[Bioc-devel] netDx: Build errors despite code working in BioC docker

[Shepherd, Lori]

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 using r-project.org> on behalf of Shraddha Pai <shraddhapai.neuro using gmail.com>
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel <bioc-devel using 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

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