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

Mon Jun 14 15:49:14 CEST 2021

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>
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> on behalf of Kern,
> Lori <Lori.Shepherd using RoswellPark.org>
> *Sent:* Monday, June 14, 2021 9:20 AM
> *To:* Wanding Zhou <zhouwanding using gmail.com>
> *Cc:* Chedraoui Silva, Tiago <txs902 using med.miami.edu>;
> bioc-devel using r-project.org <bioc-devel using r-project.org>; Gabriel Odom <
> godom using fiu.edu>; Fernanda Veitzman <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>
> Sent: Monday, June 14, 2021 9:18 AM
> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
> Cc: Gabriel Odom <godom using fiu.edu>; bioc-devel using r-project.org <
> bioc-devel using r-project.org>; Chedraoui Silva, Tiago <txs902 using med.miami.edu>;
> Fernanda Veitzman <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
> <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>
> >
>
> 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>> 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>> on behalf of Gabriel Odom <
> 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> <
> 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>>; Fernanda Veitzman <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
> 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),
> 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
>  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
>
>         [[alternative HTML version deleted]]
>
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