[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 at gmail.com>
Sent: Monday, June 14, 2021 9:18 AM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: Gabriel Odom <godom at fiu.edu>; bioc-devel at r-project.org <bioc-devel at r-project.org>; Chedraoui Silva, Tiago <txs902 at med.miami.edu>; Fernanda Veitzman <fveit001 at fiu.edu>
Subject: Re: [Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks
Sent: Monday, June 14, 2021 9:18 AM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: Gabriel Odom <godom at fiu.edu>; bioc-devel at r-project.org <bioc-devel at r-project.org>; Chedraoui Silva, Tiago <txs902 at med.miami.edu>; Fernanda Veitzman <fveit001 at 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://bioconductor.org/checkResults/devel/data-experiment-LATEST/sesameData/nebbiolo2-buildsrc.html<http://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 at roswellpark.org<mailto:Lori.Shepherd at 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Gabriel Odom <godom at fiu.edu<mailto:godom at fiu.edu>> Sent: Thursday, June 10, 2021 1:51 PM To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> Cc: Chedraoui Silva, Tiago <txs902 at med.miami.edu<mailto:txs902 at med.miami.edu>>; Fernanda Veitzman <fveit001 at fiu.edu<mailto:fveit001 at 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 at r-project.org<mailto:Bioc-devel at 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. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. 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