Luke Zappia
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/zellkonverter |
| git_branch: devel |
| git_last_commit: a64ff2d |
| git_last_commit_date: 2024-03-25 08:50:20 -0400 (Mon, 25 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:31 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2265/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.13.3 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.13.3 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings zellkonverter_1.13.3.tar.gz |
| StartedAt: 2024-03-28 10:51:07 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 11:04:39 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 811.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings zellkonverter_1.13.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.13.3’
* 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-3.19-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 29.958 1.278 31.843
writeH5AD 5.736 0.348 6.169
* 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:133:5'): 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:133:5
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 3 | PASS 134 ]
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-3.19-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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
0.188 0.046 0.217
zellkonverter.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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 methods overwritten by 'zellkonverter':
method from
py_to_r.numpy.ndarray reticulate
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
>
> test_check("zellkonverter")
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-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-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
wheel conda-forge/noarch::wheel-0.43.0-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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- anndata=0.7.6
Current channels:
- https://conda.anaconda.org/conda-forge/linux-aarch64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-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-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
wheel conda-forge/noarch::wheel-0.43.0-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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- anndata=0.7.6
Current channels:
- https://conda.anaconda.org/conda-forge/linux-aarch64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/home/biocbuild/.cache/R/basilisk/1.15.5/zellkonverter/1.13.3/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(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
[ FAIL 2 | WARN 24 | SKIP 3 | PASS 134 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:155:5', 'test-zzz-anndata.R:6:5',
'test-zzz-anndata.R:54:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:39:5'): 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:39:5
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:133:5'): 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:133:5
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 3 | PASS 134 ]
Error: Test failures
Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 29.958 | 1.278 | 31.843 | |
| AnnData-Environment | 0.007 | 0.000 | 0.007 | |
| readH5AD | 1.299 | 0.024 | 1.336 | |
| setZellkonverterVerbose | 0.000 | 0.000 | 0.001 | |
| writeH5AD | 5.736 | 0.348 | 6.169 | |