[Bioc-devel] hermes Bioconductor

[Sabanes Bove, Daniel]

Hello,

I am trying to reproduce a problem with the hermes package on BioC devel.
To this end, I installed docker, and loaded the RStudio session
from bioconductor_docker:devel.
Now the problem is that I cannot install the dependency S4Arrays because
the compilation fails with

array_selection.c: In function ‘C_Lindex2Mindex’:
array_selection.c:352:17: error: format not a string literal and no
format arguments [-Werror=format-security]
  352 |                 error(errmsg_buf());
      |                 ^~~~~
array_selection.c: In function ‘C_Mindex2Lindex’:
array_selection.c:416:17: error: format not a string literal and no
format arguments [-Werror=format-security]
  416 |                 error(errmsg_buf());
      |                 ^~~~~cc1: some warnings being treated as errors


Am I doing something wrong maybe? I expected that S4Arrays should
install just fine because

https://bioconductor.org/checkResults/devel/bioc-LATEST/S4Arrays/

shows that its checks on BioC devel pass, and I assumed that the same
Docker image is used?


Thanks for your help,

best regards

Daniel


On Thu, Jan 11, 2024 at 8:55 PM Daniel Sabanes Bove <
daniel.sabanes_bove using roche.com> wrote:

> Thanks a lot,
> we will look into this immediately.
> Best regards
> Daniel
>
> On Thu, Jan 11, 2024 at 5:37 PM CoreTeam Bioconductor <
> bioconductorcoreteam using gmail.com> wrote:
>
>> Hello Package Maintainer,
>>
>> We would like to bring to your attention that your package is failing in
>> devel across all platforms. This is very problematic. Please investigate
>> the issues and fix the package to avoid deprecation.
>>
>> https://bioconductor.org/checkResults/devel/bioc-LATEST/
>> <https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>
>>
>> If you have further questions or concerns please reach out on the
>> bioc-devel using r-project.org
>>
>> We appreciate your quick attention to this matter
>>
>> Cheers,
>> On behalf of the Bioconductor Core Team
>>
>
>
> --
> *Dr. Daniel Sabanés Bové*
> Senior Principal Data Scientist
>
> F. Hoffmann-La Roche Ltd
> PD Data Sciences - Data Science Acceleration (DSX)
> B. 663
> CH-4070 Basel
> Switzerland
>
> Discover our products at go.roche.com/statistical-engineering (internal
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>
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-- 
*Dr. Daniel Sabanés Bové*
Senior Principal Data Scientist

F. Hoffmann-La Roche Ltd
PD Data Sciences - Data Science Acceleration (DSX)
B. 663
CH-4070 Basel
Switzerland

Discover our products at go.roche.com/statistical-engineering (internal
page) and go.roche.com/statistical-engineering-presentation (public)
www.roche.com

*Confidentiality Note: *This message is intended only for the use of the
named recipient(s) and may contain confidential and/or proprietary
information. If you are not the intended recipient, please contact the
sender and delete this message. Any unauthorized use of the information
contained in this message is prohibited.

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