Hi Lori, Thanks for your quick response. The build error seems to stem from an environment issue with tensorflow=2.10.0. I was hoping the Bioconductor team could help address this in the devel branch.
Best, Ran On Mon, Mar 31, 2025 at 2:39 PM Kern, Lori <lori.sheph...@roswellpark.org> wrote: > 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-boun...@r-project.org> on behalf of RAN HU > <hu...@ucla.edu> > *Sent:* Monday, March 31, 2025 2:14 PM > *To:* Martin Grigorov <martin.grigo...@gmail.com> > *Cc:* bioc-devel@r-project.org <bioc-devel@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 <hu...@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.grigo...@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@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 <hu...@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@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@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. 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