[Bioc-devel] How to deal with external software dependencies

[RAN HU]

Hi all,

I am developing a new R package that relies on some external software.
There are some system calls written in the R function that requires the
path to those external software tools.

I am not sure what is the best practice to using external software in R
Bioconductor packages. If the external software paths are required for the
functions to run successfully, will the package fail the BiocCheck?

Any suggestions would be appreciated and thank you in advance for your
help!!!

Best,
Ran

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[Bioc-devel] Reopen cfTools issue #2608

[RAN HU]

Hi,

I am the maintainer of cfTools issue #2608. I submitted it last year but
didn't have many updates then. This issue has been closed. Now I have
modified the package and am ready to submit it again. Could you please
reopen the issue? Many thanks!

Best,
Ran

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Re: [Bioc-devel] Reopen cfTools issue #2608

[RAN HU]

Hi Lori,

I submitted a new issue #2962. Since I cannot post to the same directory
twice, this issue was also closed. Could you please open it?

Thanks,
Ran

On Tue, Mar 21, 2023 at 04:31 Kern, Lori 
wrote:

> With the recent updates to the branch renaming and given the large gap in
> time, Could you please resubmit as a new issue.
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ----------
> *From:* Bioc-devel  on behalf of RAN HU
> 
> *Sent:* Tuesday, March 21, 2023 12:51 AM
> *To:* bioc-devel@r-project.org 
> *Cc:* Peter Li 
> *Subject:* [Bioc-devel] Reopen cfTools issue #2608
>
> Hi,
>
> I am the maintainer of cfTools issue #2608. I submitted it last year but
> didn't have many updates then. This issue has been closed. Now I have
> modified the package and am ready to submit it again. Could you please
> reopen the issue? Many thanks!
>
> Best,
> Ran
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Reopen cfTools issue #2608

[RAN HU]

Thank you, Lori! I have successfully opened a new issue.

Best,
Ran

On Tue, Mar 21, 2023 at 8:36 AM Kern, Lori 
wrote:

>  I modified the code and if you try to resubmit again it should work this
> time.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* RAN HU 
> *Sent:* Tuesday, March 21, 2023 11:32 AM
> *To:* Kern, Lori 
> *Cc:* Peter Li ; bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> *Subject:* Re: [Bioc-devel] Reopen cfTools issue #2608
>
> Hi Lori,
>
> I submitted a new issue #2962. Since I cannot post to the same directory
> twice, this issue was also closed. Could you please open it?
>
> Thanks,
> Ran
>
> On Tue, Mar 21, 2023 at 04:31 Kern, Lori 
> wrote:
>
> With the recent updates to the branch renaming and given the large gap in
> time, Could you please resubmit as a new issue.
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of RAN HU
> 
> *Sent:* Tuesday, March 21, 2023 12:51 AM
> *To:* bioc-devel@r-project.org 
> *Cc:* Peter Li 
> *Subject:* [Bioc-devel] Reopen cfTools issue #2608
>
> Hi,
>
> I am the maintainer of cfTools issue #2608. I submitted it last year but
> didn't have many updates then. This issue has been closed. Now I have
> modified the package and am ready to submit it again. Could you please
> reopen the issue? Many thanks!
>
> Best,
> Ran
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
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[Bioc-devel] Windows build error

[RAN HU]

Hi all,

My package cfTools has recently been accepted. I just found that there is a
build error on Windows: Multiple platform build/check report for BioC 3.17
- BUILD results for cfTools on palomino3 (bioconductor.org)
,
citing:

==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.3.1

Please update conda by running

$ conda update -n base -c defaults conda

Quitting from lines 160-162 (cfTools-vignette.Rmd)
Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'cfTools-vignette.Rmd'

How can I fix this?

Many thanks,
Ran

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Re: [Bioc-devel] Windows build error

[RAN HU]

Dear BioC team,

I wonder if this error is caused by your Windows environment. Or is there
anything I can do to fix it?

If this Windows build error is not solved, will cfTools still be included
in the 3.17 release version?

Thanks in advance!

Best,
Ran

On Tue, Apr 18, 2023 at 4:46 PM RAN HU  wrote:

> Hi all,
>
> My package cfTools has recently been accepted. I just found that there is
> a build error on Windows: Multiple platform build/check report for BioC
> 3.17 - BUILD results for cfTools on palomino3 (bioconductor.org)
> <https://bioconductor.org/checkResults/3.17/bioc-LATEST/cfTools/palomino3-buildsrc.html>,
> citing:
>
> ==> WARNING: A newer version of conda exists. <==
>   current version: 4.12.0
>   latest version: 23.3.1
>
> Please update conda by running
>
> $ conda update -n base -c defaults conda
>
> Quitting from lines 160-162 (cfTools-vignette.Rmd)
> Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
> cannot open the connection
> --- failed re-building 'cfTools-vignette.Rmd'
>
> How can I fix this?
>
> Many thanks,
> Ran
>

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[Bioc-devel] Submit additional data package to closed issue #2963

[RAN HU]

Dear Bioc team,

I am the maintainer of the cfTools package. We hope to submit a new
experiment data package to provide large data files for cfTools' new
updates.

If I should submit the related data package to cfTools' previous github
issue #2963, could you please reopen the issue for me? Or should I open a
new issue by myself?

Many thanks,
Ran

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Re: [Bioc-devel] Submit additional data package to closed issue #2963

[RAN HU]

Hi all,

Problem solved. I have received instructions on opening a new issue for the
related package.

Thanks,
Ran

On Wed, Sep 6, 2023 at 3:58 PM RAN HU  wrote:

> Dear Bioc team,
>
> I am the maintainer of the cfTools package. We hope to submit a new
> experiment data package to provide large data files for cfTools' new
> updates.
>
> If I should submit the related data package to cfTools' previous github
> issue #2963, could you please reopen the issue for me? Or should I open a
> new issue by myself?
>
> Many thanks,
> Ran
>

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[Bioc-devel] cfTools build error

[RAN HU]

Dear Bioc Team,

I have a build error on palomino4 and kunpeng2 due to an environment
problem: Multiple platform build/check report for BioC 3.18 - All results
for package cfTools (bioconductor.org)

PackagesNotFoundError: The following packages are not available from
current channels:
  - tensorflow=2.8.0

Could you help me solve this? Thank you in advance!

Best,

Ran

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[Bioc-devel] Build error for cfTools

[RAN HU]

Hi,

I am the maintainer of the cfTools package. I found cfTools have build
errors on palomino7/8 and kunpeng2 for BioC 3.19 and 3.20, which appear to
be caused by an environment issue related to a Python dependency. This has
happened before and was solved. Could you help me solve this again? And is
there a way to avoid this error in future when there is a new release?

Thank you very much!

Best,
Ran

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Re: [Bioc-devel] Build error for cfTools

[RAN HU]

Hi Martin,

Thank you very much for your efforts in solving the problem! I
believe kunpeng2 is a relatively new platform, so we did not previously
notice the build error. The problem is understandable, and I appreciate
that we’ve worked to address it to make most platforms working.

Best,
Ran



On Fri, Aug 16, 2024 at 1:57 AM Martin Grigorov 
wrote:

> Hi Ran,
>
> Do you remember how it was solved before (for kunpeng2) ?
>
> https://anaconda.org/conda-forge/tensorflow does not provide
> linux-aarch64 build even for 2.17.0 in the conda-forge channel. Your
> package uses 2.10.0.
> The anaconda channel does provide it -
> https://anaconda.org/anaconda/tensorflow, but AFAIK using this channel is
> non-free.
>
> The builder setup docs list tensorflow as a PIP dependency:
> https://github.com/Bioconductor/BBS/blob/devel/Ubuntu-files/22.04/pip_pkgs.txt#L8
>
> biocbuild@kunpeng2 ~> pip install tensorflow
> Defaulting to user installation because normal site-packages is not
> writeable
> Requirement already satisfied: tensorflow in
> /usr/local/lib/python3.9/site-packages (2.12.0)
> Requirement already satisfied: tensorflow-cpu-aws==2.12.0 in
> /usr/local/lib64/python3.9/site-packages (from tensorflow) (2.12.0)
>
> I.e. tensorflow 2.12.0 is installed via pip, but conda does not use pip
> packages.
>
> Regards,
> Martin
>
> On Fri, Aug 16, 2024 at 4:51 AM RAN HU  wrote:
>
>> Hi,
>>
>> I am the maintainer of the cfTools package. I found cfTools have build
>> errors on palomino7/8 and kunpeng2 for BioC 3.19 and 3.20, which appear to
>> be caused by an environment issue related to a Python dependency. This has
>> happened before and was solved. Could you help me solve this again? And is
>> there a way to avoid this error in future when there is a new release?
>>
>> Thank you very much!
>>
>> Best,
>> Ran
>>
>> [[alternative HTML version deleted]]
>>
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>>
>

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