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

Tue Jun 15 23:27:16 CEST 2021

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 using 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 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>
> 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
>> <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>> 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
>> <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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
>>
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>> <https://urldefense.com/v3/__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__;JSUlJSUl!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdli0NKni6g$>
>>
>>
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>> <https://urldefense.com/v3/__https://secure-web.cisco.com/1bqZwT50er9poFDDqFv9odoW03H8D5yVGrGEoL8x39iV0iGlJo3LGXRbu0s5utfylZKoL0pJFOMT-krQn63FZPz4jbbM1csArWCEC4RljxzJVVWZMX0Fj7YfeX4K_nr9zFPMl_xeBpf7wEI_Mqu11ttlKd21i6XTPNS1C-XD0bagrpfasL4ohQhXs-ofbgnlR4fOP5H9snseyIxAmoE2yqJDSMdkApOX5Shtyb3YY_UunRkLjYkVhPXkSBIbJRyn4a2IjGh-g0qGBoXQKVloPNPUPBvsUXKoeRidToDILB-trPMPuleD4A9u2NxtDxYbJ/https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fbioc-devel*3Chttps:/*secure-web.cisco.com/1WejC--XRGIIqyln9vLBxkpQo2j4DxjnaqmQ4CtRXvKRhfWQqGIRaUaDOflzAsvm0E47XCYn62vcVS6zhgaqZtZnAtqdBXl9cGcD5o2prZ3nv1QggE-YsO-2_WwYb6Fm2CvD-4K_3CvSvuOoq2psZ2THoRyvjqZ8xWGTaFJLcTnXF4g3VFM0LWh4v3Oj2XoCzjLLk00c-G9zvdeEtN1pAFo7bJt4ynLgyIZ5WEyRbtRaZCftz6S2UlE0Cn4qdZ-aflS8thfZ4Fq2Ylg0cAbty9DUJZkY8i1RKKf0DrleLEO-3kWb1oVGPXdoPG02wOG9p/https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fbioc-devel__;JSUlJSUlJS8lJSUlJSU!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlgPAK2N0g$>
>> >
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>> <https://urldefense.com/v3/__https://secure-web.cisco.com/1bqZwT50er9poFDDqFv9odoW03H8D5yVGrGEoL8x39iV0iGlJo3LGXRbu0s5utfylZKoL0pJFOMT-krQn63FZPz4jbbM1csArWCEC4RljxzJVVWZMX0Fj7YfeX4K_nr9zFPMl_xeBpf7wEI_Mqu11ttlKd21i6XTPNS1C-XD0bagrpfasL4ohQhXs-ofbgnlR4fOP5H9snseyIxAmoE2yqJDSMdkApOX5Shtyb3YY_UunRkLjYkVhPXkSBIbJRyn4a2IjGh-g0qGBoXQKVloPNPUPBvsUXKoeRidToDILB-trPMPuleD4A9u2NxtDxYbJ/https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fbioc-devel__;JSUlJSUl!!FjuHKAHQs5udqho!c4GVYH_JPRQKYWoa4p9ayawnFXkmvhpjZF9mwBTbIymN8-kTEJkpdlicKk9IsQ$>
>>
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