Re: [Bioc-devel] report package issue to Bioconductor

[Obenchain, Valerie]

On 01/06/2017 09:53 AM, Obenchain, Valerie wrote:
> Hi,
>
> It looks like CorMut doesn't have a github repo so the best approach is
> to contact the maintainer directly or cc them (zpl...@gmail.com) instead
> of creating your own gist. Maybe you've tried this? Once the transition

I should have been more clear here and said ... "Once the Bioconductor
package repo has been transitioned from svn to git / github ...".
The goal is to have the transition finalized before the spring release.

Valerie
> from svn to git / github is complete you can open issues or submit a
> pull request directly to the package repo.
>
> Valerie
>
> On 01/03/2017 11:39 PM, Yu, Guangchuang wrote:
>> Dear all,
>>
>> Some packages never updated after they publish a paper, and they just
>> ignore bug report.
>>
>> I think we need somewhere, maybe on github, to post code review and
>> Bioconductor core team can take action if maintainer fail to fix issue.
>>
>> Here is a quick look of the CorMut package:
>> https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.
>>
>> There should be more issues than I can found with quick look of the source
>> code.
>>
>> Best wishes,
>> Guangchuang
>> ​
>
>
>
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Re: [Bioc-devel] Code quality and bug reports

[Obenchain, Valerie]

On 01/04/2017 07:53 AM, Lluís Revilla wrote:
> Dear Guangchuang and all,
>
> Quality of the packages has been a preoccupation of the project from
> the  beginning  (see
> https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for
> more references and other discussions about bug reports.) Despite not
> being in a goal of the project, it is necessary to do a reproducible
> research, which it is a goal: "To further scientific understanding by
> producing high-quality documentation and reproducible research.".
> Although it seems that this discussion appears periodically
> Bioconductor I don't know any solution in the project.
>
> I have never submitted a package to Bioconductor or CRAN, and I am
> quite new to R (and is my first mail to the list), but one thing that
> I keep thinking (before publishing a package) is the maintainability
> of it. I don't know how much time/desires will I have to dedicate to a
> package (if it is accepted) in the future, but at the same time I want
> to make useful code to be used in further research beyond my own
> project.
>
> However the Bioconductor core team may be already too busy to deal
> with the issues of all packages. Maybe it would be better to bring
> CRAN's policy to orphan packages (see:
> https://cran.r-project.org/src/contrib/Orphaned/README):

Bioconductor does have a system for dealing with orphaned packages
called End of Life:

  http://www.bioconductor.org/developers/package-end-of-life/

Deprecated packages have a strikethrough the name on the build reports,
e.g., the saps package,

  http://www.bioconductor.org/checkResults/devel/bioc-LATEST/


Valerie

>
> "Possible reasons for orphanizing a package:
>
> 1) The current maintainer actively wants to orphanize the package,
>e.g., due to no longer having time or interest to act as package
>maintainer.
>
> 2) Emails sent to the current maintainer by the CRAN admins bounced, or
>were not answered for longer periods of time.
> "
> Example of an orhpan package is clusterRepro.
>
> To orphanize a package the current maintainer could post it here on
> the devel list and ask for a maintainer on the support site, and it is
> his/her decision to whom is passed the responsibility.
> Otherwise, maybe the limit of time without answering mails/posts in
> support could be 3 months/6 months. (I don't know the CRAN decision
> when not answering mails)
>
> Once the orphaned status is reached maybe however who wants could send
> patches or take the maintenance of the package for another 3 months or
> more.
>
> This status would not make bugs easier to fix or control, but could
> mark that a package is not in the best maintenance status.
>
> Hope this helps,
>
> Lluís
>
>
> 
> Date: Wed, 4 Jan 2017 15:38:53 +0800
> From: "Yu, Guangchuang" 
> To: bioc-devel 
> Subject: [Bioc-devel] report package issue to Bioconductor
> Message-ID:
> 
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
>
> Some packages never updated after they publish a paper, and they just
> ignore bug report.
>
> I think we need somewhere, maybe on github, to post code review and
> Bioconductor core team can take action if maintainer fail to fix issue.
>
> Here is a quick look of the CorMut package:
> https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.
>
> There should be more issues than I can found with quick look of the source
> code.
>
> Best wishes,
> Guangchuang
> ?
> --
> --~--~-~--~~~---~--~~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~--~~~~--~~--~--~---
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel




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Re: [Bioc-devel] report package issue to Bioconductor

[Obenchain, Valerie]

Hi,

It looks like CorMut doesn't have a github repo so the best approach is
to contact the maintainer directly or cc them (zpl...@gmail.com) instead
of creating your own gist. Maybe you've tried this? Once the transition
from svn to git / github is complete you can open issues or submit a
pull request directly to the package repo.

Valerie

On 01/03/2017 11:39 PM, Yu, Guangchuang wrote:
> Dear all,
>
> Some packages never updated after they publish a paper, and they just
> ignore bug report.
>
> I think we need somewhere, maybe on github, to post code review and
> Bioconductor core team can take action if maintainer fail to fix issue.
>
> Here is a quick look of the CorMut package:
> https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.
>
> There should be more issues than I can found with quick look of the source
> code.
>
> Best wishes,
> Guangchuang
> ​




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Re: [Rd] seq.int/seq.default

[Martin Maechler]

> Martin Maechler 
> on Thu, 5 Jan 2017 12:39:29 +0100 writes:

> Mick Jordan 
> on Wed, 4 Jan 2017 08:15:03 -0800 writes:

>> On 1/4/17 1:26 AM, Martin Maechler wrote:
 Mick Jordan  on Tue, 3 Jan
 2017 07:57:15 -0800 writes:
>>> > This is a message for someone familiar with the
>>> implementation.  > Superficially the R code for
>>> seq.default and the C code for seq.int > appear to be
>>> semantically very similar. My question is whether, in
>>> fact, > it is intended that behave identically for all
>>> inputs.
>>> 
>>> Strictly speaking, "no": As usual, RT?Manual (;-)
>>> 
>>> The help page says in the very first paragraph
>>> ('Description'):
>>> 
>>> ‘seq’ is a standard generic with a default method.
>>> ‘seq.int’ is a primitive which can be much faster but
>>> has a few restrictions.
>>> 
>>> > I have found two cases so far where they differ, first
>>> > that seq.int will coerce a character string to a real
>>> (via > Rf_asReal) whereas seq.default appears to coerce
>>> it to NA > and then throws an error:
>>> 
>>> >> seq.default("2", "5") > Error in seq.default("2",
>>> "5") : 'from' cannot be NA, NaN or infinite >>
>>> seq.int("2", "5") > [1] 2 3 4 5
>>> >>
>>> 
>>> this may be a bit surprising (if one does _not_ look at
>>> the code), indeed, notably because seq.int() is
>>> mentioned to have more restrictions than seq() which
>>> here calls seq.default().  "Surprising" also when
>>> considering
>>> 
>>> > "2":"5" [1] 2 3 4 5
>>> 
>>> and the documentation of ':' claims 'from:to' to be the
>>> same as rep(from,to) apart from the case of factors.
>>> 
>>> --- I am considering a small change in seq.default()
>>> which would make it work for this case, compatibly with
>>> ":" and seq.int().
>>> 
>>> 
>>> > and second, that the error messages for non-numeric
>>> arguments differ:
>>> 
>>> which I find fine... if the functions where meant to be
>>> identical, we (the R developers) would be silly to have
>>> both, notably as the ".int" suffix has emerged as
>>> confusing the majority of useRs (who don't read help
>>> pages).
>>> 
>>> Rather it has been meant as saying "internal" (including
>>> "fast") also for other such R functions, but the suffix
>>> of course is a potential clash with S3 method naming
>>> schemes _and_ the fact that 'int' is used as type name
>>> for integer in other languages, notably C.
>>> 
>>> > seq.default(to=quote(b), by=2) > Error in
>>> is.finite(to) : default method not implemented for type
>>> 'symbol'
>>> 
>>> which I find a very appropriate and helpful message
>>> 
>>> > seq.int(to=quote(b), by=2) > Error in seq.int(to =
>>> quote(b), by = 2) : > 'to' cannot be NA, NaN or infinite
>>> 
>>> which is true, as well, and there's no "default method"
>>> to be mentioned, but you are right that it would be
>>> nicer if the message mentioned 'symbol' as well.

>> Thanks for the clarifications. It was surprising that
>> seq.int supported more types than seq.default. I was
>> expecting the reverse.

> exactly, me too!

>> BTW, There are a couple of, admittedly odd, cases,
>> exposed by brute force testing, where seq.int will
>> actually return "missing", which I presume is not
>> intended, and seq.default behaves differently, vis:

>>> seq.default(to=1,by=2)
>> [1] 1
>>> seq.int(to=1,by=2)

>>> > x <- seq.int(to=1,by=2) x
>> Error: argument "x" is missing, with no default

>> Lines 792 and 799 of seq.c return the incoming argument
>> (as opposed to a value based on its coercion to double
>> via asReal) and this can, as in the above example, be
>> "missing".

>> Thanks Mick Jordan

> Thanks a lot, Mick -- you are right!

> I'm fixing these (the line numbers have greatly changed in
> the mean time: Remember we work with "R-devel", i.e., the
> "trunk" : always available at
> https://svn.r-project.org/R/trunk/src/main/seq.c

This has happened in the mean time (and more is planned for
another error message).

And there's this --- where I'm pretty sure we want an error for
seq.default() as well :

> seq.int(1,7, by=1:2)
Error: 'by' must be of length 1

> seq(1,7, by=1:2)
[1] 1 3 3 7 5 7 7
Warning messages:
1: In if (n < 0L) stop("wrong sign in 'by' argument") :
  the condition has length > 1 and only the first element will be used
2: In if (n > .Machine$integer.max) stop("'by' argument is much too small") :
  the condition has length > 1 and only the first element will be used
3: In 0L:n : numerical expression has 2 elements: only the first used
4: In (0L:n) * by :
  longer object length is not a 

Re: [Bioc-devel] asBam Default Destination

[Martin Morgan]

On 01/06/2017 06:00 AM, Dario Strbenac wrote:

Good day,

The destination parameter is mandatory and has no default.


asBam(samFile)

Error in is(path, "RsamtoolsFile") :
  argument "destination" is missing, with no default

Would a good default be the same path as as the input file, but having the suffix "bam" 
instead of "sam"?



thanks for the suggestion, this (and likewise for asSam()) is 
implemented in 1.27.11.


Martin


--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

[Martin Morgan]

On 01/06/2017 06:27 AM, Anand MT wrote:

Hi Vladimir,


Thanks for suggestion. I will try this and see if it helps.


yes hover over the red dot at the end of each line and it says that the 
build version (x.y.4) is lower than the published version (x.y.31) -- 
the elements of the version number are treated as integers, and 4 is 
less than 31 as Vladimir indicates.


Also, what is the underlying reason for the file that is sometimes not 
found? It looks like something left over from some attempt at parallel 
evaluation?


Martin




From: Vladimir Kiselev 
Sent: 06 January 2017 13:24:49
To: Anand MT; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] maftools package not updated after pushing bug fixes.


Maybe 1.0.4 is smaller than 1.0.30? Try to change to 1.0.31.

On Fri, 6 Jan 2017, 05:32 Anand MT, 
> wrote:
Hi Vincent,

Thanks for reply. I swear this was OK till yesterday for updated version! This "file 
not found" issue often occurs but it resolves by itself during next builds. Anyways, 
even when everything was OK, package didn't update to newer version.




From: Vincent Carey 
>
Sent: 06 January 2017 08:27:01
To: Anand MT
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] maftools package not updated after pushing bug fixes.



On Thu, Jan 5, 2017 at 9:33 PM, Anand MT 
>>
 wrote:
Hi,


I recently pushed few bug fixes and removed some dependency packages which were 
no longer required. I did this a week ago and updated version to 1.0.4 from 
1.0.30.

Build reports are OK for updated version.

http://bioconductor.org/checkResults/release/bioc-LATEST/maftools/

Hi -- there is an error for linux build on that link.




However, release site is still at older 1.0.30. How to proceed now ?

Probably have to fix the build error --


Done !
Quitting from lines 152-153 (maftools.Rmd)
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
file not found: /dev/shm/file6fd4ebc7d82

Execution halted




Thank you.

-Anand

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