Luke Zappia
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/zellkonverter |
| git_branch: RELEASE_3_19 |
| git_last_commit: c90c58a |
| git_last_commit_date: 2024-06-21 04:52:52 -0400 (Fri, 21 Jun 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:40 -0400 (Tue, 25 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 2295/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.14.1 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: zellkonverter |
| Version: 1.14.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings zellkonverter_1.14.1.tar.gz |
| StartedAt: 2024-06-24 05:09:12 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 05:42:40 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 2008.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zellkonverter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings zellkonverter_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.14.1’
* 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 22.021 16.232 38.512
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
0.158 0.032 0.177
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
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: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.2
added / updated specs:
- python=3.11.5
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7
libexpat conda-forge/linux-64::libexpat-2.6.2-h59595ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_13
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_13
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.11.5-hab00c5b_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
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... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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 NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.10.2-pyhd8ed1ab_0
array-api-compat conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0
c-ares conda-forge/linux-64::c-ares-1.28.1-hd590300_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-1.2.0-pyhd8ed1ab_2
h5py conda-forge/linux-64::h5py-3.10.0-nompi_py311h3839ddf_100
hdf5 conda-forge/linux-64::hdf5-1.14.2-nompi_h4f84152_100
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0
libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_13
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_13
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_13
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.26.0-py311h64a7726_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/linux-64::pandas-2.1.1-py311h320fe9a_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.11-4_cp311
pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
scipy conda-forge/linux-64::scipy-1.11.3-py311h64a7726_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_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 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: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.9.2
added / updated specs:
- python=3.11.5
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7
libexpat conda-forge/linux-64::libexpat-2.6.2-h59595ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_13
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_13
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.11.5-hab00c5b_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
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... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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-64::c-ares-1.28.1-hd590300_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-64::h5py-3.9.0-nompi_py311h3839ddf_103
hdf5 conda-forge/linux-64::hdf5-1.14.2-nompi_h4f84152_100
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0
libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_13
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_13
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_13
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.26.0-py311h64a7726_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/linux-64::pandas-2.1.1-py311h320fe9a_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.11-4_cp311
pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
scipy conda-forge/linux-64::scipy-1.11.3-py311h64a7726_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_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 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: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.8.0
added / updated specs:
- python=3.8.13
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_13
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_13
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.8.13-ha86cf86_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
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... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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-7.2.1 | pyha770c72_0 27 KB conda-forge
importlib_metadata-7.2.1 | hd8ed1ab_0 9 KB conda-forge
typing_extensions-4.12.2 | pyha770c72_0 39 KB conda-forge
zipp-3.19.2 | pyhd8ed1ab_0 20 KB conda-forge
------------------------------------------------------------
Total: 96 KB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1
c-ares conda-forge/linux-64::c-ares-1.28.1-hd590300_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-64::h5py-3.6.0-nompi_py38hfbb2109_100
hdf5 conda-forge/linux-64::hdf5-1.12.1-nompi_h4df4325_104
importlib-metadata conda-forge/noarch::importlib-metadata-7.2.1-pyha770c72_0
importlib_metadata conda-forge/noarch::importlib_metadata-7.2.1-hd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_13
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_13
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_13
natsort conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.22.3-py38h99721a1_2
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pandas conda-forge/linux-64::pandas-1.4.2-py38h47df419_2
pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.8-4_cp38
pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
scipy conda-forge/linux-64::scipy-1.7.3-py38h8ce737c_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-3.19.2-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0
The following packages will be DOWNGRADED:
libzlib 1.3.1-h4ab18f5_1 --> 1.2.13-h4ab18f5_6
sqlite 3.46.0-h6d4b2fc_0 --> 3.38.2-h4ff8645_0
Downloading and Extracting Packages
importlib-metadata-7 | 27 KB | | 0%
importlib-metadata-7 | 27 KB | #####9 | 59%
importlib-metadata-7 | 27 KB | ########## | 100%
importlib_metadata-7 | 9 KB | | 0%
importlib_metadata-7 | 9 KB | ########## | 100%
importlib_metadata-7 | 9 KB | ########## | 100%
zipp-3.19.2 | 20 KB | | 0%
zipp-3.19.2 | 20 KB | ########## | 100%
zipp-3.19.2 | 20 KB | ########## | 100%
typing_extensions-4. | 39 KB | | 0%
typing_extensions-4. | 39 KB | ########## | 100%
typing_extensions-4. | 39 KB | ########## | 100%
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 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: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_13
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_13
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_13
libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.7.10-hf930737_104_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
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... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- anndata=0.7.6
- h5py=3.2.1
- hdf5=1.10.6
- natsort=7.1.1
- numpy=1.20.2
- packaging=20.9
- pandas=1.2.4
- python[version='3.7.10.*,3.7.10.*']
- scipy=1.6.3
- sqlite=3.35.5
The following NEW packages will be INSTALLED:
anndata conda-forge/linux-64::anndata-0.7.6-py37h89c1867_0
c-ares conda-forge/linux-64::c-ares-1.28.1-hd590300_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-64::h5py-3.2.1-nompi_py37ha3df211_100
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
importlib-metadata conda-forge/linux-64::importlib-metadata-4.11.4-py37h89c1867_0
importlib_metadata conda-forge/noarch::importlib_metadata-4.11.4-hd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.20.1-hf9c8cef_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.87.0-h6312ad2_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_13
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_13
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.51.0-hdcd2b5c_0
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libssh2 conda-forge/linux-64::libssh2-1.10.0-haa6b8db_3
natsort conda-forge/noarch::natsort-7.1.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.20.2-py37h038b26d_0
packaging conda-forge/noarch::packaging-20.9-pyh44b312d_0
pandas pkgs/main/linux-64::pandas-1.2.4-py37h2531618_0
pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.7-4_cp37m
pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
scipy conda-forge/linux-64::scipy-1.6.3-py37h29e03ee_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
typing_extensions conda-forge/noarch::typing_extensions-4.7.1-pyha770c72_0
zipp conda-forge/noarch::zipp-3.15.0-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
The following packages will be DOWNGRADED:
libffi 3.4.2-h7f98852_5 --> 3.3-h58526e2_2
libzlib 1.3.1-h4ab18f5_1 --> 1.2.13-h4ab18f5_6
openssl 3.3.1-h4ab18f5_0 --> 1.1.1w-hd590300_0
python 3.7.10-hf930737_104_cpython --> 3.7.10-hffdb5ce_100_cpython
sqlite 3.46.0-h6d4b2fc_0 --> 3.35.5-h74cdb3f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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(
/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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 0 | WARN 28 | SKIP 3 | PASS 152 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:178:5', 'test-zzz-anndata.R:6:5',
'test-zzz-anndata.R:54:5'
[ FAIL 0 | WARN 28 | SKIP 3 | PASS 152 ]
>
> proc.time()
user system elapsed
1552.952 72.554 1775.255
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 22.021 | 16.232 | 38.512 | |
| AnnData-Environment | 0.005 | 0.000 | 0.005 | |
| readH5AD | 0.832 | 0.065 | 0.901 | |
| setZellkonverterVerbose | 0.001 | 0.000 | 0.001 | |
| writeH5AD | 3.913 | 0.898 | 4.815 | |