Hi Conrad,
Just a friendly reminder, there is a bug in your package. Here is the build
result from the link you provided:
==========================================
--- Error message ---
--- failure: length > 1 in coercion to logical ---
--- call from argument ---
columns < 1 || columns > nColumns
--- place where the error occurs ---
if (any(columns < 1 || columns > nColumns)) {
stop("Column indices must be between 1 and ", nColumns,
"\n")
}
==========================================
The symbol `||` only applies the logical OR on the first element of two
operands. Since you need the elementwise comparison, you should use the
symbol `|` instead.
Best,
Jiefei
On Thu, Sep 17, 2020 at 2:11 PM Conrad Burden <conrad.bur...@anu.edu.au>
wrote:
>
> 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.
>
> Regards,
> Nitesh
>
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=-PsRSVf2HMnEZPj0ywkTgPZVJAwlf9uE-gVSJseq9y4&m=-2-tEmXGAUp-Qyu_D4BEN2PhDJ81VULD7dNuAIZBk9c&s=VjEsmBijpmVszBZSQCE9UN8JuAh1b09Dj2XI9Z5vM1g&e=
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
