A 404 ERROR generally has to do with accessing web resources. I looked at your vignette and it appears that this link
http://baderlab.org/netDx/supporting_data/refGene.hg18.bed Does not exist. Resources accessed by Bioconductor should be publically available. If that location is not publicly accessibly the data can not live there. If you need a place to host public data I suggest the Bioconductor AnnotationHub or ExperimentHub. Cheers, Lori Shepherd 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 Shraddha Pai <shraddhapai.ne...@gmail.com> Sent: Thursday, June 11, 2020 5:44 PM To: Bioc-devel <bioc-devel@r-project.org> Subject: [Bioc-devel] netDx: Build errors despite code working in BioC docker Hello BioC community, I have been trying unsuccessfully for a week now to update both release and dev branches of the netDx packages but am still getting build errors. Today I got a build error for the release branch: https://secure-web.cisco.com/1THF9VgEAVqGQdkK1Gugz4M1qdnd051bge4D5IxMpTOYv7mZRSDvQ6IvmsvcQh1Xc_5N7u-du_uMo645h6ZiSLuahMPE8xmFMVQyP7fFZw1BCFsNSQ-LpfMzPNn51l9ZaRS1GefMdVgHpBF5L_eeMMhA3K9scm2Lyys7bxR20xQ0BKySUiiRU8U_ES7bGMwu0mTaiuP0UcUbkCQ_tS-7BobJM5G4SFviHdd9ERzDGnqEXiRusVhrCr8uOIgPtgBxqSEF3gUbIHVoySNk1x8DonZ1veWjoE-7Of61xe1TyPqJJGDTWpuiQteFCOsGbdu0Om64XyDyr7slE9kQ-zwuaJd8hlSVw4FNOFn0iRiKlS7Y/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2FnetDx%2Fmalbec2-buildsrc.html I tried to reproduce the error in the following way: 1. I have a BioC docker that runs R 4.0.0 and Biobase 2.48.0 (from sessionInfo()). 2. I ran a fresh "git clone" to get the latest netDx. "git clone https://secure-web.cisco.com/1fKSTDcaThEf6GEuD3oF4OvI_QkP6aAAEwSW5STRXbQgyROz5rzyoCW93NMHjnzEDFLHsvAalFQhFtr_Qg5ojG18B_csfChJwfgjFgej58_bvHymqRBn0PDIjsPSRfCREsqZ19SiqWzH_-c3hH_jOVpSMMBfc3jhhiAvlbuIMTeUdq6OfxlQA8H8ZWUZsznD8yS9mqZHBM_3rAHRimO_e5brMo6KMqErI1O4-so2EAr8vHWw_oEOltZLrSrnXi8B4tkLXevvJbWh8J3Bg7_IX6Pq7U_Pbmp23PTXoWWUq4UkTuKSG9S2HPgnlpbTKn7YZjryXf9c_0SImb9sX8QL64a16OvdA4oHV65xhjXS9EdY/https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2FnetDx" , after the URL on the build page above. 3. Switched to release branch "git checkout RELEASE_3_11" 4. Reinstalled netDx "R CMD INSTALL netDx" and confirmed using sessionInfo(); netDx_1.0.1 5. Set up Renvirons as mentioned on the build page and launched R also as suggested there, after declaring the corresponding variable. 6. The offending vignette is "Predict_CaseControl_from_CNV.Rmd". So I first ran "knitr::purl("Predict_CaseControl_from_CNV.Rmd") , and then removed the suppressMessages() around the offending function call, "buildPredictor_sparseGenetic()". 7. Ran "source("Predict_CaseControl_from_CNV.R"). And it ran through successfully. What am I missing? Is it that the snapshot date it from June 10 but the build page is from June 11 so I need to wait for the changes to kick in? I'm also getting errors with the devel branch, so will probably separately write about that (sigh). Thanks,Shraddha -- Shraddha Pai, PhD http://secure-web.cisco.com/1XEZzaW2WII993HXVeWrJ29xC3iDjrN9p69iNANpk3heRN8fWRR0p-M3N2r-u0OoD0VH--V2nOw3ZtHGaBNPtVQIQFrt3suXwzgnH9narseMShrzX5tpvqAEYKJqatOEiJVLHqeZVrUgDzN9H_KK0cG2EPyojWkIQq7-4EjPtqAwXtTKe8wi_hY7tGkAwMjXiEiq-qgmN7z7b9Xc4jvBMPxTqIlMR68FZh1v6OVUgfEe280siYp9MZhguNZvMLMFVFuJ42yS8b0XYDuBEkO-b_hFsSGVf9KyQBS8g_RJNC6kSwagJRfvKZCXjeNdH4zkb3zJwFUJa7NIE2MCtKsw32xIad_FirzU9WTKcm2B8G0c/http%3A%2F%2Fshraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://secure-web.cisco.com/1RDoqupc8w03I66baJG97_eAlkJmwNqizjNkPfKrKecjRu1y1jue9yQ50WHGmOWYeP7HrqYdqk3QKnY4ZJPoBcBf_Iy_r4XEEW72jGp6we6RFtyds_DrcKy8w0jSHm3f-h1Fb-qR87slJm8nf48CSUUo9_PANDSg8vBf_2D_jRq94w7Sx8lr-L1PWGAQzUGNzvgqr77N7g_zJ_XrdeAGRu23UbveleW1s2v5ACNmI5kwAfij0vOjcmNT65ExAU67PuLbOKcGz4O-tsrBn2JUXc-XOQSRZO5UlbKy7g8eE0keWVn8m5gOmUtld-5POFuJjySDWX500OUfcZKQz3DgCWQ/http%3A%2F%2Fbaderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1K26g8xbkKLrr49oPzZIn1KA-9hvHI0CA3CYhOaFmPdqda4Crb7opKARjTKUCOaR-mFmqYAlsMM0B4tMbAjYD_yNMHhzcVlT0SxayP3UMLR6e36SMdRfpMFRFgYVvEYB0IWsOCNCK4l0OIJpNPzOPgg3zRVimsP0tf02muotMYl7WeuOC_xTQupoyQY7ivkvM0QbO69SQcr-XgNULbtx75xIyZEGRh6jI2TiAocoSNZqB5y7tkakypik3NwJ_mhIfOwxaa9e3ISSbMvD8-amSoNnoBl2b1JUAvHNsEtxsXykj6Nf-Rmu5jANEFxa6MUCAdDKCKN2w_s-LGkihq1Jdcg/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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