[Bioc-devel] MPFE Bioconductor package

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 at anu.edu.au<mailto:conrad.burden at anu.edu.au> <conrad.burden at anu.edu.au<mailto:conrad.burden at anu.edu.au>>
Web page: http://maths.anu.edu.au/people/conrad-burden


On 17 Sep 2020, at 8:36 pm, Jiefei Wang <szwjf08 at gmail.com<mailto:szwjf08 at 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 at anu.edu.au<mailto:conrad.burden at 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 at anu.edu.au<mailto:conrad.burden at anu.edu.au><mailto:conrad.burden at anu.edu.au<mailto:conrad.burden at anu.edu.au>>
Web page: http://maths.anu.edu.au/people/conrad-burden


On 17 Sep 2020, at 1:16 pm, Stone, Matt <mstone at fredhutch.org<mailto:mstone at fredhutch.org><mailto:
mstone at fredhutch.org<mailto:mstone at 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org> on behalf of
Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at 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 at r-project.org<mailto:bioc-devel at r-project.org>
<mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> mailing list where other people can
help you more readily.

   Best,

   Nitesh

   From: Conrad Burden <conrad.burden at anu.edu.au<mailto:conrad.burden at anu.edu.au>>
   Date: Wednesday, September 16, 2020 at 10:16 PM
   To: "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at 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 at anu.edu.au<mailto:conrad.burden at anu.edu.au><mailto:conrad.burden at anu.edu.au<mailto:conrad.burden at 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 at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org><mailto:Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at 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 at anu.edu.au<mailto:conrad.burden at anu.edu.au>
<mailto:conrad.burden at anu.edu.au<mailto:conrad.burden at 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 at anu.edu.au<mailto:conrad.burden at anu.edu.au><mailto:conrad.burden at anu.edu.au<mailto:conrad.burden at 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 at roswellpark.org<mailto:nitesh.turaga at 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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