[Bioc-devel] hermes Bioconductor
Sabanes Bove, Daniel
d@n|e|@@@b@ne@_bove @end|ng |rom roche@com
Fri Jan 12 16:58:33 CET 2024
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 <stvjc using channing.harvard.edu>
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 <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
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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
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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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