[Bioc-devel] MPFE Bioconductor package
Conrad Burden
conr@d@burden @end|ng |rom @nu@edu@@u
Sun Sep 20 03:52:48 CEST 2020
Thanks everyone with your help with this. Apologies for the grumpiness in my last email. If a similar problem arises again I use the recommended mailing list.
- cheers, Conrad
On 19 Sep 2020, at 3:52 am, Vincent Carey <stvjc using channing.harvard.edu<mailto:stvjc using channing.harvard.edu>> wrote:
Thanks Jiefei! I wanted to acknowledge Conrad's comments too -- we will
discuss them as a group in our monthly technical advisory board meeting to
assess adequacy of documentation and support resources for conditions
like these. Our project must make use of a variety of technologies to meet
the needs and interests of users and developers, and input from the community
is vital to ensuring that our materials are up-to-date and sufficiently detailed
to support independent progress through challenging situations. Community inputs
that help to remedy shortcomings in our documents are extremely valuable.
On Fri, Sep 18, 2020 at 12:36 PM Jiefei Wang <szwjf08 using gmail.com<mailto:szwjf08 using gmail.com>> wrote:
Hi Conrad,
Glad to hear that you have solved the problem. Sorry for hearing your bad
experience, I guess it could be better if you can ask your question in a
git mailing list(If there is one) because it is really not a package
administrative problem which the Bioconductor core team is responsible for.
What Nitesh said does not mean you should sort it out for your self, it
just means you should ask it in a better place, and he forwarded your email
to here. Bioc mailing list is mostly for package development, so you can
get two responses for that(Even though we did not correctly understand your
question). Please do not feel anxious about it, you are welcome to ask for
help.
Best,
Jiefei
On Fri, Sep 18, 2020 at 12:46 PM Conrad Burden <conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>>
wrote:
>
> Hi guys,
>
> It seems to be working now. There is one warning message, which I believe
> is just to tell me that the package had been "deprecated” (which
> apparently does not mean what my Oxford English Dictionary tells me it
> means).
>
> Could you please confirm whether I have to do anything else for it to go
> into the next release?
>
> By the way, I should have pointed out from the beginning that my problem
> was NOT with debugging the R code. I had that sorted out almost
> immediately back in April (but thanks for confirming that you came up with
> the same solution Jiefei). My problem was with working out how to get this
> trivial 1-line change into the bioconductor system. If one is not already
> familiar with unix, GitHub, ssh keys, repositories and heaven knows what
> else, and if one doesn’t know the terminology, the on-liine instructions
> are impossible to follow, assuming, that is, one can find the right web
> page to start with. I was somewhat put off by asking further by the
> sentence "Unfortunately we are not able to devote time towards individual
> packages”, which I took to mean “go away, stop bothering us, and sort it
> out for yourself”.
>
> cheers, 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> <conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>>
> Web page: http://maths.anu.edu.au/people/conrad-burden
>
>
> On 17 Sep 2020, at 8:36 pm, Jiefei Wang <szwjf08 using gmail.com<mailto:szwjf08 using gmail.com>> wrote:
>
> 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.burden using anu.edu.au<mailto:conrad.burden using 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.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au><mailto:conrad.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au>>
>> Web page: http://maths.anu.edu.au/people/conrad-burden
>>
>>
>> On 17 Sep 2020, at 1:16 pm, Stone, Matt <mstone using fredhutch.org<mailto:mstone using fredhutch.org><mailto:
>> mstone using fredhutch.org<mailto:mstone using 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-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org> on behalf of
>> Nitesh.Turaga using RoswellPark.org<mailto:Nitesh.Turaga using 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 using r-project.org<mailto:bioc-devel using r-project.org>
>> <mailto: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<mailto:conrad.burden using anu.edu.au>>
>> Date: Wednesday, September 16, 2020 at 10:16 PM
>> To: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org<mailto: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://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.burden using anu.edu.au<mailto:conrad.burden using anu.edu.au><mailto:conrad.burden using anu.edu.au<mailto:conrad.burden using 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.Turaga using RoswellPark.org<mailto:Nitesh.Turaga using RoswellPark.org><mailto: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>
>> <mailto: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><mailto:conrad.burden using anu.edu.au<mailto:conrad.burden using 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.turaga using roswellpark.org<mailto: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://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
>>
>>
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