[Bioc-devel] hermes Bioconductor

[Vincent Carey]

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)
> > www.roche.com
> >
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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
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