| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:21 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 2261/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.12.1 (landing page) Luke Zappia
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | NA | ||||||||
|
To the developers/maintainers of the zellkonverter package: - 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: 1.12.1 |
| 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_1.12.1.tar.gz |
| StartedAt: 2024-04-18 07:54:17 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 08:06:24 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 727.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/zellkonverter.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.12.1’
* 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 ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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 36.444 4.115 48.155
writeH5AD 11.735 0.982 15.560
* 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: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
Backtrace:
▆
1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:102:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate::conda_create(...)
8. └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
[ FAIL 2 | WARN 24 | SKIP 3 | PASS 125 ]
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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
0.236 0.072 0.315
zellkonverter.Rcheck/tests/testthat.Rout.fail
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 methods overwritten by 'zellkonverter':
method from
py_to_r.numpy.ndarray reticulate
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... failed
PackagesNotFoundError: The following packages are not available from current channels:
- python=3.7.10
Current channels:
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-arm64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-arm64
- 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.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
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... failed
PackagesNotFoundError: The following packages are not available from current channels:
- python=3.7.10
Current channels:
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-arm64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-arm64
- 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.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/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(
[ FAIL 2 | WARN 24 | SKIP 3 | PASS 125 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:147:5', 'test-zzz-anndata.R:6:5',
'test-zzz-anndata.R:54:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:31:5'): Reading H5AD works with version 0.7.6 ───────────
Error: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
Backtrace:
▆
1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:31:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate::conda_create(...)
8. └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-write.R:102:5'): writeH5AD works as expected with version 0.7.6 ──
Error: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
Backtrace:
▆
1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:102:5
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
6. └─reticulate::conda_install(...)
7. └─reticulate::conda_create(...)
8. └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
[ FAIL 2 | WARN 24 | SKIP 3 | PASS 125 ]
Error: Test failures
Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 36.444 | 4.115 | 48.155 | |
| AnnData-Environment | 0.006 | 0.002 | 0.008 | |
| readH5AD | 1.623 | 0.129 | 1.899 | |
| setZellkonverterVerbose | 0.000 | 0.001 | 0.002 | |
| writeH5AD | 11.735 | 0.982 | 15.560 | |