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

Fri Jun 12 17:28:08 CEST 2020

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  Is there a reasoning for using an archived version instead of a current version?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.neuro using gmail.com>
Sent: Friday, June 12, 2020 10:32 AM
To: Bioc-devel <bioc-devel using r-project.org>; Shepherd, Lori <Lori.Shepherd using 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.neuro using gmail.com<mailto:shraddhapai.neuro using 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.Shepherd using roswellpark.org<mailto:Lori.Shepherd using 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.Shepherd using roswellpark.org<mailto:Lori.Shepherd using 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-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Shraddha Pai <shraddhapai.neuro using gmail.com<mailto:shraddhapai.neuro using gmail.com>>
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel <bioc-devel using r-project.org<mailto: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

--
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University of Toronto

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The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

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--
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
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