[Bioc-devel] hermes Bioconductor

[Vincent Carey]

Oops, I misread this, and can reproduce.  You can clone the current source
out of github in the
container and install it there.

docker run -ti bioconductor/bioconductor_docker:devel bash

   3  git clone https://github.com/bioconductor/S4Arrays
    4  R CMD INSTALL S4Arrays

On Fri, Jan 12, 2024 at 9:51 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> I cannot reproduce this with a current pull of the devel container.
> BiocManager installation
> of S4Vectors succeeded.  Please provide the version given in environment
> variable
> BIOCONDUCTOR_DOCKER_VERSION, I used 3.19.13
>
> R Under development (unstable) (2024-01-03 r85769)
> Platform: x86_64-pc-linux-gnu
> Running under: Ubuntu 22.04.3 LTS
>
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;
>  LAPACK version 3.10.0
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> time zone: Etc/UTC
> tzcode source: system (glibc)
>
> attached base packages:
> [1] stats4    stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] S4Vectors_0.41.3    BiocGenerics_0.49.1
>
> loaded via a namespace (and not attached):
> [1] BiocManager_1.30.22 compiler_4.4.0      tools_4.4.0
>
> On Fri, Jan 12, 2024 at 9:30 AM Sabanes Bove, Daniel via Bioc-devel <
> bioc-devel using r-project.org> wrote:
>
>> 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
>> > page) and go.roche.com/statistical-engineering-presentation (public)
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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
>>
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