[Bioc-devel] EWCE Bioconductor package

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Feb 11 15:47:00 CET 2021

When a package is defuncted and removed from Bioconductor, push access is no longer granted.

The package has been out of Bioconductor for several releases and will have to be re-submitted and undergo a formal review through the submission tracker.


As stated in the package lifecycle documentation:



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 Murphy, Alan E <a.murphy using imperial.ac.uk>
Sent: Thursday, February 11, 2021 7:46 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Nathan Skene <nathan.skene using gmail.com>
Subject: [Bioc-devel] EWCE Bioconductor package

Hi all,

My apologies in advance if this is not the correct mailing list for this question, regarding development to the EWCE Bioconductor package.

I work as part of Dr. Nathan Skene's group who submitted the package EWCE<https://secure-web.cisco.com/1sx525Q-bQneoyLW4yHBUObMMrMG0LTbnZfrXekcT9C3BUwLeiiZ9iUPNIP-wKORuLgEp6AX2pgrDH2BBsmWGAiePOSu7efUtmKDcygCUcXFt2dsj0kYFmm-Xlos9hs37021atLamsnQEfbtqOdHYQz2wtWoggI-WtzwASwzYWLnR2Q44tmO3ojckLnFzUnqLpdpBLzHMntnC_tTv_DU2Jov-UHb1cf7L_7x05_6M_651LzOaG4OLWsX53w9rIvrAvS9bf4X6nA48KRJMZEevLhxMQWSqv5myH6oHowcatlu6VbPseluKHyT3wJcvZpmK/https%3A%2F%2Fbioconductor.riken.jp%2Fpackages%2F3.5%2Fbioc%2Fhtml%2FEWCE.html%23since> to Bioconductor some years ago. The package fell out of maintenance and as such was deprecated from Bioconductor 3.6. We are working to update and hopefully, reinstate the package but are running into issues when pushing any changes to Bioconductor. We have been following instructions here<http://secure-web.cisco.com/1ZqSdbN61YyYYV3KiXShkC0ceYqoBoDgeVozbANodfbwCLpGUwnvwfxWZKUIOWHfgBFcDqV8B2KJEt_6IqgbzubjUlGoKfK2aaEMhqyPxaLLng389G_UMR3LkScYMVLYOz-d8x4yO5F27ldVbM4ctNzBXwOtPck3SKtY34RBPiL0vDXbn4Gn2EiCnvbgx8KQS4gAbh02HEvZB2wylI0AHFo9KwA2laZIcRAlIuLQ8VUVsd2L1EjOcWrQ1cDRJRZjvp32MQ4Zg94DIq_Kwk9krb8ERgnIdwJPawv7WgslW4Msjll2oBWFfEvaMzfl8aSwG/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F> to try and sync our Github updates with the Bioconductor version but can't seem to push the new, merged version to Bioconductor.

To test the cause of the issue, we cloned the repo:

git clone https://secure-web.cisco.com/12B2YQDIm_cMn-0q1F-RByiCbf2gIjefbocAxQ9Ufhu3GxJ8AD8wnMFMiOK4CWqYfcl6TSMUdYfIQ1xHqzHRiGIhDC-LBJbCTZmHw8F3rT59gUPfbo3OYZJmZyqctSYPHUMMNLElFxKh7xyf2YjWTCBkZhgDaT9F9XobPWAZpVapV_6QGSOvvgYHk8FM_EqfYzmkzKQEUaU8vaK8iLfiEBSYzKn_FD6zL0MRyVny3Ibw7C7acqKfKHgSNHuWIEwKhH09SJvFMmXlvyp_JYezufnoQ4D5FAi8wEiy1sqRhu-1p5CcjKrd3nke_-SbFOsTn/https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2FEWCE

And updated the version of the package in the DESCRIPTION file and tried pushing the change, using Nathan's account which is associated with the package. However, we still can't push to Bioconductor, getting the error:

-bash-4.2$ git push origin master
FATAL: W any packages/EWCE n.skene DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.Please make sure you have the correct access rights
and the repository exists.

It appears it does recognise Nathan's account but doesn't think he has access rights to the repo. It is worth noting that EWCE is also not listed on his account's webpage.

We are wondering if this issue is caused by EWCE being deprecated and if so, what are the necessary steps to reinstate it?

Kind regards,

Alan Murphy
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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