64::zlib-1.2.13-h68df207_6
zstd conda-forge/linux-aarch64::zstd-1.5.6-h02f22dd_0
The following packages will be DOWNGRADED:
libsqlite 3.46.1-hc4a20ef_0 --> 3.46.0-hf51ef55_0
libzlib 1.3.1-h68df207_1 --> 1.2.13-h68df207_6
sqlite 3.46.1-h578a6b9_0 --> 3.38.2-hc74f5b8_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.8.30-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_1
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc conda-forge/linux-aarch64::libgcc-14.1.0-he277a41_1
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.1.0-he9431aa_1
libgomp conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_1
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.46.1-hc4a20ef_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.1.0-h3f4de04_1
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-hf1166c9_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1
ncurses conda-forge/linux-aarch64::ncurses-6.5-hcccb83c_1
openssl conda-forge/linux-aarch64::openssl-3.3.2-h86ecc28_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.46.1-h578a6b9_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested anndata 0.7.6**
- package python-3.7.10-h47f6e27_104_cpython requires sqlite >=3.36.0,<4.0a0, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ anndata 0.7.6** does not exist (perhaps a typo or a missing channel);
├─ h5py 3.2.1** is installable with the potential options
│ ├─ h5py 3.2.1 would require
│ │ └─ python_abi 3.7.* *_cp37m with the potential options
│ │ ├─ python_abi 3.7, which can be installed;
│ │ └─ python_abi 3.7 would require
│ │ └─ python 3.7.* *_cpython, which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7] would require
│ │ │ └─ sqlite >=3.36.0,<4.0a0 , which can be installed;
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12] would require
│ │ ├─ pypy3.8 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ │ ├─ pypy3.9 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ └─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9] would require
│ │ │ └─ sqlite >=3.37.0,<4.0a0 , which can be installed;
│ │ └─ python 3.9.13 would require
│ │ └─ sqlite >=3.38.5,<4.0a0 , which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ └─ h5py 3.2.1 would require
│ ├─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9], which can be installed (as previously explained);
│ │ └─ python 3.9.13, which can be installed (as previously explained);
│ └─ python_abi 3.9.* *_cp39, which can be installed;
├─ python 3.7.10.*,3.7.10.* is installable with the potential options
│ ├─ python 3.7.10 conflicts with any installable versions previously reported;
│ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ └─ python 3.7.10 would require
│ └─ python_abi 3.7.* *_cp37m, which conflicts with any installable versions previously reported;
├─ scipy 1.6.3** is installable with the potential options
│ ├─ scipy 1.6.3 would require
│ │ └─ python_abi 3.7 *_pypy37_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy 1.6.3 would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ └─ scipy 1.6.3 would require
│ ├─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9], which can be installed (as previously explained);
│ │ └─ python 3.9.13, which can be installed (as previously explained);
│ └─ python_abi 3.9.* *_cp39, which can be installed;
└─ sqlite 3.35.5** is not installable because it conflicts with any installable versions previously reported.
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.8.30-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_1
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc conda-forge/linux-aarch64::libgcc-14.1.0-he277a41_1
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.1.0-he9431aa_1
libgomp conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_1
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.46.1-hc4a20ef_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.1.0-h3f4de04_1
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-hf1166c9_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1
ncurses conda-forge/linux-aarch64::ncurses-6.5-hcccb83c_1
openssl conda-forge/linux-aarch64::openssl-3.3.2-h86ecc28_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.46.1-h578a6b9_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.3.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested anndata 0.7.6**
- package python-3.7.10-h47f6e27_104_cpython requires sqlite >=3.36.0,<4.0a0, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ anndata 0.7.6** does not exist (perhaps a typo or a missing channel);
├─ h5py 3.2.1** is installable with the potential options
│ ├─ h5py 3.2.1 would require
│ │ └─ python_abi 3.7.* *_cp37m with the potential options
│ │ ├─ python_abi 3.7, which can be installed;
│ │ └─ python_abi 3.7 would require
│ │ └─ python 3.7.* *_cpython, which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7] would require
│ │ │ └─ sqlite >=3.36.0,<4.0a0 , which can be installed;
│ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12] would require
│ │ ├─ pypy3.8 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ │ ├─ pypy3.9 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ │ └─ sqlite >=3.37.1,<4.0a0 , which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ └─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9] would require
│ │ │ └─ sqlite >=3.37.0,<4.0a0 , which can be installed;
│ │ └─ python 3.9.13 would require
│ │ └─ sqlite >=3.38.5,<4.0a0 , which can be installed;
│ ├─ h5py 3.2.1 would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ └─ h5py 3.2.1 would require
│ ├─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9], which can be installed (as previously explained);
│ │ └─ python 3.9.13, which can be installed (as previously explained);
│ └─ python_abi 3.9.* *_cp39, which can be installed;
├─ python 3.7.10.*,3.7.10.* is installable with the potential options
│ ├─ python 3.7.10 conflicts with any installable versions previously reported;
│ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ └─ python 3.7.10 would require
│ └─ python_abi 3.7.* *_cp37m, which conflicts with any installable versions previously reported;
├─ scipy 1.6.3** is installable with the potential options
│ ├─ scipy 1.6.3 would require
│ │ └─ python_abi 3.7 *_pypy37_pp73, which conflicts with any installable versions previously reported;
│ ├─ scipy 1.6.3 would require
│ │ ├─ python >=3.8,<3.9.0a0 with the potential options
│ │ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ │ ├─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ │ │ └─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ └─ scipy 1.6.3 would require
│ ├─ python >=3.9,<3.10.0a0 with the potential options
│ │ ├─ python [3.7.10|3.8.10|3.8.12|3.9.6|3.9.7], which can be installed (as previously explained);
│ │ ├─ python [3.8.12|3.8.13|3.9.10|3.9.12], which can be installed (as previously explained);
│ │ ├─ python [3.9.0|3.9.1|...|3.9.5], which can be installed;
│ │ ├─ python [3.9.10|3.9.9], which can be installed (as previously explained);
│ │ └─ python 3.9.13, which can be installed (as previously explained);
│ └─ python_abi 3.9.* *_cp39, which can be installed;
└─ sqlite 3.35.5** is not installable because it conflicts with any installable versions previously reported.
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.17.2/zellkonverter/1.15.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
[ FAIL 2 | WARN 30 | SKIP 4 | PASS 143 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-read.R:178:5', 'test-read.R:212:5',
'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:54:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:62:5'): Reading H5AD works with version 0.7.6 ───────────
Error: one or more Python packages failed to install [error code 1]
Backtrace:
▆
1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:62:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
── Error ('test-write.R:136:5'): writeH5AD works as expected with version 0.7.6 ──
Error: one or more Python packages failed to install [error code 1]
Backtrace:
▆
1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:136:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
[ FAIL 2 | WARN 30 | SKIP 4 | PASS 143 ]
Error: Test failures
Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 28.257 | 1.743 | 30.737 | |
| AnnData-Environment | 0.008 | 0.000 | 0.008 | |
| readH5AD | 1.330 | 0.111 | 1.453 | |
| setZellkonverterVerbose | 0.001 | 0.000 | 0.000 | |
| writeH5AD | 5.987 | 0.532 | 6.536 | |