| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:53 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the zellkonverter package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2167/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.9.0 (landing page) Luke Zappia
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: zellkonverter |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings zellkonverter_1.9.0.tar.gz |
| StartedAt: 2023-02-28 18:51:47 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 19:04:51 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 783.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings zellkonverter_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/zellkonverter.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.17-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 R 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 38.878 3.835 53.009
writeH5AD 14.221 1.775 23.704
* 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:40'): 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:40:4
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
[ FAIL 2 | WARN 21 | SKIP 3 | PASS 94 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘zellkonverter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
0.202 0.032 0.217
zellkonverter.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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.numpy.ndarray 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: /home/biocbuild/.cache/R/basilisk/1.11.2/zellkonverter/1.9.0/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_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-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-3.0.8-hb4cce97_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
wheel conda-forge/noarch::wheel-0.38.4-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
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/zellkonverter/1.9.0/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
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.
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/1.11.2/zellkonverter/1.9.0/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_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-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-3.0.8-hb4cce97_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
wheel conda-forge/noarch::wheel-0.38.4-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
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/zellkonverter/1.9.0/zellkonverterAnnDataEnv-0.7.6
added / updated specs:
- python=3.7.10
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
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.
[ FAIL 2 | WARN 21 | SKIP 3 | PASS 94 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (3)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:14'): 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:14:4
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
── Error ('test-write.R:40'): 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:40:4
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate:::stopf(fmt, result)
[ FAIL 2 | WARN 21 | SKIP 3 | PASS 94 ]
Error: Test failures
Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 38.878 | 3.835 | 53.009 | |
| AnnData-Environment | 0.017 | 0.004 | 0.021 | |
| readH5AD | 1.647 | 0.096 | 1.755 | |
| setZellkonverterVerbose | 0.014 | 0.004 | 0.018 | |
| writeH5AD | 14.221 | 1.775 | 23.704 | |