[Bioc-devel] Build error for cfTools

[Kern, Lori]

Yes it does as it has not built at all for the given cycle, it would not be available via BiocManager to the end user.  You can verify that it has not yet built by looking at the bottom of the  package landing page at Package Archive section and having nothing available for the windows section:  https://bioconductor.org/packages/3.21/bioc/html/cfTools.html

The release branch is frozen as of this afternoon.  You may continue to push updates to the devel branch at this time to fix the package.


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 <bioc-devel-bounces using r-project.org> on behalf of RAN HU <huran using ucla.edu>
Sent: Monday, March 31, 2025 2:14 PM
To: Martin Grigorov <martin.grigorov using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Build error for cfTools

Hi,

I noticed that there is still a build error on Windows Server for cfTools:
https://secure-web.cisco.com/1-Um4ceU76UyX5hMdEdCT8j3ZwrgembVcUUEgdnjQr75L45yWfwAWJw18vFcHE8z6yHzXiMp7Gk-ako1YXkYhciAkPxu5fvoMFwdUp_oogb1nB55-J-x0UJHg2425SFQurdqyBm36WDl8blUOfeVyvFwZx_I9sg3WNsb_nTqkcsl3pC4Uifr0jnbHxkdV89edmVsIESMo6FvOOUXBagKQ-di-N_kTyRGijQTE9jRYlD1WPQXXvvKIGQ14AlPGAokZy7umB7Ufbyq8kcTu7eUGXOswQMaFgiVSZtoSgT_sJu7sdb-bGp8_Y5sWzwFF0N1K/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FcfTools%2Fpalomino7-buildsrc.html
Does this prevent Windows users from installing or using the R package?

If so, I’d really appreciate the opportunity to work together to resolve
this issue and help ensure it doesn't occur in future releases.

Thank you for your time and support!

Best,
Ran

On Fri, Aug 16, 2024 at 1:43 PM RAN HU <huran using ucla.edu> wrote:

> 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 <martin.grigorov using gmail.com>
> wrote:
>
>> Hi Ran,
>>
>> Do you remember how it was solved before (for kunpeng2) ?
>>
>> https://secure-web.cisco.com/1DxWtYDXCt6jlIM0wyefLN7m86Y-m2UbYkic6JxwNNQvzEDLIhs87hw_dLMtZfYiCKQKmFmWDFN7sDWWFEIJQVXuIv_XQTqRumvb8Hd9n6XP6gl_R4403IUx_ICLDbFispB_psjrk0bQepnYAF5bFFJkm9Dj2cp189J5CHMBkUUnvaYQvcnKoDI1gAlqacr9lt_BhW-7oILF1Oyx_hGXDRK3QIrvBLcvSPAG1qoPLoJZCCRAiFYXKEfuADIWNWelHPS6BIsItDtnMAc0S39t65-xjkzAPHxFRlUm3RDSb-7vdVQ3Fgarz02LtQ8ijb-R0/https%3A%2F%2Fanaconda.org%2Fconda-forge%2Ftensorflow 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://secure-web.cisco.com/1MQwIJXbjL7p1LUymz79K8PMKmuqZbUONwN_kmjzHybqCcgmAonc6EdKH9a6i2FfIf2dAgueJ6UIoXSki8R1Bp7L4PWFzkZWAx-jYFJh9CHPGQhyES4bNNvfu-Rugbu1Dnuyun8kl95aw9V5cm85lXkjZgYsPFO3LSPB998L57pz82UG96d2OqCDCPyCeQbCPrSvDgIEcu1XZjuEF0kitOtMUhmBiT6Bawkt9wGchepa0IefA4kjYfBLP69qsAe-2wGx4HoOxKBG5lIlYT0ekeQprIQ7PeqykGAmraIZz_GOhdhzaFQmLKWmzMWOpP4zD/https%3A%2F%2Fanaconda.org%2Fanaconda%2Ftensorflow, but AFAIK using this channel
>> is non-free.
>>
>> The builder setup docs list tensorflow as a PIP dependency:
>> https://secure-web.cisco.com/1wp95CAy9DrfWvFPfdVTCcNDL2DCHx2XiSUJNWa4GtmEOg9XMUlNuqmlbqruq59NarlGeOtKGp-5r5Y4P3fxccirrlJdbm8ChtvNe8cosCB2RL1kpiXVqS01NWvf4b8znrGHC4Owl-T_jSxoBOli_8GdrsaPp6cd0FlPeJqR2WvC9FtiFjIRSTnPBgUoXgyLgX7jYHMBZLgfQDxDdIXscsU-CwduM3RiIfzvJOxGqXf_1LZNZxS4w6v7GdYXwL8b0M4bYF8Y2ekX3DjFLNBYjxLV1Kdc3FjYFhlQmZGqMAzuCO3YTxktflZywxi3-mKaf/https%3A%2F%2Fgithub.com%2FBioconductor%2FBBS%2Fblob%2Fdevel%2FUbuntu-files%2F22.04%2Fpip_pkgs.txt%23L8
>>
>> biocbuild using 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 <huran using ucla.edu> 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]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://secure-web.cisco.com/1FbKLT68dQ2oquQY4FHeNKlzB6V4twdKQR3v2jgXCBTyPfgmAnzmGsgcyCNPAE_t64XG-vsBoJ_L7OKzAx2V40chloMOGT5BtuErB-Bxzu1YCiN6pdHAJEigXyfLOMjkyYJ5TiO2PCrL_OEsCIr4zOVOHvXCZd_R8WfWBu26AoARJE9JdQoft1ZUKrFMM6CcVFAuKA7pKVSJCG0lGxbZdsUo0onZ5wJR9Z48GWRHQjo124vQJUSKjVciEMR7tol4AC4gC24ED9QVzWlTUv3kYHb_Bxa1pONfFAbgSSqZdKnMxCiP707ZW-oO04ClWQyHM/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>>>
>>

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1FbKLT68dQ2oquQY4FHeNKlzB6V4twdKQR3v2jgXCBTyPfgmAnzmGsgcyCNPAE_t64XG-vsBoJ_L7OKzAx2V40chloMOGT5BtuErB-Bxzu1YCiN6pdHAJEigXyfLOMjkyYJ5TiO2PCrL_OEsCIr4zOVOHvXCZd_R8WfWBu26AoARJE9JdQoft1ZUKrFMM6CcVFAuKA7pKVSJCG0lGxbZdsUo0onZ5wJR9Z48GWRHQjo124vQJUSKjVciEMR7tol4AC4gC24ED9QVzWlTUv3kYHb_Bxa1pONfFAbgSSqZdKnMxCiP707ZW-oO04ClWQyHM/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



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.
	[[alternative HTML version deleted]]