[Bioc-devel] Devel build report errors

[Martin Grigorov]

On Mon, Jul 8, 2024 at 11:21 AM Martin Grigorov <mgrigorov using apache.org>
wrote:

> Hi,
>
>
> On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira <
> rodrigo.arcoverdi using 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]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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