Luke Zappia
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:32 -0500 (Sat, 09 Nov 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" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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. |
| Package: zellkonverter |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.16.0.tar.gz |
| StartedAt: 2024-11-09 16:27:00 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 16:36:10 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 550.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zellkonverter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘/Users/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 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 7.917 0.851 10.292
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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-apple-darwin20
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
0.070 0.016 0.083
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
Retrieving notices: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.6
added / updated specs:
- python=3.12.2
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.12.2 |hdf0ec26_0_cpython 12.5 MB conda-forge
------------------------------------------------------------
Total: 12.5 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0
libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1
openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0
pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0
python conda-forge/osx-arm64::python-3.12.2-hdf0ec26_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.6
added / updated specs:
- anndata=0.10.6
- h5py=3.10.0
- hdf5=1.14.3
- natsort=8.4.0
- numpy=1.26.4
- packaging=24.0
- pandas=2.2.1
- python[version='3.12.2.*,3.12.2.*']
- scipy=1.12.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
anndata-0.10.6 | pyhd8ed1ab_0 96 KB conda-forge
c-ares-1.34.3 | h5505292_0 175 KB conda-forge
h5py-3.10.0 |nompi_py312hac0f6fd_101 1.0 MB conda-forge
numpy-1.26.4 | py312h8442bc7_0 5.8 MB conda-forge
pandas-2.2.1 | py312h88edd18_0 13.8 MB conda-forge
scipy-1.12.0 | py312h9d7df2b_2 14.8 MB conda-forge
------------------------------------------------------------
Total: 35.7 MB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.10.6-pyhd8ed1ab_0
array-api-compat conda-forge/noarch::array-api-compat-1.9.1-pyhd8ed1ab_0
c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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/osx-arm64::h5py-3.10.0-nompi_py312hac0f6fd_101
hdf5 conda-forge/osx-arm64::hdf5-1.14.3-nompi_hec07895_105
krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0
libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0
libblas conda-forge/osx-arm64::libblas-3.9.0-25_osxarm64_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-25_osxarm64_openblas
libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0
libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0
libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
liblapack conda-forge/osx-arm64::liblapack-3.9.0-25_osxarm64_openblas
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0
libopenblas conda-forge/osx-arm64::libopenblas-0.3.28-openmp_hf332438_1
libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/osx-arm64::numpy-1.26.4-py312h8442bc7_0
packaging conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0
pandas conda-forge/osx-arm64::pandas-2.2.1-py312h88edd18_0
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/osx-arm64::python_abi-3.12-5_cp312
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/osx-arm64::scipy-1.12.0-py312h9d7df2b_2
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.2
added / updated specs:
- python=3.11.5
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.11.5 |h47c9636_0_cpython 14.0 MB conda-forge
------------------------------------------------------------
Total: 14.0 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0
libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1
openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0
pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0
python conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/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
---------------------------|-----------------
anndata-0.10.2 | pyhd8ed1ab_0 94 KB conda-forge
h5py-3.10.0 |nompi_py311h393cb7e_100 1.0 MB conda-forge
hdf5-1.14.2 |nompi_h3aba7b3_100 3.3 MB conda-forge
numpy-1.26.0 | py311hb8f3215_0 6.5 MB conda-forge
packaging-23.2 | pyhd8ed1ab_0 48 KB conda-forge
pandas-2.1.1 | py311h9e438b8_1 13.7 MB conda-forge
scipy-1.11.3 | py311h93d07a4_1 14.4 MB conda-forge
------------------------------------------------------------
Total: 39.0 MB
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-1.9.1-pyhd8ed1ab_0
c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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/osx-arm64::h5py-3.10.0-nompi_py311h393cb7e_100
hdf5 conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100
krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0
libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0
libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0
libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0
libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0
libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_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/osx-arm64::python_abi-3.11-5_cp311
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.9.2
added / updated specs:
- python=3.11.5
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0
libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1
openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0
pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0
python conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/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 packages will be downloaded:
package | build
---------------------------|-----------------
anndata-0.9.2 | pyhd8ed1ab_0 85 KB conda-forge
h5py-3.9.0 |nompi_py311h4794d1a_103 1.1 MB conda-forge
------------------------------------------------------------
Total: 1.2 MB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.9.2-pyhd8ed1ab_0
c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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/osx-arm64::h5py-3.9.0-nompi_py311h4794d1a_103
hdf5 conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100
krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0
libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0
libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0
libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0
libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0
libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0
natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
numpy conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pandas conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_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/osx-arm64::python_abi-3.11-5_cp311
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.8.0
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.8.13 |hd3575e6_0_cpython 12.3 MB conda-forge
------------------------------------------------------------
Total: 12.3 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1
openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0
pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0
python conda-forge/osx-arm64::python-3.8.13-hd3575e6_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0
sqlite conda-forge/osx-arm64::sqlite-3.47.0-hcd14bea_1
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: osx-arm64
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: 24.9.2
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/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
---------------------------|-----------------
anndata-0.8.0 | pyhd8ed1ab_1 74 KB conda-forge
h5py-3.6.0 |nompi_py38hacf61ce_100 1.1 MB conda-forge
importlib_metadata-8.5.0 | hd8ed1ab_0 9 KB conda-forge
natsort-8.1.0 | pyhd8ed1ab_0 35 KB conda-forge
numpy-1.22.3 | py38h4084d66_2 5.7 MB conda-forge
packaging-21.3 | pyhd8ed1ab_0 36 KB conda-forge
pandas-1.4.2 | py38h6724fcd_2 11.6 MB conda-forge
scipy-1.7.3 | py38h7b4f323_1 19.1 MB conda-forge
sqlite-3.38.2 | h7e3ccbd_0 1.7 MB conda-forge
------------------------------------------------------------
Total: 39.3 MB
The following NEW packages will be INSTALLED:
anndata conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1
c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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/osx-arm64::h5py-3.6.0-nompi_py38hacf61ce_100
hdf5 conda-forge/osx-arm64::hdf5-1.12.1-nompi_hd9dbc9e_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
krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0
libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
libcurl conda-forge/osx-arm64::libcurl-8.8.0-h7b6f9a7_1
libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0
libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1
libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0
natsort conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0
numpy conda-forge/osx-arm64::numpy-1.22.3-py38h4084d66_2
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pandas conda-forge/osx-arm64::pandas-1.4.2-py38h6724fcd_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/osx-arm64::python_abi-3.8-5_cp38
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
scipy conda-forge/osx-arm64::scipy-1.7.3-py38h7b4f323_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/osx-arm64::zlib-1.2.13-hfb2fe0b_6
zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0
The following packages will be DOWNGRADED:
libsqlite 3.47.0-hbaaea75_1 --> 3.46.0-hfb93653_0
libzlib 1.3.1-h8359307_2 --> 1.2.13-hfb2fe0b_6
sqlite 3.47.0-hcd14bea_1 --> 3.38.2-h7e3ccbd_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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.
[ FAIL 0 | WARN 28 | SKIP 6 | PASS 152 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• 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'
• On Mac aarch64 (2): 'test-read.R:70:5', 'test-write.R:164:5'
[ FAIL 0 | WARN 28 | SKIP 6 | PASS 152 ]
>
> proc.time()
user system elapsed
122.896 42.731 258.488
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 7.917 | 0.851 | 10.292 | |
| AnnData-Environment | 0.002 | 0.001 | 0.003 | |
| readH5AD | 0.274 | 0.021 | 0.298 | |
| setZellkonverterVerbose | 0.001 | 0.000 | 0.000 | |
| writeH5AD | 1.156 | 0.135 | 1.306 | |