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List: bioc-devel
Subject: Re: [Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks
From: Wanding Zhou <zhouwanding () gmail ! com>
Date: 2021-06-15 21:27:16
Message-ID: CAK+Q8bOL0=HnoKDZptMnxu7qS1O+yUh0CyUczviCRb6tpKQ6VQ () mail ! gmail ! com
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Hi Gabriel,
Yeah, that should be correct. The build seems fixed on Bioconductor I just
checked.
Wanding
On Tue, Jun 15, 2021 at 12:40 PM Gabriel Odom <godom@fiu.edu> wrote:
> 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@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@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@r-project.org> on behalf of Kern,
> > Lori <Lori.Shepherd@RoswellPark.org>
> > *Sent:* Monday, June 14, 2021 9:20 AM
> > *To:* Wanding Zhou <zhouwanding@gmail.com>
> > *Cc:* Chedraoui Silva, Tiago <txs902@med.miami.edu>;
> > bioc-devel@r-project.org <bioc-devel@r-project.org>; Gabriel Odom <
> > godom@fiu.edu>; Fernanda Veitzman <fveit001@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@gmail.com>
> > Sent: Monday, June 14, 2021 9:18 AM
> > To: Kern, Lori <Lori.Shepherd@RoswellPark.org>
> > Cc: Gabriel Odom <godom@fiu.edu>; bioc-devel@r-project.org <
> > bioc-devel@r-project.org>; Chedraoui Silva, Tiago <txs902@med.miami.edu>;
> > Fernanda Veitzman <fveit001@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/14wC2r7uMzHAbZME5HNyl8y3THlgTIwq2nJ1nnqRIKG1chTxUF8H34 \
> > UzOHihRZC7SDCP2PDTKoqrRcfo5PRsbwSu8p2rP5_cWFgQW6pAHZodfi-enkPE_-JHNwoPK92gAi_NnrPS \
> > COiaJlX0-JI5SBrU7OclFZmr95RmFsiRTwA_SkAukghYSWOqtGRssFlY53CIkQKO08aaTw6jI-9V5XAdmq \
> > lcqrj1i0C5grb-B5y0IsSXsHjPq_uFO8gelmkQqV7k9cIdFBDKd7c8r6EugHkO4WvOCoxSeMUqzT1fpL8M \
> > qDMvnBJKkgU-UQO566eI7/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fdata- \
> > experiment-LATEST%2FsesameData%2Fnebbiolo2-buildsrc.html<http://secure-web.cisco.c \
> > om/1Wqopyj6WX11lkKJCcYWkMTdFk6tVlIE0fNHVxlLeCXdaeUnhenjnlg3yUH9XMiuSFy0B9vk2gpimLo \
> > m8gF33P8HUA6LNPdeNYvZKibiS7ebYcVKrHve0OJNiqWuTWpRnJbaZ2Pc4SoqYr5GqhU3pViuUYPRW7jVW \
> > RvsITRMZfiILDKetophnVSPVhUNRjvmNl3DEDZ3uIqFNIp_QEk1gsQ9pQO6Q8F5YwaDrsuRBdXI_6pPvNg \
> > KNY806BHmtMGuvSIqZXDSkACRShKyoB609tTBL7HwrNPtNoMjRB2Z6juNBjQPkwA8wUNBjWv9DxJlr/htt \
> > p%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fdata-experiment-LATEST%2FsesameData%2Fnebbiolo2-buildsrc.html
> > <https://urldefense.com/v3/__http://secure-web.cisco.com/14wC2r7uMzHAbZME5HNyl8y3 \
> > THlgTIwq2nJ1nnqRIKG1chTxUF8H34UzOHihRZC7SDCP2PDTKoqrRcfo5PRsbwSu8p2rP5_cWFgQW6pAHZ \
> > odfi-enkPE_-JHNwoPK92gAi_NnrPSCOiaJlX0-JI5SBrU7OclFZmr95RmFsiRTwA_SkAukghYSWOqtGRs \
> > sFlY53CIkQKO08aaTw6jI-9V5XAdmqlcqrj1i0C5grb-B5y0IsSXsHjPq_uFO8gelmkQqV7k9cIdFBDKd7 \
> > c8r6EugHkO4WvOCoxSeMUqzT1fpL8MqDMvnBJKkgU-UQO566eI7/http*3A*2F*2Fbioconductor.org* \
> > 2FcheckResults*2Fdevel*2Fdata-experiment-LATEST*2FsesameData*2Fnebbiolo2-buildsrc. \
> > html*3Chttp:/*secure-web.cisco.com/1Wqopyj6WX11lkKJCcYWkMTdFk6tVlIE0fNHVxlLeCXdaeU \
> > nhenjnlg3yUH9XMiuSFy0B9vk2gpimLom8gF33P8HUA6LNPdeNYvZKibiS7ebYcVKrHve0OJNiqWuTWpRn \
> > JbaZ2Pc4SoqYr5GqhU3pViuUYPRW7jVWRvsITRMZfiILDKetophnVSPVhUNRjvmNl3DEDZ3uIqFNIp_QEk \
> > 1gsQ9pQO6Q8F5YwaDrsuRBdXI_6pPvNgKNY806BHmtMGuvSIqZXDSkACRShKyoB609tTBL7HwrNPtNoMjR \
> > B2Z6juNBjQPkwA8wUNBjWv9DxJlr/http*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel* \
> > 2Fdata-experiment-LATEST*2FsesameData*2Fnebbiolo2-buildsrc.html__;JSUlJSUlJSUlLyUlJSUlJSUl!!Fj
> >
uHKAHQs5udqho!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@roswellpark.org
> > <mailto:Lori.Shepherd@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@r-project.org<mailto:
> > bioc-devel-bounces@r-project.org>> on behalf of Gabriel Odom <
> > godom@fiu.edu<mailto:godom@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 <txs902@med.miami.edu<mailto:
> > txs902@med.miami.edu>>; Fernanda Veitzman <fveit001@fiu.edu<mailto:
> > fveit001@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-bDosj2WZQlQzabUbU \
> > w-sSN6lEC-B6l3_OJo_RSlBFh4j7Rjr3HpXJn16WzrsjJ3wF4_C4yy3YR3tOGL0L1VeTZ7FYrAF6XHbRcS \
> > 3EkDimq7a_wpzO1NgverSf5l9K6TsLwXVjoNx06G4G9Ca76BET29gO6_mD2RyaevSEWOsPiQ4vYTfmMcrK \
> > 4HkbE58yJmLmuMmwkWU1JSvtx6-fm_o9g2wdpyztI8aQ/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2064
> > <https://urldefense.com/v3/__https://secure-web.cisco.com/1LJYIf7eE_SLkrPc-raY2Tf \
> > rjVLvxvy25vUgb2qyF7dnrGbAVuMe-y9M92LmMJZPf7OZS4Zzw4czMrxNuuCQk3Mh4BXq7KToBlTJ6Wg09 \
> > N1mRJIIxMidq-bDosj2WZQlQzabUbUw-sSN6lEC-B6l3_OJo_RSlBFh4j7Rjr3HpXJn16WzrsjJ3wF4_C4 \
> > yy3YR3tOGL0L1VeTZ7FYrAF6XHbRcS3EkDimq7a_wpzO1NgverSf5l9K6TsLwXVjoNx06G4G9Ca76BET29 \
> > gO6_mD2RyaevSEWOsPiQ4vYTfmMcrK4HkbE58yJmLmuMmwkWU1JSvtx6-fm_o9g2wdpyztI8aQ/https*3 \
> > A*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-Zi6Ty7B1fjWZ7lIh1 \
> > FIhDb7ZTgZWrrlAeTktUkCcwIZmoOr_NOj8wGRorNymIlJkbM_OZ9tXF7loND6qtHWOAGyLrDEvU9Yack4 \
> > zl4GZYI6wTzcdr2Gd31XB2eb9G1LdpqiIpPY7m2sAT0VPJ04EX_FbBlbo_G0RKWHzJNs6p6ILdBryIiOUf \
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> > ZPSQ0uAErYYcSW7rU8eC40tO2ctZ032ONQ4GCwlOk5Lw/https%3A%2F%2Ftravis-ci.com%2Fgithub%2FTransBioInfoLab%2FcoMethDMR%2Fbuilds%2F228394255
> > <https://urldefense.com/v3/__https://secure-web.cisco.com/1j2Lm3Ar4WQmwywzgNFqh4t \
> > T1aPJE0I8o00-Zi6Ty7B1fjWZ7lIh1FIhDb7ZTgZWrrlAeTktUkCcwIZmoOr_NOj8wGRorNymIlJkbM_OZ \
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> > Yg7rcGBdVHcvolT2k9rT8RqHT-qOIcZPSQ0uAErYYcSW7rU8eC40tO2ctZ032ONQ4GCwlOk5Lw/https*3 \
> > A*2F*2Ftravis-ci.com*2Fgithub*2FTransBioInfoLab*2FcoMethDMR*2Fbuilds*2F228394255__ \
> > ;JSUlJSUlJSU!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlhNepO3pw$>),
> > but instantly fails on Bioconductor (
> > http://secure-web.cisco.com/1_JOpYlcb26Br20C8xzcwa5dZN4HaNbPd23ADPLxcNF191FKN4lUx4 \
> > OM5jOINXAoGkByRNgNEr-VfiSdvABVAfPbk6WLrPVAjEA46btRh0GpYlT2eWfywAPHT0A8H1RHXz9ULN52 \
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> > zEEpoEt_3hrvJJMgzoYlFf2LsWWDm9OUMw3UqVor8d-B0y4uPfXxx4wWiF93L5rse-fLht_Muo0xos00WH \
> > -2uqmT-SwroZ9Gawn2qSeUyAfaiQg-tSZIOsUtKPC5Q/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FcoMethDMR_buildreport_20210610114
> > <https://urldefense.com/v3/__http://secure-web.cisco.com/1_JOpYlcb26Br20C8xzcwa5d \
> > ZN4HaNbPd23ADPLxcNF191FKN4lUx4OM5jOINXAoGkByRNgNEr-VfiSdvABVAfPbk6WLrPVAjEA46btRh0 \
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> > IR_tKPNX_JzWcxN9TZtPJk6UPbBkuFzEEpoEt_3hrvJJMgzoYlFf2LsWWDm9OUMw3UqVor8d-B0y4uPfXx \
> > x4wWiF93L5rse-fLht_Muo0xos00WH-2uqmT-SwroZ9Gawn2qSeUyAfaiQg-tSZIOsUtKPC5Q/http*3A* \
> > 2F*2Fbioconductor.org*2Fspb_reports*2FcoMethDMR_buildreport_20210610114__;JSUlJSU! \
> > !FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlgvDT3DFQ$> \
> > 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
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
> >
> > https://secure-web.cisco.com/13Kk3L1299v2slZnlxS0A7jQHspZUxsF4ynFFRxOU19eChzGmhwve \
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> > dE6tj3ZoFv4NZEN2tmheLY5sa4yTTiIZYGPPso2jcrcQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
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> > trPMPuleD4A9u2NxtDxYbJ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-deve \
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> > EO-3kWb1oVGPXdoPG02wOG9p/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> > <https://urldefense.com/v3/__https://secure-web.cisco.com/1bqZwT50er9poFDDqFv9odo \
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> > h*2Fmailman*2Flistinfo*2Fbioc-devel__;JSUlJSUlJS8lJSUlJSU!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlgPAK2N0g$>
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