Sorry my mistake.
Looking at the devel branch -- it looks like accessing the ensembl archives is the issue in biomart. Ensembl/biomart connectivity is known to be spotty. I believe caching is already implemented in the biomart backend and you could verify with the maintainer but if not caching when its a successfully download would be beneficial. Is there a reasoning for using an archived version instead of a current version? For release - I'm sorry for the confusion, I copied the link wrong. 404 still does indicate a file not found. It is odd as I can also test locally and do not run into ERRORs. I can try and hop on the builders next week to try and dig a little further into why/what cannot be found. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Shraddha Pai <shraddhapai.ne...@gmail.com> Sent: Friday, June 12, 2020 10:32 AM To: Bioc-devel <bioc-devel@r-project.org>; Shepherd, Lori <lori.sheph...@roswellpark.org> Subject: Fwd: [Bioc-devel] netDx: Build errors despite code working in BioC docker Forgot to cc the group. Also, this is the correct link: http://download.baderlab.org/netDx/supporting_data/refGene.hg18.bed<http://secure-web.cisco.com/1BG3zQjrC4UXZnY6W31nyWRYP1FitXbJGL62ML_BhhL94zaaIolEoaxXzHx5QjIRwzDUCauCke2kWQfkC9xdmncnnubfy7pIvU6jLQT462RVSpcpiw2ZIh68sCagt1kcDudQdEiqUiA0Nw1FE8FPCBMBwTgmx55qgSV24LG0lr4VqmMudk3NVjXEsUJcNou9G7U5yhVdBv8Kxv1l8vG_b_7cj_NNDXONQY6UmchPoRhO3gbppmkmxZvlDyHhGMECwR4oEs29KyTblmT6FvTZnU_wocFiiOMxvizuQY_iFxODZhuGKE7olnWNkR1GpT7_zVxdsSSjy_rdAaHo8SgdSBg/http%3A%2F%2Fdownload.baderlab.org%2FnetDx%2Fsupporting_data%2FrefGene.hg18.bed> Hosting it on our end isn't an issue. S ---------- Forwarded message --------- From: Shraddha Pai <shraddhapai.ne...@gmail.com<mailto:shraddhapai.ne...@gmail.com>> Date: Fri, Jun 12, 2020 at 10:24 AM Subject: Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker To: Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> Hi Lori, Which line number and file did you find the above link in? I'm looking at both the RELEASE_3_11 and master, within the Predict_CaseControl_from_CNV.Rmd file. In all instances, the link to refGene.hg18.bed appears to be correct. I did find that the bed on the server was rw_r__r__ so I used a chmod 755 it. That shouldn't affect the situation because the file was world-readable before. Thanks,S On Fri, Jun 12, 2020 at 8:30 AM Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote: 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<http://secure-web.cisco.com/1TP-zIIaBfWsvlmHEcSZvDlHiwO38Y1zaiQ2rt1cYpD7qKJyqAfq-48yQLNYkGyiGHapd5n2sXvCBW6Or3qpzoiQ3as-2so5egDRF5T4fA5351kAA9e5xkLH-K6xynbenplj_we7KO2bPVjeegaUmsWEzLgtr9BcQt8dQ_E-8LPPzsdumv9DEe2KQV6cn6wJXpXqi-ci6kzrm22BUdcqtcAY4JJxgZJEdLytmx9CaglTrVxITe29gEl1Fp_IsbUWdyHzt4Z4Pt8N4AOvN5XKIZFdBrzEieLx1WauItREZd5n_HpBCAYOT7yS_g378F03ZqGgxvgUA5AUgJ5wN_NYEaA/http%3A%2F%2Fbaderlab.org%2FnetDx%2Fsupporting_data%2FrefGene.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<mailto:bioc-devel-boun...@r-project.org>> on behalf of Shraddha Pai <shraddhapai.ne...@gmail.com<mailto:shraddhapai.ne...@gmail.com>> Sent: Thursday, June 11, 2020 5:44 PM To: Bioc-devel <bioc-devel@r-project.org<mailto: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<mailto: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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Thank you. -- -- Shraddha Pai, PhD http://shraddhapai.com<http://secure-web.cisco.com/1Ver_8BG-M0UV5Y8aX6X91t5WVRx5SJk2FyOGSMyRKwtZ6C54_NnXq2a09ubObfmX1SKW93R_b1vog3aZ-HZbh5Y7IDj7BIqGOUYOrCu-gJ5TzMF_pouoRWmqwPgOdYDe89-gSaQhi8PEm42zP2oNSA7ydV7dh9PVm-OiOmWBBSbkoGVA1RPkg2AUxBE6SIh7Ceng95vSVs50ZUMmxBtAzbK3ldi96ge1qfggANEjJfH9LBIK9u-wDDUGlcMeb3yVaD3Dq2Lq0uFF9h_0TsxGpfsFvkZvESO04cS-orBgWmwwaug-5hJ0A1oAmqtyK7951cCG38fIGiMQ-0LFKwD9n-XgnR8F-8Lwvsl1cvn-AYY/http%3A%2F%2Fshraddhapai.com%2F> ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org<http://secure-web.cisco.com/1NC7yS0nv4LGgulf1KtFXumWbU0IHvdT8O0NQ4xbUrmQg5ikFUyJmFRavNnNaIHT2mMcjDG8dPg8LfRr5OgCx9OITArZ4oH5MfM90_F3Vfoig6n1P5mI3sGcAgvXXGiGVU2BEu5wglymx90-tZhdjVrvYk2qJlcBIZS4OY_PjlE9gGxQDca4p98CGaHHrtCPVHqZVCWBV5kydk7iCGI5GGlew1Nl3Msv0gz2eX4xPILWEIBe_ecGpbiL0MLNZkn9JlAenGKa1IsPz6WcG5bBvMlfO5zSYmq4sERZYcrcFvF4G7kbPWmC_vCSMuthr4vmHsHHgJDhb3oMNdsgy6hLUCA/http%3A%2F%2Fbaderlab.org> The Donnelly Centre for Cellular and Biomolecular Research University of Toronto -- -- Shraddha Pai, PhD http://shraddhapai.com<http://secure-web.cisco.com/1Ver_8BG-M0UV5Y8aX6X91t5WVRx5SJk2FyOGSMyRKwtZ6C54_NnXq2a09ubObfmX1SKW93R_b1vog3aZ-HZbh5Y7IDj7BIqGOUYOrCu-gJ5TzMF_pouoRWmqwPgOdYDe89-gSaQhi8PEm42zP2oNSA7ydV7dh9PVm-OiOmWBBSbkoGVA1RPkg2AUxBE6SIh7Ceng95vSVs50ZUMmxBtAzbK3ldi96ge1qfggANEjJfH9LBIK9u-wDDUGlcMeb3yVaD3Dq2Lq0uFF9h_0TsxGpfsFvkZvESO04cS-orBgWmwwaug-5hJ0A1oAmqtyK7951cCG38fIGiMQ-0LFKwD9n-XgnR8F-8Lwvsl1cvn-AYY/http%3A%2F%2Fshraddhapai.com%2F> ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org<http://secure-web.cisco.com/1NC7yS0nv4LGgulf1KtFXumWbU0IHvdT8O0NQ4xbUrmQg5ikFUyJmFRavNnNaIHT2mMcjDG8dPg8LfRr5OgCx9OITArZ4oH5MfM90_F3Vfoig6n1P5mI3sGcAgvXXGiGVU2BEu5wglymx90-tZhdjVrvYk2qJlcBIZS4OY_PjlE9gGxQDca4p98CGaHHrtCPVHqZVCWBV5kydk7iCGI5GGlew1Nl3Msv0gz2eX4xPILWEIBe_ecGpbiL0MLNZkn9JlAenGKa1IsPz6WcG5bBvMlfO5zSYmq4sERZYcrcFvF4G7kbPWmC_vCSMuthr4vmHsHHgJDhb3oMNdsgy6hLUCA/http%3A%2F%2Fbaderlab.org> The Donnelly Centre for Cellular and Biomolecular Research University of Toronto This email message may contain legally privileged and/or confidential information. 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