Hi Matt, Nitesh, Thanks for replying quickly and for sending the link to the full check report, which I had not been able to find.
I think I have worked out what the problem might be. I have found the page “Troubleshooting Build Report” which tells me "Changes pushed to Bioconductor before 4:45 will be reflected in the following day’s build report that is posted around 1:00 PM EST”, which I assume is US eastern standard time. I pushed my changes (MPFE v1.5.2) to the Bioconductor repository at approximately 2:30pm Canberra time yesterday, 16 September, which is 12:30 am 16 September on the east coast of the US. It won’t appear in the build report unitl 1:00pm 17 September US time, which is 3:00am 18 September in Canberra. I’ll check it again tomorrow. Sorry to put you to all this trouble. - cheers, Conrad. A/Prof. Conrad Burden Mathematical Sciences Institute Building 145 Australian National University Phone: 61-2-61250730 E-mail: conrad.bur...@anu.edu.au<mailto:conrad.bur...@anu.edu.au> Web page: http://maths.anu.edu.au/people/conrad-burden On 17 Sep 2020, at 1:16 pm, Stone, Matt <mst...@fredhutch.org<mailto:mst...@fredhutch.org>> wrote: Hi Dr. Burden, The "ERROR" links on that report page link to the full check reports for each platform. Here is the report from malbec1, one of the Linux machines. http://bioconductor.org/checkResults/3.12/bioc-LATEST/MPFE/malbec1-checksrc.html If you're not familiar with the output of R CMD check, it runs a series of diagnostic checks and reports any detected issues. In order of decreasing severity, they are ERROR, WARNING, and NOTE. The Bioconductor guidelines [1] indicate that errors and warnings must be fixed in order for the package to be accepted. (You can find more details on the checks in the R Packages book [2].) This check report found one ERROR, one WARNING, and one NOTE. The ERROR was caused by an error in one of the documented examples in the file `MPFE-Ex.R`, which you can see in this excerpt from the report: ============================================= * checking examples ... ERROR Running examples in ‘MPFE-Ex.R’ failed The error most likely occurred in: base::assign(".ptime", proc.time(), pos = "CheckExEnv") ### Name: MPFE-package ### Title: MPFE ### Aliases: MPFE-package MPFE ### Keywords: amplicon, bisulphite sequencing, bisufite sequencing, ### methylation ### ** Examples data(patternsExample) estimates <- estimatePatterns(patternsExample, epsilon=0.02, eta=0.01) ============================================= In my experience, errors in the examples are caused by either a) buggy or outdated code in the example or b) a bug in one of the package functions that the example uses. Here, I would guess that either a bug exists in the estimatePatterns() function, or the data loaded from patternsExample isn't as expected. You can reproduce and debug the error by running the example yourself. For the other two checks: The WARNING was caused by the current deprecation status of MPFE (which I'm guessing you're in the process of updating). The NOTE suggests you explicitly import some functions that haven't yet been declared in the NAMESPACE. I'm relatively new to Bioconductor and so I don't know if this is mandated, but I would suggest fixing this as well. Hope this was helpful! Matt [1] https://www.bioconductor.org/developers/package-guidelines/ [2] https://r-pkgs.org/r-cmd-check.html#check-checks On 9/16/20, 7:28 PM, "Bioc-devel on behalf of Turaga, Nitesh" <bioc-devel-boun...@r-project.org on behalf of nitesh.tur...@roswellpark.org> wrote: 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@r-project.org<mailto:bioc-devel@r-project.org> mailing list where other people can help you more readily. Best, Nitesh From: Conrad Burden <conrad.bur...@anu.edu.au> Date: Wednesday, September 16, 2020 at 10:16 PM To: "Turaga, Nitesh" <nitesh.tur...@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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=eC4mws_XHyw54OmYzImxdEYWMjiUMOVQI94y7enC3eo&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1-5FlTlsPGdiweUgsTA1ZSetCA6Wa7Cx0nRRhn-2DKMD9QOgfthLn1yQMkxrS8lEIYgyLi6eDkxv4Wm8hJ2ip-2DZ4qgfVJPc6238pgfe6HqXcyA1-5FS1ku06TrAYNPKiMfHXlMv2KBdkHrqtAz9dXO-5Ft-2DwzGY5K-5Fp4uIqEA2VUJOpkHGqQzblgjAapiGRVkGHTp-5FPff7SfT8fLkVSZ-2DAfrIXkpVKEevWX4s3g-5F4SaHC9-5FTQUaZsgQncY9BeXNHVrjcEBmhQ2RKHzJs0kvsR8redxDy6l7EF8MaBty9sjZkZQSrE0pzAUBk-5FQdV89XPPG0jeVaciSlTIz36WWSvFao4fdAMh3drpFUCZRbh-2Df5sivj7HEWo_https-253A-252F-252Fbioconductor.org-252Fdevelopers-252Fhow-2Dto-252Fgit-252F&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=My4fbcyVNcRJkKeB9ox5fMuMnJXWKCRELmXQ_5RmsEQ&e= >. Having spent the morning rummaging around on your web pages I have finally found a report at https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.12_bioc-2DLATEST_MPFE_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=ItngR8K1kdOFPKIhtS04i5sVjVcMmZSBHHBH83KMwQo&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1F3EIY-2DQ4mY1uMM701WuI38wU45d1aOwF8Sbl-2D3q9TBOM2RFp4aNUo7zHZ228S13gGOPH5HjbXAS1WRPseNh2-2DCYIcBjElI0-2DnIjvPITUPTab6IQ102px53X5YpjPBhCb3vtHs0kFMvDxbTT0ATDrX7nFj36o3TKgUDq8uUgH8oGOJdC8wZokuZiotc-5F0ay3E5oUeZ7cMHdS4KqkEUy7JkNa3b3d68wn5BkhQScER2k04Cg1JMOEwPCLpgNkj0RgLjI43nMKdtYfiEWE1eBocIetj2NXOiqyhLAKaWWskPcATgWQwHF4OAHlLtV-2DB0JXEZfiSdr7CGpYOrsB-2DTu7OX5dqhjl6CGPr73nu1N8l8O8_http-253A-252F-252Fbioconductor.org-252FcheckResults-252F3.12-252Fbioc-2DLATEST-252FMPFE-252F&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=xJS0TUL-PuPNqSUr6E8T1SRkOeee-ftq0PL40CTxCO4&e= > 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.bur...@anu.edu.au<mailto:conrad.bur...@anu.edu.au> Web page: https://urldefense.proofpoint.com/v2/url?u=http-3A__maths.anu.edu.au_people_conrad-2Dburden&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=Dw3YO3Okz8SDjKE6cwFYGSfH2eYVStHqunHPHYR_OY0&e= On 7 Apr 2020, at 8:51 pm, Turaga, Nitesh <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@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.bur...@anu.edu.au<mailto:conrad.bur...@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.bur...@anu.edu.au<mailto:conrad.bur...@anu.edu.au> Web page: https://urldefense.proofpoint.com/v2/url?u=http-3A__maths.anu.edu.au_people_conrad-2Dburden&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=Dw3YO3Okz8SDjKE6cwFYGSfH2eYVStHqunHPHYR_OY0&e= On 7 Apr 2020, at 3:40 am, nitesh.tur...@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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_MPFE_https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_MPFE_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=DF8VnTeQgSC5nT379GlAkN32YDNfgj40YHDJf-y_wOM&e= 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. 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