[Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks

Gabriel Odom godom @end|ng |rom ||u@edu
Tue Jun 15 18:40:26 CEST 2021 

Thank you Lori and Wanding :)
We are using the default settings for the cache location. Our call to the sesameData:: package is simply sesameDataCache("HM450", showProgress = FALSE)
What should we do in the mean time?

On Jun 14, 2021, at 9:49 AM, Wanding Zhou <zhouwanding using gmail.com<mailto:zhouwanding using gmail.com>> wrote:


Note: This message originated from outside the FIU Faculty/Staff email system.

Thank you for the fix and suggestions, Lori!

Wanding

On Mon, Jun 14, 2021 at 9:34 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
I'm looking at the caching code in sesameData.  I think there could be some code cleanup and some things things that should be changed.  I'll try to put together some comments and time pending a pull request.

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 Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Sent: Monday, June 14, 2021 9:20 AM
To: Wanding Zhou <zhouwanding using gmail.com<mailto:zhouwanding using gmail.com>>
Cc: Chedraoui Silva, Tiago <txs902 using med.miami.edu<mailto:txs902 using med.miami.edu>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>; Gabriel Odom <godom using fiu.edu<mailto:godom using fiu.edu>>; Fernanda Veitzman <fveit001 using fiu.edu<mailto:fveit001 using fiu.edu>>
Subject: Re: [Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks

This is an issue on the Bioconductor builds. I will fix momentarily and should be reflected in tomorrow's build report.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Wanding Zhou <zhouwanding using gmail.com<mailto:zhouwanding using gmail.com>>
Sent: Monday, June 14, 2021 9:18 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Cc: Gabriel Odom <godom using fiu.edu<mailto:godom using fiu.edu>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>; Chedraoui Silva, Tiago <txs902 using med.miami.edu<mailto:txs902 using med.miami.edu>>; Fernanda Veitzman <fveit001 using fiu.edu<mailto:fveit001 using fiu.edu>>
Subject: Re: [Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks

Looks like sesameData build is experiencing the same problem.

http://secure-web.cisco.com/14wC2r7uMzHAbZME5HNyl8y3THlgTIwq2nJ1nnqRIKG1chTxUF8H34UzOHihRZC7SDCP2PDTKoqrRcfo5PRsbwSu8p2rP5_cWFgQW6pAHZodfi-enkPE_-JHNwoPK92gAi_NnrPSCOiaJlX0-JI5SBrU7OclFZmr95RmFsiRTwA_SkAukghYSWOqtGRssFlY53CIkQKO08aaTw6jI-9V5XAdmqlcqrj1i0C5grb-B5y0IsSXsHjPq_uFO8gelmkQqV7k9cIdFBDKd7c8r6EugHkO4WvOCoxSeMUqzT1fpL8MqDMvnBJKkgU-UQO566eI7/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fdata-experiment-LATEST%2FsesameData%2Fnebbiolo2-buildsrc.html<http://secure-web.cisco.com/1Wqopyj6WX11lkKJCcYWkMTdFk6tVlIE0fNHVxlLeCXdaeUnhenjnlg3yUH9XMiuSFy0B9vk2gpimLom8gF33P8HUA6LNPdeNYvZKibiS7ebYcVKrHve0OJNiqWuTWpRnJbaZ2Pc4SoqYr5GqhU3pViuUYPRW7jVWRvsITRMZfiILDKetophnVSPVhUNRjvmNl3DEDZ3uIqFNIp_QEk1gsQ9pQO6Q8F5YwaDrsuRBdXI_6pPvNgKNY806BHmtMGuvSIqZXDSkACRShKyoB609tTBL7HwrNPtNoMjRB2Z6juNBjQPkwA8wUNBjWv9DxJlr/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fdata-experiment-LATEST%2FsesameData%2Fnebbiolo2-buildsrc.html<https://urldefense.com/v3/__http://secure-web.cisco.com/14wC2r7uMzHAbZME5HNyl8y3THlgTIwq2nJ1nnqRIKG1chTxUF8H34UzOHihRZC7SDCP2PDTKoqrRcfo5PRsbwSu8p2rP5_cWFgQW6pAHZodfi-enkPE_-JHNwoPK92gAi_NnrPSCOiaJlX0-JI5SBrU7OclFZmr95RmFsiRTwA_SkAukghYSWOqtGRssFlY53CIkQKO08aaTw6jI-9V5XAdmqlcqrj1i0C5grb-B5y0IsSXsHjPq_uFO8gelmkQqV7k9cIdFBDKd7c8r6EugHkO4WvOCoxSeMUqzT1fpL8MqDMvnBJKkgU-UQO566eI7/http*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel*2Fdata-experiment-LATEST*2FsesameData*2Fnebbiolo2-buildsrc.html*3Chttp:/*secure-web.cisco.com/1Wqopyj6WX11lkKJCcYWkMTdFk6tVlIE0fNHVxlLeCXdaeUnhenjnlg3yUH9XMiuSFy0B9vk2gpimLom8gF33P8HUA6LNPdeNYvZKibiS7ebYcVKrHve0OJNiqWuTWpRnJbaZ2Pc4SoqYr5GqhU3pViuUYPRW7jVWRvsITRMZfiILDKetophnVSPVhUNRjvmNl3DEDZ3uIqFNIp_QEk1gsQ9pQO6Q8F5YwaDrsuRBdXI_6pPvNgKNY806BHmtMGuvSIqZXDSkACRShKyoB609tTBL7HwrNPtNoMjRB2Z6juNBjQPkwA8wUNBjWv9DxJlr/http*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel*2Fdata-experiment-LATEST*2FsesameData*2Fnebbiolo2-buildsrc.html__;JSUlJSUlJSUlLyUlJSUlJSUl!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdljKUxIP4Q$>>

error in evaluating the argument 'x' in selecting a method for function 'query': Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/ExperimentHub
  filename: experimenthub.index.rds

I will do some more test from my side as well. Thanks,

Wanding

On Mon, Jun 14, 2021 at 6:56 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org><mailto:Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>>> wrote:
Let me check the location of the cache on the builders.

Did you create a specific cache for these files or were you using the default?




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><mailto:bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>>> on behalf of Gabriel Odom <godom using fiu.edu<mailto:godom using fiu.edu><mailto:godom using fiu.edu<mailto:godom using fiu.edu>>>
Sent: Thursday, June 10, 2021 1:51 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org><mailto:bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org><mailto:bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>>
Cc: Chedraoui Silva, Tiago <txs902 using med.miami.edu<mailto:txs902 using med.miami.edu><mailto:txs902 using med.miami.edu<mailto:txs902 using med.miami.edu>>>; Fernanda Veitzman <fveit001 using fiu.edu<mailto:fveit001 using fiu.edu><mailto:fveit001 using fiu.edu<mailto:fveit001 using fiu.edu>>>
Subject: [Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks

Hi folks,
We are submitting the package coMethDMR to Bioconductor (https://secure-web.cisco.com/1LJYIf7eE_SLkrPc-raY2TfrjVLvxvy25vUgb2qyF7dnrGbAVuMe-y9M92LmMJZPf7OZS4Zzw4czMrxNuuCQk3Mh4BXq7KToBlTJ6Wg09N1mRJIIxMidq-bDosj2WZQlQzabUbUw-sSN6lEC-B6l3_OJo_RSlBFh4j7Rjr3HpXJn16WzrsjJ3wF4_C4yy3YR3tOGL0L1VeTZ7FYrAF6XHbRcS3EkDimq7a_wpzO1NgverSf5l9K6TsLwXVjoNx06G4G9Ca76BET29gO6_mD2RyaevSEWOsPiQ4vYTfmMcrK4HkbE58yJmLmuMmwkWU1JSvtx6-fm_o9g2wdpyztI8aQ/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2064<https://urldefense.com/v3/__https://secure-web.cisco.com/1LJYIf7eE_SLkrPc-raY2TfrjVLvxvy25vUgb2qyF7dnrGbAVuMe-y9M92LmMJZPf7OZS4Zzw4czMrxNuuCQk3Mh4BXq7KToBlTJ6Wg09N1mRJIIxMidq-bDosj2WZQlQzabUbUw-sSN6lEC-B6l3_OJo_RSlBFh4j7Rjr3HpXJn16WzrsjJ3wF4_C4yy3YR3tOGL0L1VeTZ7FYrAF6XHbRcS3EkDimq7a_wpzO1NgverSf5l9K6TsLwXVjoNx06G4G9Ca76BET29gO6_mD2RyaevSEWOsPiQ4vYTfmMcrK4HkbE58yJmLmuMmwkWU1JSvtx6-fm_o9g2wdpyztI8aQ/https*3A*2F*2Fgithub.com*2FBioconductor*2FContributions*2Fissues*2F2064__;JSUlJSUlJQ!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlii8u8-wQ$>
This package requires HM450 and EPIC data (probe IDs) available for package functionality. We currently have a check on package load that these two data components are in cache.
Our package passes checks on local and Travis (https://secure-web.cisco.com/1j2Lm3Ar4WQmwywzgNFqh4tT1aPJE0I8o00-Zi6Ty7B1fjWZ7lIh1FIhDb7ZTgZWrrlAeTktUkCcwIZmoOr_NOj8wGRorNymIlJkbM_OZ9tXF7loND6qtHWOAGyLrDEvU9Yack4zl4GZYI6wTzcdr2Gd31XB2eb9G1LdpqiIpPY7m2sAT0VPJ04EX_FbBlbo_G0RKWHzJNs6p6ILdBryIiOUfRamGe5aU5WifgydF0_alcKCAHwlarFaUqLi0w4RZgN6ODJZJbgbXYg7rcGBdVHcvolT2k9rT8RqHT-qOIcZPSQ0uAErYYcSW7rU8eC40tO2ctZ032ONQ4GCwlOk5Lw/https%3A%2F%2Ftravis-ci.com%2Fgithub%2FTransBioInfoLab%2FcoMethDMR%2Fbuilds%2F228394255<https://urldefense.com/v3/__https://secure-web.cisco.com/1j2Lm3Ar4WQmwywzgNFqh4tT1aPJE0I8o00-Zi6Ty7B1fjWZ7lIh1FIhDb7ZTgZWrrlAeTktUkCcwIZmoOr_NOj8wGRorNymIlJkbM_OZ9tXF7loND6qtHWOAGyLrDEvU9Yack4zl4GZYI6wTzcdr2Gd31XB2eb9G1LdpqiIpPY7m2sAT0VPJ04EX_FbBlbo_G0RKWHzJNs6p6ILdBryIiOUfRamGe5aU5WifgydF0_alcKCAHwlarFaUqLi0w4RZgN6ODJZJbgbXYg7rcGBdVHcvolT2k9rT8RqHT-qOIcZPSQ0uAErYYcSW7rU8eC40tO2ctZ032ONQ4GCwlOk5Lw/https*3A*2F*2Ftravis-ci.com*2Fgithub*2FTransBioInfoLab*2FcoMethDMR*2Fbuilds*2F228394255__;JSUlJSUlJSU!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlhNepO3pw$>), but instantly fails on Bioconductor (http://secure-web.cisco.com/1_JOpYlcb26Br20C8xzcwa5dZN4HaNbPd23ADPLxcNF191FKN4lUx4OM5jOINXAoGkByRNgNEr-VfiSdvABVAfPbk6WLrPVAjEA46btRh0GpYlT2eWfywAPHT0A8H1RHXz9ULN52jKnZnzZ14QLCg8pENr-CTAaHA0b2Az1tNLndC5A0hPXXXs86BwPkIR_tKPNX_JzWcxN9TZtPJk6UPbBkuFzEEpoEt_3hrvJJMgzoYlFf2LsWWDm9OUMw3UqVor8d-B0y4uPfXxx4wWiF93L5rse-fLht_Muo0xos00WH-2uqmT-SwroZ9Gawn2qSeUyAfaiQg-tSZIOsUtKPC5Q/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FcoMethDMR_buildreport_20210610114<https://urldefense.com/v3/__http://secure-web.cisco.com/1_JOpYlcb26Br20C8xzcwa5dZN4HaNbPd23ADPLxcNF191FKN4lUx4OM5jOINXAoGkByRNgNEr-VfiSdvABVAfPbk6WLrPVAjEA46btRh0GpYlT2eWfywAPHT0A8H1RHXz9ULN52jKnZnzZ14QLCg8pENr-CTAaHA0b2Az1tNLndC5A0hPXXXs86BwPkIR_tKPNX_JzWcxN9TZtPJk6UPbBkuFzEEpoEt_3hrvJJMgzoYlFf2LsWWDm9OUMw3UqVor8d-B0y4uPfXxx4wWiF93L5rse-fLht_Muo0xos00WH-2uqmT-SwroZ9Gawn2qSeUyAfaiQg-tSZIOsUtKPC5Q/http*3A*2F*2Fbioconductor.org*2Fspb_reports*2FcoMethDMR_buildreport_20210610114__;JSUlJSU!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlgvDT3DFQ$>
 003.html

What solutions have people used in the past to require access to such large data sets without including them in the package?
Warm regards and many thanks,
Gabriel

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