[Bioc-devel] hermes Bioconductor

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 at 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 at 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 at r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

--
*Dr. Daniel Saban?s Bov?*
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.

--
*Dr. Daniel Saban?s Bov?*
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.

        [[alternative HTML version deleted]]

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 at 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 at 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 at 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 at r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

--
*Dr. Daniel Saban?s Bov?*
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.

--
*Dr. Daniel Saban?s Bov?*
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.

        [[alternative HTML version deleted]]

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 at 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 at 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 at 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 at 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 at r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

--
*Dr. Daniel Saban?s Bov?*
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.

--
*Dr. Daniel Saban?s Bov?*
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.

        [[alternative HTML version deleted]]

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