Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker
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.sheph...@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 an archived version instead of a current version?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 > *Sent:* Friday, June 12, 2020 10:32 AM > *To:* Bioc-devel ; Shepherd, Lori > > *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* > 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 > > > 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> 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 on behalf of > Shraddha Pai > *Sent:* Thursday, June 11, 2020 5:44 PM > *To:* Bioc-devel > *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
Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker
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 Sent: Friday, June 12, 2020 10:32 AM To: Bioc-devel ; Shepherd, Lori 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 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 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 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 mailto:bioc-devel-boun...@r-project.org>> on behalf of Shraddha Pai mailto:shraddhapai.ne...@gmail.com>> Sent: Thursday, June 11, 2020 5:44 PM To: Bioc-devel 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_QkP6aAAEwSW5STRXbQgyROz5rzyoCW93NMHjn
Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker
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 on behalf of Shraddha Pai
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel
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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