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

Fri Jun 12 17:41:39 CEST 2020

Hi Lori,
Thanks for confirming. Indeed, the new set of netDx build errors on all
operating systems seem to be caused by an inability to fetch the hg18 gene
definitions from biomaRt. I would rather keep the example running (and
package maintenance) simple by just hosting the gene definition file needed
for the examples on our server (download.baderlab.org).

Understanding why the builder cannot find the hg18 file on
download.baderlab.org would be great. I'll stay tuned.

Thanks,Shraddha

On Fri, Jun 12, 2020 at 11:28 AM Shepherd, Lori <
Lori.Shepherd using roswellpark.org> wrote:

> 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 an archived version instead of a current version?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>
> 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
> <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> 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
> <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
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> 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
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> 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

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