[Bioc-devel] MPFE Bioconductor package

[Turaga, Nitesh]

Hi Conrad,

Sorry to hear you’ve had such a hard time with the Bioconductor GIT ecosystem. Please keep in mind that for a new build to be triggered you have to update the version number in the DESCRIPTION file of the package( The “x.y.z” version format needs the “z” to be incremented ).

Also, I highly encourage you to email the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> mailing list where other people can help you more readily.

Best,

Nitesh

From: Conrad Burden <conrad.burden using anu.edu.au>
Date: Wednesday, September 16, 2020 at 10:16 PM
To: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org>
Subject: Re: MPFE Bioconductor package


Dear Nitesh,

I have spent some considerable time trying to fix the MPFE package which I inherited from dead colleagues.  I was easily able to determine that the fix required to the R source code is a trivial one line change.  By contrast I have spent at least a week of my valuable time tryng to get the fix into your system using the available online instructions.  It is no exaggeration to say has been a stressful and unpleasant experience.  With help from colleagues who understand github, yesterday I finally managed to get something uploaded using instructions at https://bioconductor.org/developers/how-to/git/<https://secure-web.cisco.com/1_lTlsPGdiweUgsTA1ZSetCA6Wa7Cx0nRRhn-KMD9QOgfthLn1yQMkxrS8lEIYgyLi6eDkxv4Wm8hJ2ip-Z4qgfVJPc6238pgfe6HqXcyA1_S1ku06TrAYNPKiMfHXlMv2KBdkHrqtAz9dXO_t-wzGY5K_p4uIqEA2VUJOpkHGqQzblgjAapiGRVkGHTp_Pff7SfT8fLkVSZ-AfrIXkpVKEevWX4s3g_4SaHC9_TQUaZsgQncY9BeXNHVrjcEBmhQ2RKHzJs0kvsR8redxDy6l7EF8MaBty9sjZkZQSrE0pzAUBk_QdV89XPPG0jeVaciSlTIz36WWSvFao4fdAMh3drpFUCZRbh-f5sivj7HEWo/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F>.  Having spent the morning rummaging around on your web pages I have finally found a report at http://bioconductor.org/checkResults/3.12/bioc-LATEST/MPFE/<http://secure-web.cisco.com/1F3EIY-Q4mY1uMM701WuI38wU45d1aOwF8Sbl-3q9TBOM2RFp4aNUo7zHZ228S13gGOPH5HjbXAS1WRPseNh2-CYIcBjElI0-nIjvPITUPTab6IQ102px53X5YpjPBhCb3vtHs0kFMvDxbTT0ATDrX7nFj36o3TKgUDq8uUgH8oGOJdC8wZokuZiotc_0ay3E5oUeZ7cMHdS4KqkEUy7JkNa3b3d68wn5BkhQScER2k04Cg1JMOEwPCLpgNkj0RgLjI43nMKdtYfiEWE1eBocIetj2NXOiqyhLAKaWWskPcATgWQwHF4OAHlLtV-B0JXEZfiSdr7CGpYOrsB-Tu7OX5dqhjl6CGPr73nu1N8l8O8/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2FMPFE%2F> which apparently says it didn’t work.

Will you PLEASE, PLEASE, PLEASE at least give me a hint about how I find out what went wrong.

Sincerely,
A/Prof. Conrad Burden
Mathematical Sciences Institute
Building 145
Australian National University

Phone: 61-2-61250730
E-mail: conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>
Web page: http://maths.anu.edu.au/people/conrad-burden


On 7 Apr 2020, at 8:51 pm, Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org<mailto:Nitesh.Turaga using RoswellPark.org>> wrote:

Hi Conrad,

I'm sorry to hear about your colleagues.

Unfortunately we are not able to devote time towards individual packages, but we can deprecate the package and un-deprecate it at a later time when the issues are fixed (whenever you have some time to look at it). This is not an issue in anyway.

For now, we will go ahead and deprecate this.

Best regards,

Nitesh


On Apr 6, 2020, at 7:45 PM, Conrad Burden <conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>> wrote:


Dear Nitesh,

Thank you for your email regarding the MPFE package.  I was involved in the development of this package 6 years ago with 3 colleagues, two of whom I am sorry to say are now deceased, and one of whom is no longer working in academia or bioinformatics.  Although I developed the theory behind this package and wrote some of the R code, I generally left the Bioconductor side of things to my colleagues.  I am almost entirely ignorant of the use of Github to the extent of not even understanding the phrase "committing and pushing changes to your package”.  Also, my research has moved on to other areas of applied mathematics.

It is possible that I could return to this one day and sort it out.  For the time being however, I am extremely busy with running a lecture course remotely from home and trying to meet a deadline for resubmitting a paper.  Unless someone at your end is able to sort out the problem, I’m sorry to say we are just going to have to leave it go at least for the time being.

Very best regards, Conrad.

A/Prof. Conrad Burden
Mathematical Sciences Institute
Building 145
Australian National University

Phone: 61-2-61250730
E-mail: conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>
Web page: http://maths.anu.edu.au/people/conrad-burden



On 7 Apr 2020, at 3:40 am, nitesh.turaga using roswellpark.org wrote:

MPFE Bioconductor Package Report

Nitesh Turaga1

1Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA

April 06, 2020

Package: MPFE

Dear Conrad Burden,

I am contacting you concerning the MPFE package, on the release and devel branch of Bioconductor, for which you are listed as the maintainer.

The latest build/check report shows that your package is failing on one or more platforms. Please resolve the issues for your package’s continued inclusion in Bioconductor.

https://bioconductor.org/checkResults/release/bioc-LATEST/MPFE/https://bioconductor.org/checkResults/devel/bioc-LATEST/MPFE/

Note,

• The last day for commits to the release branch is Monday April 10, if you want to get a build report.The branch freeze is on April 14.

• Similarly, Friday April 24 for last day to pass R CMD build/check on ‘devel’ to get a build report. Commits can go through until the freeze happens to create the RELEASE_3_11 branch on Monday April 27.

Please let me know if you have any questions.

P.S. vignette error, please fix.

Regards,
Nitesh

Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


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