Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Michael Love 
Fine with me to make results() into a generic.

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Hervé Pagès 
Fixed in BiocGenerics 0.48.1: 
https://github.com/Bioconductor/BiocGenerics/commit/5fd6dfe93786292484dc53023ec681391f4559e0

With this version of BiocGenerics, SNPhood passes CHECK on my laptop 
(Ubuntu Linux). We'll see how it goes on Thursday's report. (The fix was 
too late for today's builds -- they already started -- so it won't 
reflect on tomorrow's report.)

Sorry again for the trouble.

Cheers,

H.

PS: Making results() an S4 generic defined in BiocGenerics would still 
be a good idea though, because a SNPhood user could still decide to 
_explicitly_ load DESeq2 with library(DESeq2) after they've loaded 
SNPhood, which would also break results(). I'll leave this to the 
authors/maintainers of SNPhood and/or DESeq2 to open an issue on the 
BiocGenerics repo to request this if they are interested.

On 10/31/23 13:49, Hervé Pagès wrote:
>
> Hmm.. so I was curious and did a little bit more investigation about this.
>
> The other package that also defines a results() function is DESeq2, 
> and it gets attached to the search path after calling 
> analyzeSNPhood(). You can actually observe this phenomena with the 
> following code:
>
>     library(SNPhood)
>     library(SNPhoodData)
>     search()  # DESeq2 is NOT attached
>     example(analyzeSNPhood)
>     search()  # DESeq2 is attached
>
> What's intriguing is that this only happens in BioC 3.18. In BioC 
> 3.17, running the analyzeSNPhood example does NOT alter the search 
> path. After spending some time tracking this down, it turns out that 
> the reason for this change of behaviour is a small tweak I made 
> recently to the updateObject() generic in BiocGenerics. An unfortunate 
> one that I will correct now.
>
> @Christian: A fix is on its way so you have nothing to do.
>
> Sorry for the trouble.
>
> H.
>
> On 10/31/23 09:44, Hervé Pagès wrote:
>>
>> On 10/31/23 07:22, Wolfgang Huber wrote:
>>
>>> Dear Christian
>>>
>>> If your vignette attaches another package that exports a “results” 
>>> function, after it attached SNPhood which defines its own results function, 
>>> then the R interpreter has no other choice than doing what it does.
>>>
>>> Other people adding additional functionality to their packages is probably 
>>> not something one can really complain about, so I see three options
>>> - you use SNPhood::results in your vignette
>>> - you don’t attach the other package, and rather just use what you need 
>>> from it using “::”
>>> - you convince Hervé to add ‘results' to BiocGenerics and everyone who 
>>> exports such a function converts it to a method for that generic.
>>
>> My pleasure, and that's the cleanest solution. But it will only help 
>> if the package that defines the "other" results() function is a 
>> Bioconductor package and not a CRAN package. Has this package been 
>> identified?
>>
>> A 4th option is to make sure that the other package gets loaded 
>> _before_ SNPhood e.g. by putting an explicit library(> package>) before library(SNPhood) in your vignette, even though 
>> that's kind of hacky.
>>
>> Best,
>>
>> H.
>>
>>> Thank you and kind regards
>>> Wolfgang
>>>
>>> --
>>> Wolfgang Huber
>>> EMBL
>>> https://www.huber.embl.de/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
 Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  
 ha scritto:

 For my package SNPhood that did not receive any code changes or updates
 in quite a while, I suddenly see errors with Bioc 3.18:
 https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html

 Error: processing vignette 'workflow.Rmd' failed with diagnostics:
 unused argument (type = "allelicBias")

 This comes from this line I think:

 names(results(SNPhood.o, type = "allelicBias"))

 For literally years, this didnt cause any problems, and the results
 function is actually (re)defined in the SNPhood package:

 results <- function(SNPhood.o, type, elements = NULL)

 I am not sure now what causes this. Should I use the syntax
 SNPhood::results to make it clear, or I am wrongly assuming that the
 wrong result function is taken that causes the error?

 Any pointers?


 Best

 Christian


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 ___
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 https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> ___
>>> Bioc-devel@r-project.org  mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> -- 
>> Hervé Pagès
>>
>> Bioconductor Core Team
>> hpages.on.git...@gmail.com
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Hervé Pagès 
Thanks Ali! Only problem is that I have too much control on too many 
infrastructure components so it's too easy for me to mess up other 
people's stuff :-(

On 10/31/23 14:00, Ali Sajid Imami wrote:
> Herve, I see the work you do and stand in awe. I can only wish I could 
> some day be in a similar place. For now, I am content with submitting 
> packages for 3.19. :)
>
>> On Oct 31, 2023, at 4:49 PM, Hervé Pagès  
>> wrote:
>>
>> Hmm.. so I was curious and did a little bit more investigation about 
>> this.
>>
>> The other package that also defines a results() function is DESeq2, and
>> it gets attached to the search path after calling analyzeSNPhood(). You
>> can actually observe this phenomena with the following code:
>>
>> library(SNPhood)
>> library(SNPhoodData)
>> search()  # DESeq2 is NOT attached
>> example(analyzeSNPhood)
>> search()  # DESeq2 is attached
>>
>> What's intriguing is that this only happens in BioC 3.18. In BioC 3.17,
>> running the analyzeSNPhood example does NOT alter the search path. After
>> spending some time tracking this down, it turns out that the reason for
>> this change of behaviour is a small tweak I made recently to the
>> updateObject() generic in BiocGenerics. An unfortunate one that I will
>> correct now.
>>
>> @Christian: A fix is on its way so you have nothing to do.
>>
>> Sorry for the trouble.
>>
>> H.
>>
>> On 10/31/23 09:44, Hervé Pagès wrote:
>>>
>>> On 10/31/23 07:22, Wolfgang Huber wrote:
>>>
 Dear Christian

 If your vignette attaches another package that exports a “results” 
 function, after it attached SNPhood which defines its own results 
 function, then the R interpreter has no other choice than doing 
 what it does.

 Other people adding additional functionality to their packages is 
 probably not something one can really complain about, so I see 
 three options
 - you use SNPhood::results in your vignette
 - you don’t attach the other package, and rather just use what you 
 need from it using “::”
 - you convince Hervé to add ‘results' to BiocGenerics and everyone 
 who exports such a function converts it to a method for that generic.
>>>
>>> My pleasure, and that's the cleanest solution. But it will only help
>>> if the package that defines the "other" results() function is a
>>> Bioconductor package and not a CRAN package. Has this package been
>>> identified?
>>>
>>> A 4th option is to make sure that the other package gets loaded
>>> _before_ SNPhood e.g. by putting an explicit library(>> package>) before library(SNPhood) in your vignette, even though that's
>>> kind of hacky.
>>>
>>> Best,
>>>
>>> H.
>>>
 Thank you and kind regards
 Wolfgang

 --
 Wolfgang Huber
 EMBL
 https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian 
> Arnold  ha scritto:
>
> For my package SNPhood that did not receive any code changes or 
> updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
>
> This comes from this line I think:
>
> names(results(SNPhood.o, type = "allelicBias"))
>
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
>
> results <- function(SNPhood.o, type, elements = NULL)
>
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
>
> Any pointers?
>
>
> Best
>
> Christian
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
 ___
 Bioc-devel@r-project.org  mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> --
>>> Hervé Pagès
>>>
>>> Bioconductor Core Team
>>> hpages.on.git...@gmail.com
>>
>> --
>> Hervé Pagès
>>
>> Bioconductor Core Team
>> hpages.on.git...@gmail.com
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.orgmailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Ali Sajid Imami 
Herve, I see the work you do and stand in awe. I can only wish I could some
day be in a similar place. For now, I am content with submitting packages
for 3.19. :)


Regards,
Dr. Ali Sajid Imami
LinkedIn 


On Tue, Oct 31, 2023 at 4:50 PM Hervé Pagès 
wrote:

> Hmm.. so I was curious and did a little bit more investigation about this.
>
> The other package that also defines a results() function is DESeq2, and
> it gets attached to the search path after calling analyzeSNPhood(). You
> can actually observe this phenomena with the following code:
>
>  library(SNPhood)
>  library(SNPhoodData)
>  search()  # DESeq2 is NOT attached
>  example(analyzeSNPhood)
>  search()  # DESeq2 is attached
>
> What's intriguing is that this only happens in BioC 3.18. In BioC 3.17,
> running the analyzeSNPhood example does NOT alter the search path. After
> spending some time tracking this down, it turns out that the reason for
> this change of behaviour is a small tweak I made recently to the
> updateObject() generic in BiocGenerics. An unfortunate one that I will
> correct now.
>
> @Christian: A fix is on its way so you have nothing to do.
>
> Sorry for the trouble.
>
> H.
>
> On 10/31/23 09:44, Hervé Pagès wrote:
> >
> > On 10/31/23 07:22, Wolfgang Huber wrote:
> >
> >> Dear Christian
> >>
> >> If your vignette attaches another package that exports a “results”
> function, after it attached SNPhood which defines its own results function,
> then the R interpreter has no other choice than doing what it does.
> >>
> >> Other people adding additional functionality to their packages is
> probably not something one can really complain about, so I see three options
> >> - you use SNPhood::results in your vignette
> >> - you don’t attach the other package, and rather just use what you need
> from it using “::”
> >> - you convince Hervé to add ‘results' to BiocGenerics and everyone who
> exports such a function converts it to a method for that generic.
> >
> > My pleasure, and that's the cleanest solution. But it will only help
> > if the package that defines the "other" results() function is a
> > Bioconductor package and not a CRAN package. Has this package been
> > identified?
> >
> > A 4th option is to make sure that the other package gets loaded
> > _before_ SNPhood e.g. by putting an explicit library( > package>) before library(SNPhood) in your vignette, even though that's
> > kind of hacky.
> >
> > Best,
> >
> > H.
> >
> >> Thank you and kind regards
> >> Wolfgang
> >>
> >> --
> >> Wolfgang Huber
> >> EMBL
> >> https://www.huber.embl.de/
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold<
> chrarn...@web.de>  ha scritto:
> >>>
> >>> For my package SNPhood that did not receive any code changes or updates
> >>> in quite a while, I suddenly see errors with Bioc 3.18:
> >>>
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
> >>>
> >>> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> >>> unused argument (type = "allelicBias")
> >>>
> >>> This comes from this line I think:
> >>>
> >>> names(results(SNPhood.o, type = "allelicBias"))
> >>>
> >>> For literally years, this didnt cause any problems, and the results
> >>> function is actually (re)defined in the SNPhood package:
> >>>
> >>> results <- function(SNPhood.o, type, elements = NULL)
> >>>
> >>> I am not sure now what causes this. Should I use the syntax
> >>> SNPhood::results to make it clear, or I am wrongly assuming that the
> >>> wrong result function is taken that causes the error?
> >>>
> >>> Any pointers?
> >>>
> >>>
> >>> Best
> >>>
> >>> Christian
> >>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org  mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> ___
> >> Bioc-devel@r-project.org  mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.git...@gmail.com
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Hervé Pagès 
Hmm.. so I was curious and did a little bit more investigation about this.

The other package that also defines a results() function is DESeq2, and 
it gets attached to the search path after calling analyzeSNPhood(). You 
can actually observe this phenomena with the following code:

     library(SNPhood)
     library(SNPhoodData)
     search()  # DESeq2 is NOT attached
     example(analyzeSNPhood)
     search()  # DESeq2 is attached

What's intriguing is that this only happens in BioC 3.18. In BioC 3.17, 
running the analyzeSNPhood example does NOT alter the search path. After 
spending some time tracking this down, it turns out that the reason for 
this change of behaviour is a small tweak I made recently to the 
updateObject() generic in BiocGenerics. An unfortunate one that I will 
correct now.

@Christian: A fix is on its way so you have nothing to do.

Sorry for the trouble.

H.

On 10/31/23 09:44, Hervé Pagès wrote:
>
> On 10/31/23 07:22, Wolfgang Huber wrote:
>
>> Dear Christian
>>
>> If your vignette attaches another package that exports a “results” function, 
>> after it attached SNPhood which defines its own results function, then the R 
>> interpreter has no other choice than doing what it does.
>>
>> Other people adding additional functionality to their packages is probably 
>> not something one can really complain about, so I see three options
>> - you use SNPhood::results in your vignette
>> - you don’t attach the other package, and rather just use what you need from 
>> it using “::”
>> - you convince Hervé to add ‘results' to BiocGenerics and everyone who 
>> exports such a function converts it to a method for that generic.
>
> My pleasure, and that's the cleanest solution. But it will only help 
> if the package that defines the "other" results() function is a 
> Bioconductor package and not a CRAN package. Has this package been 
> identified?
>
> A 4th option is to make sure that the other package gets loaded 
> _before_ SNPhood e.g. by putting an explicit library( package>) before library(SNPhood) in your vignette, even though that's 
> kind of hacky.
>
> Best,
>
> H.
>
>> Thank you and kind regards
>> Wolfgang
>>
>> --
>> Wolfgang Huber
>> EMBL
>> https://www.huber.embl.de/
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  
>>> ha scritto:
>>>
>>> For my package SNPhood that did not receive any code changes or updates
>>> in quite a while, I suddenly see errors with Bioc 3.18:
>>> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>>>
>>> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
>>> unused argument (type = "allelicBias")
>>>
>>> This comes from this line I think:
>>>
>>> names(results(SNPhood.o, type = "allelicBias"))
>>>
>>> For literally years, this didnt cause any problems, and the results
>>> function is actually (re)defined in the SNPhood package:
>>>
>>> results <- function(SNPhood.o, type, elements = NULL)
>>>
>>> I am not sure now what causes this. Should I use the syntax
>>> SNPhood::results to make it clear, or I am wrongly assuming that the
>>> wrong result function is taken that causes the error?
>>>
>>> Any pointers?
>>>
>>>
>>> Best
>>>
>>> Christian
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org  mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> ___
>> Bioc-devel@r-project.org  mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Hervé Pagès 
On 10/31/23 07:22, Wolfgang Huber wrote:

> Dear Christian
>
> If your vignette attaches another package that exports a “results” function, 
> after it attached SNPhood which defines its own results function, then the R 
> interpreter has no other choice than doing what it does.
>
> Other people adding additional functionality to their packages is probably 
> not something one can really complain about, so I see three options
> - you use SNPhood::results in your vignette
> - you don’t attach the other package, and rather just use what you need from 
> it using “::”
> - you convince Hervé to add ‘results' to BiocGenerics and everyone who 
> exports such a function converts it to a method for that generic.

My pleasure, and that's the cleanest solution. But it will only help if 
the package that defines the "other" results() function is a 
Bioconductor package and not a CRAN package. Has this package been 
identified?

A 4th option is to make sure that the other package gets loaded _before_ 
SNPhood e.g. by putting an explicit library() before 
library(SNPhood) in your vignette, even though that's kind of hacky.

Best,

H.

>
> Thank you and kind regards
> Wolfgang
>
> --
> Wolfgang Huber
> EMBL
> https://www.huber.embl.de/
>
>
>
>
>
>
>
>
>
>> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  ha 
>> scritto:
>>
>> For my package SNPhood that did not receive any code changes or updates
>> in quite a while, I suddenly see errors with Bioc 3.18:
>> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>>
>> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
>> unused argument (type = "allelicBias")
>>
>> This comes from this line I think:
>>
>> names(results(SNPhood.o, type = "allelicBias"))
>>
>> For literally years, this didnt cause any problems, and the results
>> function is actually (re)defined in the SNPhood package:
>>
>> results <- function(SNPhood.o, type, elements = NULL)
>>
>> I am not sure now what causes this. Should I use the syntax
>> SNPhood::results to make it clear, or I am wrongly assuming that the
>> wrong result function is taken that causes the error?
>>
>> Any pointers?
>>
>>
>> Best
>>
>> Christian
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org  mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> ___
> Bioc-devel@r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Julien Wollbrett 
Hi,

Sorry... it looks like I replied to the wrong email

De : Bioc-devel  de la part de Julien 
Wollbrett 
Envoyé : mardi 31 octobre 2023 16:04
À : Wolfgang Huber ; Christian Arnold 

Cc : bioc-devel@r-project.org 
Objet : Re: [Bioc-devel] Package problems due to results() function from other 
package?

Bonjour,


Quelle magnifique nouvelle.


Nous ne serons malheureusement pas disponible avant le 30 novembre car nous 
partons ce vendredi pour un mois de vacances dans nos familles respectives.Nous 
serions potentiellement disponibles demain ou jeudi mais j'imagine que cela 
n'est pas du tout compatible avec votre planning.

Est ce qu'il serait possible de vous rencontrer en d�cemb ou est ce que notre 
absence risque de nous causer pr�judice pour la place en


De : Bioc-devel  de la part de Wolfgang Huber 

Envoy� : mardi 31 octobre 2023 15:22
� : Christian Arnold 
Cc : bioc-devel@r-project.org 
Objet : Re: [Bioc-devel] Package problems due to results() function from other 
package?

Dear Christian

If your vignette attaches another package that exports a �results� function, 
after it attached SNPhood which defines its own results function, then the R 
interpreter has no other choice than doing what it does.

Other people adding additional functionality to their packages is probably not 
something one can really complain about, so I see three options
- you use SNPhood::results in your vignette
- you don�t attach the other package, and rather just use what you need from it 
using �::�
- you convince Herv� to add �results' to BiocGenerics and everyone who exports 
such a function converts it to a method for that generic.

Thank you and kind regards
Wolfgang

--
Wolfgang Huber
EMBL
https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  ha 
> scritto:
>
> For my package SNPhood that did not receive any code changes or updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
>
> This comes from this line I think:
>
> names(results(SNPhood.o, type = "allelicBias"))
>
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
>
> results <- function(SNPhood.o, type, elements = NULL)
>
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
>
> Any pointers?
>
>
> Best
>
> Christian
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Julien Wollbrett 
Bonjour,


Quelle magnifique nouvelle.


Nous ne serons malheureusement pas disponible avant le 30 novembre car nous 
partons ce vendredi pour un mois de vacances dans nos familles respectives.Nous 
serions potentiellement disponibles demain ou jeudi mais j'imagine que cela 
n'est pas du tout compatible avec votre planning.

Est ce qu'il serait possible de vous rencontrer en d�cemb ou est ce que notre 
absence risque de nous causer pr�judice pour la place en


De : Bioc-devel  de la part de Wolfgang Huber 

Envoy� : mardi 31 octobre 2023 15:22
� : Christian Arnold 
Cc : bioc-devel@r-project.org 
Objet : Re: [Bioc-devel] Package problems due to results() function from other 
package?

Dear Christian

If your vignette attaches another package that exports a �results� function, 
after it attached SNPhood which defines its own results function, then the R 
interpreter has no other choice than doing what it does.

Other people adding additional functionality to their packages is probably not 
something one can really complain about, so I see three options
- you use SNPhood::results in your vignette
- you don�t attach the other package, and rather just use what you need from it 
using �::�
- you convince Herv� to add �results' to BiocGenerics and everyone who exports 
such a function converts it to a method for that generic.

Thank you and kind regards
Wolfgang

--
Wolfgang Huber
EMBL
https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  ha 
> scritto:
>
> For my package SNPhood that did not receive any code changes or updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
>
> This comes from this line I think:
>
> names(results(SNPhood.o, type = "allelicBias"))
>
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
>
> results <- function(SNPhood.o, type, elements = NULL)
>
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
>
> Any pointers?
>
>
> Best
>
> Christian
>
>
> [[alternative HTML version deleted]]
>
> ___
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Re: [Bioc-devel] Package problems due to results() function from other package?

2023-10-31 Thread Wolfgang Huber 
Dear Christian

If your vignette attaches another package that exports a “results” function, 
after it attached SNPhood which defines its own results function, then the R 
interpreter has no other choice than doing what it does.

Other people adding additional functionality to their packages is probably not 
something one can really complain about, so I see three options
- you use SNPhood::results in your vignette
- you don’t attach the other package, and rather just use what you need from it 
using “::”
- you convince Hervé to add ‘results' to BiocGenerics and everyone who exports 
such a function converts it to a method for that generic.

Thank you and kind regards
Wolfgang

--
Wolfgang Huber
EMBL
https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold  ha 
> scritto:
> 
> For my package SNPhood that did not receive any code changes or updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
> 
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
> 
> This comes from this line I think:
> 
> names(results(SNPhood.o, type = "allelicBias"))
> 
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
> 
> results <- function(SNPhood.o, type, elements = NULL)
> 
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
> 
> Any pointers?
> 
> 
> Best
> 
> Christian
> 
> 
> [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] Package problems due to results() function from other package?

2023-10-28 Thread Christian Arnold 
For my package SNPhood that did not receive any code changes or updates
in quite a while, I suddenly see errors with Bioc 3.18:
https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html

Error: processing vignette 'workflow.Rmd' failed with diagnostics:
unused argument (type = "allelicBias")

This comes from this line I think:

names(results(SNPhood.o, type = "allelicBias"))

For literally years, this didnt cause any problems, and the results
function is actually (re)defined in the SNPhood package:

results <- function(SNPhood.o, type, elements = NULL)

I am not sure now what causes this. Should I use the syntax
SNPhood::results to make it clear, or I am wrongly assuming that the
wrong result function is taken that causes the error?

Any pointers?


Best

Christian


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