[Bioc-devel] netDx: Build errors despite code working in BioC docker
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-bounces at r-project.org> on behalf of Shraddha Pai <shraddhapai.neuro at gmail.com>
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel <bioc-devel at r-project.org>
Subject: [Bioc-devel] netDx: Build errors despite code working in BioC docker
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel <bioc-devel at 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 at 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. 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.