[Bioc-devel] nebbiolo1 build error in Glimma
There was reported issues with the caching of the ZeiselBrainData. I have reset the cache and hopefully this should clear up over the weekend. If it does not we can further investigate on our end but I do not think there is anything you need to do at this time. Cheers, 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 at r-project.org> on behalf of Shian Su <su.s at wehi.edu.au>
Sent: Thursday, March 10, 2022 6:59 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] nebbiolo1 build error in Glimma
Sent: Thursday, March 10, 2022 6:59 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] nebbiolo1 build error in Glimma
Hi all, I?m trying to figure out why my package is failing to build on nebbiolo1 (Ubuntu 20.04). https://secure-web.cisco.com/19fh39OLbcA_qQ7Chvyt1bDyRmg1ntpwrey4SrccHwr-MDLK7rrYKrfH-g8L9Am3u-23Se7kNcbwnZBFkhqBy9FBI8pD4qBhVov0n_-JDbqkUhRRSg6FFO7iL9gCzlTjW1FYRBzNOOG3MuFpU_xfPqN2DogHJyrI7QSMQz06T85Lv27RFCprfTch3viKV1CaWhYUI2SlSFsEvUUdQTOx0ns22Klab6N4MAdg-wKP9nBWABomGKsNljueLVT07lor7Pa7MnUCbjV9vKt-aKZHUkbZP-laI9zrYS_8kETTjHGm9h0EwKs9nRSU3e21rAnui/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.15%2Fbioc-LATEST%2FGlimma%2Fnebbiolo1-buildsrc.html I believe it spontaneously failed last November without any changes from me, so I had hoped it would go away on its own. The package has no problem building on the Mac and Windows servers, on my personal Mac, Windows and Ubuntu machines, and on the Bioconductor docker image. The offending lines appear to be library(scRNAseq) sce <- ZeiselBrainData(ensembl=TRUE) Error: processing vignette 'single_cell_edger.Rmd' failed with diagnostics: undefined columns selected The only thing I can think of is that somehow ExperimentHub is behaving differently on that particular build server? Any help is appreciated. Kind regards, Shian Su ---- Shian Su PhD Student, Ritchie Lab 6W, Epigenetics and Development Walter & Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville VIC 3052, Australia [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia http://secure-web.cisco.com/1pKMZEe5ZtreUoFmuLei8dqWPoP9Je_mlb_s4y34XUazPqlqlpk2bDc0FzZ3TLwfsEO1b2T2SF_O24y0lIva5J5gViCCfVEf_L4N0u0ysOfh1hv8wEFP8bOX0o-oYMPCHteeScV6pXzoTRj6Zmqdmnj-4BNsLwrQ6qoKodubZCNHDuaLCXPhmqRSIHePO5aTjI-epp5BdbtHXisrilW60ukySgieK5sdnHV9TCW2sJYZ5mZQbXP4y32kimKpSr08-uBH9rrbWRRmm7oeq_aKhGfejD57DcBZULY7Jb5diSbudDyT4Ys6qz1gmCltvSN0t/http%3A%2F%2Fwww.wehi.edu.au<https://secure-web.cisco.com/137oqBFgGauWx__toE53ddKIWeBIt2rGWQb6nsAkKYSwe0E2Z6Ow0acZfIBxq0U0v9DAhpYV7eUGMfYvZ0mO7Shy1MjW6sLBTjD6Ld-QKxL1oHrpKc0GjtyEVle82LSKN6qaZ2u0VyMnYtC3HJ6pp01K0RkNqG0_a3FU7P2SaLXG6EjKtnRvB-_QKvgnoglxfFFD99_hfcG_ea58sDFq0AepC9iT5uzLk_smMFpknRmnCwk-Q1UqkWFlVKBePhh_99gyD7zISjhBlGV9xJnVqawoLDs8XQhAf0cI1YAqr-0Q6SmAdeT9Lp07mvtiikSFj/https%3A%2F%2Fwehi.edu.au> Twitter<https://secure-web.cisco.com/1UVdzLN9tnzg0GbzkGdcmuvDWu-6GL35OV_uf0VJdrlRKA4dCqX2RIZEg_Hu4Tonldsvor8L-MI5B3iWNQnCFmCwjG9aKGVClAa7C-HpK5scLl6MCZTC2nRQ5hjWbxrMMznmVknKjRZj-WyF6suXB9F3kxyeH3vhKsLKyzTzGy4TW5z746iUxd89Zra5jpRQOnQ_Of34sW8JhsvEcIeRS5omCfjIKwxVk3DRIOwr6b7qhWg4OeheBgu-m7OXpQ3HaiYeBGfAuUJXlfM5-ryWVWVZ2DH5d0o_MGXbeJVqGZj9ilyhEL39igdX8j1mNUUN1TEiEOtKyS9PzBlewdFI1Eg/https%3A%2F%2Ftwitter.com%2FWEHI_research> | Facebook<https://secure-web.cisco.com/1Ik0cLUBAcpvslpOqfvOpTvFwkQMOW-RAUoe67ALbJLD7AYbjlnLUgbDdAP9DRT5S7n1wXPlG97BVuGtOPH2fX1K_OhNi0P-dG-qJc-J6UiemJ_BoyWtr3nwfL1KyBximw6oxt1KNcpM7tJAzYqIcS8jUoev_ikO85ZuiNcPDTRoiIrNrTCaEXLuyQOdlcc-fDN47paP_8pAYXaKsGcaaZa6QhohVHi63-74uwFNmJ-kxSZNfu63bmFZPhvQIOL6X97kG1-iF9vscKS_Y9ZfYRN8IKjjIH-FLaLgjF7x408QiZqJ0Y4OKMmqcGrCSLuHgpPxFSKcrNxYQvQBAO-DmNw/https%3A%2F%2Fwww.facebook.com%2FWEHIresearch%2F> | Instagram<https://secure-web.cisco.com/1EPZ3MARkhg6vBf5rhgMnCBoqxp9wc80IlAP8JTwFM9wIYZj10vGDRDKGj8Gu8Nz-C9CtHSXJNjr_s1LzfLPb7tYYzNOSPKfiNkEdQ4VmPDLc-vsGc-KD9RGpTe4gZqGtqpnaoDfReVGaH9JZE120M3Du0H_CQW7jqbUglhlcyNNiX0111OaVu0stMssJrKnKAGanTcaLZkjVJfl6bQPKVBNUcrRv1Er2eCBpXW--CDKwoI6yvoj8bZNvkhKm-UE7PTR8nMvU1c8WrmAzRhP24tti2hWUQQgmDKDiIIPZPtad2Gk1isB-5foTF1bxAyDcnw0uuVrXw3RuwwwTdUHZBg/https%3A%2F%2Fwww.instagram.com%2Fwehi_research> | Youtube<https://secure-web.cisco.com/1ufz3qAsLQywD3eT1D9V7HjxLRdie95hnKfbaEqi2L080dkvVJC6WB-KC5N3xZT_KbV7ScevFQiN69EgWfdSnIasY-fvQWfKSp6Oq3JkdkPwBKQeJptKNANXqERZui_OVNowiU2L_00lNhVlJCewXb2GIKRUj829T6Q1LPgGQbAh7z19VcvpdxuDhMJEdGBW5RGJCfnIs2gw4Ri394aStQTt4m5jP908S3kivNt2C9O7fQ2_bJDBy_JgDJ6oQNFykpzTvbsxB3qWi3uXwBs1kU-jyU4eQ-BAeStdt-UvEACidgm0dGStMkuYdX46QCuhAvumfwTflAqjpVEfuKn1R8Q/https%3A%2F%2Fwww.youtube.com%2Fuser%2FWEHImovies> | LinkedIn<https://secure-web.cisco.com/1XlmcEIIamFbZ6sSDX_nVxioJ-BRtIwQFUvAHlVE4eJP14TJQ_FBxf6knNwT7x8sn0aJ3dOGDb7UoTUsAu_bOGBXZOe0MjcjRgVo112EqPNXbP1QPgH2Se7oROEhSti2xM90rFAezQrs3jyQyVvrhqs1kaPssAo2w8CqFT-8WNjF6xg7GpYugsNUFmPpVQ1ZvUsGstFw7vfvX67P4ca4S84-HhuhHrgeRRksuwAux8bpo7GFdsIu1EhpxzzqZe7c-bZdvhOoLh3d97WdSfc3xfq9tPkzFIlpjKBwDFIf_Cnds4WPFIV1CdcyPy3quHjWwAZ2zgXUnZMF3rVJObJ8h6Q/https%3A%2F%2Fwww.linkedin.com%2Fcompany%2Fwehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. 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