date:20240112

Re: [Bioc-devel] hermes Bioconductor

2024-01-12 Thread Sabanes Bove, Daniel via Bioc-devel

Thanks Vincent,
that helped!
Naive question: Would it not be expected behavior that when we are in the
BioC devel docker container, we automatically install the GitHub devel
branch versions of the packages? (Not sure how that would be easy to
default as behavior but I think it would be a nice feature)


On Fri, Jan 12, 2024 at 4:22 PM Vincent Carey 
wrote:

> 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 
> 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-8LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8LC_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] stats4stats graphics  grDevices utils datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] S4Vectors_0.41.3BiocGenerics_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@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_b...@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 <
>>> > bioconductorcoret...@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@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
>>> >
>>> > *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 mes

Re: [Bioc-devel] hermes Bioconductor

2024-01-12 Thread 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 
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-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_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] stats4stats graphics  grDevices utils datasets  methods
> [8] base
>
> other attached packages:
> [1] S4Vectors_0.41.3BiocGenerics_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@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_b...@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 <
>> > bioconductorcoret...@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@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
>> >
>> > *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 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 messag

Re: [Bioc-devel] hermes Bioconductor

2024-01-12 Thread 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-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
[1] S4Vectors_0.41.3BiocGenerics_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@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_b...@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 <
> > bioconductorcoret...@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@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
> >
> > *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 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.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information i

Re: [Bioc-devel] hermes Bioconductor

2024-01-12 Thread Sabanes Bove, Daniel via Bioc-devel

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_b...@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 <
> bioconductorcoret...@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/
>> 
>>
>> If you have further questions or concerns please reach out on the
>> bioc-devel@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
>
> *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 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.

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] hermes Bioconductor

Re: [Bioc-devel] hermes Bioconductor

Re: [Bioc-devel] hermes Bioconductor

Re: [Bioc-devel] hermes Bioconductor

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