Luke Zappia
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/zellkonverter |
| git_branch: RELEASE_3_20 |
| git_last_commit: d492566 |
| git_last_commit_date: 2024-10-29 10:49:36 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:36 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 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 2283/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.16.0 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2025-04-01 11:50:02 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 12:00:08 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 605.8 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.16.0’
* 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 19.459 1.118 21.396
* 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:167:5'): 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:167:5
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 24 | SKIP 4 | PASS 152 ]
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-4.4.3/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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
0.199 0.023 0.209
zellkonverter.Rcheck/tests/testthat.Rout.fail
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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/1.18.0/zellkonverter/1.16.0/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-2025.1.31-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1
libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2
libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2
liblzma conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0
liblzma-devel conda-forge/linux-aarch64::liblzma-devel-5.6.4-h86ecc28_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_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-h8382b9d_2
setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.49.1-h578a6b9_2
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-5.6.4-h2dbfc1b_0
xz-gpl-tools conda-forge/linux-aarch64::xz-gpl-tools-5.6.4-h2dbfc1b_0
xz-tools conda-forge/linux-aarch64::xz-tools-5.6.4-h86ecc28_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: 25.3.0
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**
- nothing provides libsqlite 3.49.0 h5eb1b54_0 needed by sqlite-3.49.0-h578a6b9_0
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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ ├─ sqlite 3.49.0 would require
│ │ │ │ └─ libsqlite 3.49.0 h5eb1b54_0, which does not exist (perhaps a missing channel);
│ │ │ ├─ sqlite 3.36.0, which can be installed;
│ │ │ └─ sqlite 3.37.0, 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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ ├─ pypy3.9 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ └─ sqlite >=3.37.1,<4.0a0 with the potential options
│ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ ├─ 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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ ├─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ │ └─ sqlite 3.37.0, which can be installed;
│ │ └─ python 3.9.13 would require
│ │ └─ sqlite >=3.38.5,<4.0a0 with the potential options
│ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ ├─ 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.
sys:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
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/1.18.0/zellkonverter/1.16.0/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-2025.1.31-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1
libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2
libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2
liblzma conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0
liblzma-devel conda-forge/linux-aarch64::liblzma-devel-5.6.4-h86ecc28_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_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-h8382b9d_2
setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.49.1-h578a6b9_2
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-5.6.4-h2dbfc1b_0
xz-gpl-tools conda-forge/linux-aarch64::xz-gpl-tools-5.6.4-h2dbfc1b_0
xz-tools conda-forge/linux-aarch64::xz-tools-5.6.4-h86ecc28_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: 25.3.0
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**
- nothing provides libsqlite 3.49.0 h5eb1b54_0 needed by sqlite-3.49.0-h578a6b9_0
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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ ├─ sqlite 3.49.0 would require
│ │ │ │ └─ libsqlite 3.49.0 h5eb1b54_0, which does not exist (perhaps a missing channel);
│ │ │ ├─ sqlite 3.36.0, which can be installed;
│ │ │ └─ sqlite 3.37.0, 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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ ├─ pypy3.9 7.3.8.* , which requires
│ │ │ └─ sqlite >=3.37.1,<4.0a0 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ └─ sqlite >=3.37.1,<4.0a0 with the potential options
│ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ ├─ 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 with the potential options
│ │ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ │ ├─ sqlite [3.37.1|3.38.2|3.38.3|3.38.4], which can be installed;
│ │ │ ├─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ │ │ └─ sqlite 3.37.0, which can be installed;
│ │ └─ python 3.9.13 would require
│ │ └─ sqlite >=3.38.5,<4.0a0 with the potential options
│ │ ├─ sqlite [3.38.5|3.39.0|...|3.49.1], which can be installed;
│ │ └─ sqlite 3.49.0, which cannot be installed (as previously explained);
│ ├─ 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.
[ FAIL 2 | WARN 24 | SKIP 4 | PASS 152 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-read.R:192:5', 'test-read.R:234:5',
'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:63:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:72:5'): 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:72:5
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:167:5'): 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:167:5
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 24 | SKIP 4 | PASS 152 ]
Error: Test failures
Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 19.459 | 1.118 | 21.396 | |
| AnnData-Environment | 0.006 | 0.000 | 0.006 | |
| readH5AD | 0.932 | 0.051 | 0.992 | |
| setZellkonverterVerbose | 0 | 0 | 0 | |
| writeH5AD | 2.575 | 0.260 | 2.925 | |