Likely it is a compatibility issue with python version and available modules. You might look at updating the package to be compatible with a more recent version of tensorflow
The core team is preparing for the release and might not be able to help debug this until post release. Maybe someone in the community would like to offer any further help 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 <hu...@ucla.edu> Sent: Monday, March 31, 2025 2:50 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Cc: Martin Grigorov <martin.grigo...@gmail.com>; bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Build error for cfTools 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<mailto: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<https://secure-web.cisco.com/1vWuKJB-IkFvqot213Q3OwUG9l6_wfwSfI52wpQtPss_2bel4zJVdneQSMb7OQTYWqx40vXIv7kSyPZP0p3k7gq1ZNQY8-0uPGBJnORyOqrripkWDWUW2255L5ZyJcUDorTgMcfCc1peKxvBXOsLqsSTzLljK8zgfQQOyyVYbhmjfSjyPV4AYwgKw831VVtCY6h3rtKLBEPpyaPOfiN7PpX_PfBHXQanT8aIpzJVhmIjnNSf_rk2DOSJphcyWwHLGflx4insKsfOvmC3IMNS4WEo_QcBt8kFK0k79jNY9-KFSsD0dnRby_C-RNZbhuu7N/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fbioc%2Fhtml%2FcfTools.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<mailto:bioc-devel-boun...@r-project.org>> on behalf of RAN HU <hu...@ucla.edu<mailto:hu...@ucla.edu>> Sent: Monday, March 31, 2025 2:14 PM To: Martin Grigorov <martin.grigo...@gmail.com<mailto:martin.grigo...@gmail.com>> Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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