Thank you for the fix and suggestions, Lori! Wanding
On Mon, Jun 14, 2021 at 9:34 AM Kern, Lori <lori.sheph...@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-boun...@r-project.org> on behalf of Kern, > Lori <lori.sheph...@roswellpark.org> > *Sent:* Monday, June 14, 2021 9:20 AM > *To:* Wanding Zhou <zhouwand...@gmail.com> > *Cc:* Chedraoui Silva, Tiago <txs...@med.miami.edu>; > bioc-devel@r-project.org <bioc-devel@r-project.org>; Gabriel Odom < > go...@fiu.edu>; Fernanda Veitzman <fveit...@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 <zhouwand...@gmail.com> > Sent: Monday, June 14, 2021 9:18 AM > To: Kern, Lori <lori.sheph...@roswellpark.org> > Cc: Gabriel Odom <go...@fiu.edu>; bioc-devel@r-project.org < > bioc-devel@r-project.org>; Chedraoui Silva, Tiago <txs...@med.miami.edu>; > Fernanda Veitzman <fveit...@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.sheph...@roswellpark.org > <mailto:lori.sheph...@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-boun...@r-project.org<mailto: > bioc-devel-boun...@r-project.org>> on behalf of Gabriel Odom < > go...@fiu.edu<mailto:go...@fiu.edu>> > Sent: Thursday, June 10, 2021 1:51 PM > To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> < > bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> > Cc: Chedraoui Silva, Tiago <txs...@med.miami.edu<mailto: > txs...@med.miami.edu>>; Fernanda Veitzman <fveit...@fiu.edu<mailto: > fveit...@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]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > > https://secure-web.cisco.com/13Kk3L1299v2slZnlxS0A7jQHspZUxsF4ynFFRxOU19eChzGmhwvePJKemVJ9AY-y4K5HScAxBLMace2mrc-vVV7A4yzzM2YTgZo_VWM1gcrL_-tmlmxb-qsLNMGNlpf3W113RiecKMZN0UTUPoSWBnId982tbwz3fCJY_Emc_TdvTBq4U6lORSLzd5hHiTRxXjEjKwn_TzeyPkY6I6u1NVS7Ibc42xoafr7oW9meqMlx01Plkom1e1RdBtMvh5cclQOJTDaDsPj-t5dWOs5HThpgDigIvlZeLg7LG_DMF9dE6tj3ZoFv4NZEN2tmheLY5sa4yTTiIZYGPPso2jcrcQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > This email message may contain legally privileged and/or confidential > information. 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