[Bioc-devel] Bioconductor package devel site not updating

Mon Jun 22 18:25:31 CEST 2020

It was the issue on the Bioconductor side.  If you look at the page now it looks like everything is updated.  Let us know if anything does not appear correct.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Hoffman, Gabriel <gabriel.hoffman using mssm.edu>
Sent: Friday, June 19, 2020 8:00 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: Bioconductor package devel site not updating

Hi Lori,

Thanks for your help.  It looks like you found the issue, but here is my original message.  (I�m not sure why it didn�t go through)

Best,

Gabriel

Hi,

I maintain the variancePartition package and I recently posted an update v1.19.4 to the development branch (BioC 3.12).  The build was successful: http://bioconductor.org/packages/devel/bioc/html/variancePartition.html<http://secure-web.cisco.com/1OyTHHUsZY3VsP1fPtVX8zsmeaxZcZkgT8ylIH3E8VUQs2-13amHCQjt8X7-Zo2zmICuxJuG_9r9phDTlNEIoLti5Hu_nRc3dWHIfhbgq1wjR_uLwbBhfx2l2q-vR8SYyAwrK0wvHdIVZO5AHH8XGP7RUPBfT05KePvVn_wX0OwqLoW-nwEqMXKg08U4i0_hOWAWqJUJOqNbYipgR_vxbvSgKpohxTM_64q_pnAkqGtMgUsn-SpF06xhG3Oy-LwwSjZiaZuI7nEj5-qx7g-KK7wdBV-Rmv6-vwEWiBBWP0qLfKwoBDvVu4K1LV4L4pvu1t1d_gyc1hDS11y28qD1ie_cXE-MYiIcgn4cnf4yCtvo/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FvariancePartition.html> . The vignettes and manual were correctly updated to this version.

My issue is that the webpage did not update.  It is still on v1.19.1.  This causes three problems.

  1.  The link to download the source package doesn�t work because it points to variancePartition_1.19.1.tar.gz.
  2.  I added a new vignette.  I can load it if I specify the URL directly (http://bioconductor.org/packages/devel/bioc/vignettes/variancePartition/inst/doc/FAQ.html<http://secure-web.cisco.com/1-lncMzHuEQWU3uOX8U2aV8WN_8s3cg8q-DPxUJyabGmvYdqkGtL0X70arCoDTXeeHE_s61kRE6Am5KeqMo-PxdJJs4rDtuO2hlrfHME_u0G_Lv7lYFhYlAIDJ2xGdCWbGNkquZrklX5dx4LHz0QYbSEN2MfbSCyAbbS0a-lUCQRQbeU8204wNugf6a5ly87OcgPQoJmsoXU1mJmhVKT5y4ezUtf9YS7Hj0p6Wf1A2MYtGx1cGqhJhHFGlsegve4nZGN6cPVSAo0xWNdcDebJMw4GrDg79meNCyMtkotsbmBar-KlthZiv043CpoPlwA3sbD_iGzxpDgs4ZiidJXtPy3iiH2DWOjljkvWlctzkt4/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FvariancePartition%2Finst%2Fdoc%2FFAQ.html>) but the webpage doesn�t link to it because the page is the old version.
  3.  This version makes some changes requested by reviewers, and I need the webpage to update before I can resubmit my manuscript.

My question is: Is the issue with the webpage on Bioconductor�s side, or is it an issue with my package?

(I get the old page on multiple browsers and multiple machines, so it isn�t a caching issue)

Thanks

Gabriel

From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, June 19, 2020 at 7:08 AM
To: "Hoffman, Gabriel" <gabriel.hoffman using mssm.edu>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: Bioconductor package devel site not updating

USE CAUTION: External Message.

Hello,

The message you sent appears blank.  So I'll take my best guess at what you are referring to:

Please see this post indicating that we are having trouble with our website and are in process of fixing it.  We have located the issue and pushed a fix and once applied the landing pages should generate properly.

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html<https://secure-web.cisco.com/1Ry8QVshv1h8LZw09yFl2sSqlNV0dhUCNDOLFBIZTAnbhs9ohcFLwUlHM_d1jttdUiO1XzVsuZRy3aYzg0wFCvGCjef8-D0gfQMzP7Aj_0HqUKI4PyRhRU3FdQF9OyC9gczcLT2IDdOztuMhppoWDJyfLfbuRNbwCBPZnvPMzERKd_Bxnmm8gYnL0DgC-SaRZnjebeitKrDIOvjNNmc3P1xzYqn4fH2E6gwiUFNc3rBIbo_gFFq89aB_tv2OirJJMVxcLxuLNGKGLZ-LDkkj7wmqPhKapmgc8ljU7Ck53LLK2ROBfii9_uQYJq9uJIK-Smr2N9m1nbpoDiYUP0rJdWg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DJune_016923.html%26d%3DDwMFAw%26c%3DshNJtf5dKgNcPZ6Yh64b-A%26r%3DKdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk%26m%3D-WIBPVmkz719yBNTRf_Ycqugpy7a70f6i0rKzBKUTv0%26s%3DTPQSupVoQleHsY2i_4PnuwGoD6SEj8hXd5_XXfMQRUo%26e%3D>

Please check the build reports for the version numbers that are being used to build the package.

http://bioconductor.org/checkResults/<https://secure-web.cisco.com/10fUrbyz6IHKb3XRo880qoYQ3tghmrxRCvh9-T2Rwo6iqjQc2UhdBv-h0LS7nRIvqq3JGzMS7gfRamf3HPA7al2pacr4YOp1SHAqZjzuwlwpIJqaiJlio8Z0FzXzvUa3D5XSGxp6gxF6BQ1epRzgXiOTffoyXJ_LOsvB_9Tm3Gxh0zr3NnNrgeHT3IiZQzYvH8c2dIR6MQr8IaKvH7dSkpYveqTIGJRUA3TkBwk6MymEoHA3jWI_XPD2MekEyBF21Qqz_BTqnvYLDhCg0LZY8ECZId3WgfbCYMJfCNlUNjDkrNUZZU8IJz-3UVHNQsE9eq-u4JPSbG0UlN8Y0CUewUw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__bioconductor.org_checkResults_%26d%3DDwMFAw%26c%3DshNJtf5dKgNcPZ6Yh64b-A%26r%3DKdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk%26m%3D-WIBPVmkz719yBNTRf_Ycqugpy7a70f6i0rKzBKUTv0%26s%3DZmdgkn_PDLzCRnp0ONOkhaPVueqyb_pq7tnbpF0kfm4%26e%3D>

Keeping in mind there can be up to a 48 hour delay to see the results as described here:

http://bioconductor.org/developers/how-to/troubleshoot-build-report/<https://secure-web.cisco.com/1J8Y7cCckTBcNJv1D8V9IyorLzThKvGx-IESfiG1d5P0sFoexueX7GZs6olMHFOagJ4kQ5tiFgKA3Dmj-SyUc5wvh-0CZlTjjCKAskDJtyvhP_lUwVfI6z3kt7aGImhClp4PEKkdTTyx8fAwHL5NQTeqaz0SOD_pAxlgSAHfxwgWnBCeyF5dg829h26Ok1VbqnWqeg3UFeJS-9vOXiJ5J9TNE0iJoWXBZhQGBBUoOET1GcrjREd4s9vKKmVRR6F4g9qLl-9VJ9CQ9FKymLtMq-JbLbpu90e6GOd8Ii-3SxmwEtwWSW4BaKiyOPSZKfB7rBuAoRQmKnavT7Ba25A1cOQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__bioconductor.org_developers_how-2Dto_troubleshoot-2Dbuild-2Dreport_%26d%3DDwMFAw%26c%3DshNJtf5dKgNcPZ6Yh64b-A%26r%3DKdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk%26m%3D-WIBPVmkz719yBNTRf_Ycqugpy7a70f6i0rKzBKUTv0%26s%3DyJzrOiKvullMMAKe9g_scXqrOBajEdpRYgeXJAftJT8%26e%3D>

If none of these applied to your issue, please provide more detail on what package you maintain and specifics on what you are experiencing.

Thank you.

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 Hoffman, Gabriel <gabriel.hoffman using mssm.edu>
Sent: Thursday, June 18, 2020 9:37 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Bioconductor package devel site not updating

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