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

Fri Jun 12 16:32:03 CEST 2020

Forgot to cc the group.
Also, this is the correct link:
http://download.baderlab.org/netDx/supporting_data/refGene.hg18.bed

Hosting it on our end isn't an issue.
S

---------- Forwarded message ---------
From: Shraddha Pai <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>

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> 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
>
> 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,
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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 ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

-- 
--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

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