Hi all, We are trying to implement a new tool in scifer package, and I have a few questions about compatibility and build reports. 1. I am getting the following error in build for Linux (openEuler 22.03 LTS-SP1) / aarch64. ``` error: dependency ?sangerseqR? is not available for package ?scifer? ``` However, when I check the devel build report for sangerseqR it seems to be passing without errors and only its dependent packages are getting this error. 1. Besides that, we are having the same error in Windows and macOS 13.6.5 Ventura. This new function we are trying to implement relies on a conda environment (basilisk). The issue is that the packages we need in conda are not available for all the platforms so I get an error that the packages we need are not found. ``` PackagesNotFoundError: The following packages are not available from current channels: - dnaio=1.2.1 - igblast=1.22.0 ``` 1. Finally, is it mandatory to be compatible with windows? Hope someone can help ? Best regards, Rodrigo
[Bioc-devel] Devel build report errors
4 messages · Rodrigo Arcoverde Cerveira, Martin Grigorov, Vincent Carey
Hi, On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira <
rodrigo.arcoverdi at gmail.com> wrote:
Hi all, We are trying to implement a new tool in scifer package, and I have a few questions about compatibility and build reports. 1. I am getting the following error in build for Linux (openEuler 22.03 LTS-SP1) / aarch64. ``` error: dependency ?sangerseqR? is not available for package ?scifer? ``` However, when I check the devel build report for sangerseqR it seems to be passing without errors and only its dependent packages are getting this error.
I will check what?s issue on openEuler! The installation of some packages timed out after the update of R to 4.4.1. Everything should be back to normal in the next few days!
1. Besides that, we are having the same error in Windows and macOS
13.6.5 Ventura. This new function we are trying to implement relies on a
conda environment (basilisk). The issue is that the packages we need in
conda are not available for all the platforms so I get an error that the
packages we need are not found.
```
PackagesNotFoundError: The following packages are not available from
current channels:
- dnaio=1.2.1
- igblast=1.22.0
```
1. Finally, is it mandatory to be compatible with windows?
Hope someone can help ?
Best regards,
Rodrigo
[[alternative HTML version deleted]]
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On Mon, Jul 8, 2024 at 11:21?AM Martin Grigorov <mgrigorov at apache.org> wrote:
Hi, On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira < rodrigo.arcoverdi at gmail.com> wrote:
Hi all, We are trying to implement a new tool in scifer package, and I have a few questions about compatibility and build reports. 1. I am getting the following error in build for Linux (openEuler 22.03 LTS-SP1) / aarch64. ``` error: dependency ?sangerseqR? is not available for package ?scifer? ``` However, when I check the devel build report for sangerseqR it seems to be passing without errors and only its dependent packages are getting this error.
I will check what?s issue on openEuler! The installation of some packages timed out after the update of R to 4.4.1. Everything should be back to normal in the next few days!
BiocManager::install(c("sangerseqR"))
Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Installing package(s) 'sangerseqR' trying URL ' https://bioconductor.org/packages/3.20/bioc/src/contrib/sangerseqR_1.41.0.tar.gz ' Content type 'application/x-gzip' length 2903474 bytes (2.8 MB) ================================================== downloaded 2.8 MB * installing *source* package ?sangerseqR? ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sangerseqR) It should be good now!
1. Besides that, we are having the same error in Windows and macOS
13.6.5 Ventura. This new function we are trying to implement relies on a
conda environment (basilisk). The issue is that the packages we need in
conda are not available for all the platforms so I get an error that the
packages we need are not found.
```
PackagesNotFoundError: The following packages are not available from
current channels:
- dnaio=1.2.1
- igblast=1.22.0
```
1. Finally, is it mandatory to be compatible with windows?
Hope someone can help ?
Best regards,
Rodrigo
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Sorry to hear you are having problems. I tried to run the igblast example in a current installation. I set BASILISK_MINICONDA_VERSION=py311_23.11.0-2 to get faster mamba resolution (but this setting cannot be used on windows AFAIK, so is not used in build system) and I hit warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY failed LibMambaUnsatisfiableError: Encountered problems while solving: - package dnaio-1.2.1-py310h7c593f9_0 requires xopen >=1.4.0, but none of the providers can be installed Could not solve for environment specs The following package could not be installed ?? dnaio 1.2.1** is not installable because it requires ?? xopen >=1.4.0 , which conflicts with any installable versions previously reported. Now I don't claim this to be representative of the build system but it does illustrate an issue you will have to deal with. It is valuable to use the python session-info (pypi) to determine the active versions of all dependencies after a successful run of igblast in your package. Then pin them all in your basilisk.R As for abandoning the windows platform, it can be done but you lose access to a large potential user base. On Mon, Jul 8, 2024 at 4:14?AM Rodrigo Arcoverde Cerveira <
rodrigo.arcoverdi at gmail.com> wrote:
Hi all,
We are trying to implement a new tool in scifer package, and I have a few
questions about compatibility and build reports.
1. I am getting the following error in build for Linux (openEuler 22.03
LTS-SP1) / aarch64.
```
error: dependency ?sangerseqR? is not available for package ?scifer?
```
However, when I check the devel build report for sangerseqR it seems to be
passing without errors and only its dependent packages are getting this
error.
1. Besides that, we are having the same error in Windows and macOS
13.6.5 Ventura. This new function we are trying to implement relies on a
conda environment (basilisk). The issue is that the packages we need in
conda are not available for all the platforms so I get an error that the
packages we need are not found.
```
PackagesNotFoundError: The following packages are not available from
current channels:
- dnaio=1.2.1
- igblast=1.22.0
```
1. Finally, is it mandatory to be compatible with windows?
Hope someone can help ?
Best regards,
Rodrigo
[[alternative HTML version deleted]]
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