Re: [Bioc-devel] IFAA Bioconductor

2024-01-18 Thread Zhigang Li 
Hi Martin,

Thanks for the explanation. We will change all related functions in
MatrixExtra to the following format:
importMethodsFrom(MatrixExtra, crossprod)

Thanks,

Zhigang
https://sites.google.com/view/zlab


On Tue, Jan 16, 2024 at 1:18 PM Martin Morgan 
wrote:

> In R-devel I typed
>
>
>
> news()
>
>
>
> and noted
>
>
>
> - The matrix multiplication functions crossprod() and tcrossprod() are now
> also primitive and S3 generic,
>
>
>
> So I wonder if this has changed the 'rules' for how to declare the import
> -- previous behavior was along the lines of 'if the methods are exported,
> then the generic is also (implicitly) exported' and vice versa. I'm guess
> that the generic is no longer exported with the methods, which is how S3
> works. If you're using the methods, then maybe
>
>
>
> importMethodsFrom(MatrixExtra, crossprod)
>
>
>
> if one wants to use the methods. Or, since the S4 generic crossprod is
> defined in the Matrix package,
>
>
>
> importFrom(Matrix, crossprod)
>
>
>
> if one wants to use the S4 generic (e.g., to create a new S4 method).
>
>
>
> This is just a guess, and it's not really clear to me whether this
> behavior apparently associated with the change in crossprod to base is
> intentional or accidental; a post to R-devel might be in order…
>
>
>
> I would avoid import(MatrixExtra) on principle, but perhaps it is a last
> resort.
>
>
>
> Also I'll mention that I could reproduce the problem under R-devel, and
> that changing to importMethodsFrom(MatrixExtra, crossprod) got me past this
> stage (but now I also need to make a change for tcrossprod…)
>
>
>
> Martin Morgan
>
>
>
> *From: *Bioc-devel  on behalf of
> Zuguang Gu 
> *Date: *Tuesday, January 16, 2024 at 11:49 AM
> *To: *Zhigang Li 
> *Cc: *bioc-devel@r-project.org 
> *Subject: *Re: [Bioc-devel] IFAA Bioconductor
>
> I saw MatrixExtra defines several S4 methods/dispatches for the generic
> `crossprod()` which is actually defined in base.
>
> Maybe you can import the whole MatrixExtra namespace?
>
> import(MatrixExtra)
>
>
>
> On Tue, 16 Jan 2024 at 16:14, Zhigang Li  wrote:
>
> > Hi There,
> >
> > It seems that the error says :
> > "
> > ** byte-compile and prepare package for lazy loading
> >
> > Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'
> >
> > "
> >
> > But we checked and the package "MatrixExtra" still has the function
> > "crossprod". And in the NAMESPACE file, there is a row for
> > "importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
> > error happened. And there was no error for the previous version. Would
> you
> > mind providing some advice? Thanks.
> >
> > Regards,
> > Zhigang
> > https://sites.google.com/view/zlab
> >
> >
> > On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <
> > > bioconductorcoret...@gmail.com> wrote:
> > >
> > >> Hello Package Maintainer,
> > >>
> > >> We would like to bring to your attention that your package is failing
> in
> > >> devel across all platforms. This is very problematic. Please
> investigate
> > >> the issues and fix the package to avoid deprecation.
> > >>
> > >> https://bioconductor.org/checkResults/devel/bioc-LATEST/
> > >> <
> >
> https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>
> > >>
> > >> If you have further questions or concerns please reach out on the
> > >> bioc-devel@r-project.org
> > >>
> > >> We appreciate your quick attention to this matter
> > >>
> > >> Cheers,
> > >> On behalf of the Bioconductor Core Team
> > >>
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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>

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Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Martin Morgan 
In R-devel I typed

news()

and noted

- The matrix multiplication functions crossprod() and tcrossprod() are now also 
primitive and S3 generic,

So I wonder if this has changed the 'rules' for how to declare the import -- 
previous behavior was along the lines of 'if the methods are exported, then the 
generic is also (implicitly) exported' and vice versa. I'm guess that the 
generic is no longer exported with the methods, which is how S3 works. If 
you're using the methods, then maybe

importMethodsFrom(MatrixExtra, crossprod)

if one wants to use the methods. Or, since the S4 generic crossprod is defined 
in the Matrix package,

importFrom(Matrix, crossprod)

if one wants to use the S4 generic (e.g., to create a new S4 method).

This is just a guess, and it's not really clear to me whether this behavior 
apparently associated with the change in crossprod to base is intentional or 
accidental; a post to R-devel might be in order…

I would avoid import(MatrixExtra) on principle, but perhaps it is a last resort.

Also I'll mention that I could reproduce the problem under R-devel, and that 
changing to importMethodsFrom(MatrixExtra, crossprod) got me past this stage 
(but now I also need to make a change for tcrossprod…)

Martin Morgan

From: Bioc-devel  on behalf of Zuguang Gu 

Date: Tuesday, January 16, 2024 at 11:49 AM
To: Zhigang Li 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] IFAA Bioconductor
I saw MatrixExtra defines several S4 methods/dispatches for the generic
`crossprod()` which is actually defined in base.

Maybe you can import the whole MatrixExtra namespace?

import(MatrixExtra)



On Tue, 16 Jan 2024 at 16:14, Zhigang Li  wrote:

> Hi There,
>
> It seems that the error says :
> "
> ** byte-compile and prepare package for lazy loading
>
> Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'
>
> "
>
> But we checked and the package "MatrixExtra" still has the function
> "crossprod". And in the NAMESPACE file, there is a row for
> "importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
> error happened. And there was no error for the previous version. Would you
> mind providing some advice? Thanks.
>
> Regards,
> Zhigang
> https://sites.google.com/view/zlab
>
>
> On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <
> > bioconductorcoret...@gmail.com> wrote:
> >
> >> Hello Package Maintainer,
> >>
> >> We would like to bring to your attention that your package is failing in
> >> devel across all platforms. This is very problematic. Please investigate
> >> the issues and fix the package to avoid deprecation.
> >>
> >> https://bioconductor.org/checkResults/devel/bioc-LATEST/
> >> <
> https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow><https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow%3e>
> >>
> >> If you have further questions or concerns please reach out on the
> >> bioc-devel@r-project.org
> >>
> >> We appreciate your quick attention to this matter
> >>
> >> Cheers,
> >> On behalf of the Bioconductor Core Team
> >>
> >
>
> [[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] IFAA Bioconductor

2024-01-16 Thread Zuguang Gu 
I saw MatrixExtra defines several S4 methods/dispatches for the generic
`crossprod()` which is actually defined in base.

Maybe you can import the whole MatrixExtra namespace?

import(MatrixExtra)



On Tue, 16 Jan 2024 at 16:14, Zhigang Li  wrote:

> Hi There,
>
> It seems that the error says :
> "
> ** byte-compile and prepare package for lazy loading
>
> Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'
>
> "
>
> But we checked and the package "MatrixExtra" still has the function
> "crossprod". And in the NAMESPACE file, there is a row for
> "importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
> error happened. And there was no error for the previous version. Would you
> mind providing some advice? Thanks.
>
> Regards,
> Zhigang
> https://sites.google.com/view/zlab
>
>
> On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <
> > bioconductorcoret...@gmail.com> wrote:
> >
> >> Hello Package Maintainer,
> >>
> >> We would like to bring to your attention that your package is failing in
> >> devel across all platforms. This is very problematic. Please investigate
> >> the issues and fix the package to avoid deprecation.
> >>
> >> https://bioconductor.org/checkResults/devel/bioc-LATEST/
> >> <
> https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>
> >>
> >> If you have further questions or concerns please reach out on the
> >> bioc-devel@r-project.org
> >>
> >> We appreciate your quick attention to this matter
> >>
> >> Cheers,
> >> On behalf of the Bioconductor Core Team
> >>
> >
>
> [[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] IFAA Bioconductor

2024-01-16 Thread Ramos Perez, Marcel via Bioc-devel 
Hi Zhigang,

AFAICT, I don't see `crossprod` as an exported symbol in `MatrixExtra`.

> library(MatrixExtra)

> ls("package:MatrixExtra")

Did you mean Matrix:: or base:: crossprod?

Best regards,

Marcel


On 1/16/24 10:14 AM, Zhigang Li wrote:

Hi There,

It seems that the error says :
"
** byte-compile and prepare package for lazy loading

Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'

"

But we checked and the package "MatrixExtra" still has the function
"crossprod". And in the NAMESPACE file, there is a row for
"importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
error happened. And there was no error for the previous version. Would you
mind providing some advice? Thanks.

Regards,
Zhigang
https://sites.google.com/view/zlab


On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <


bioconductorcoret...@gmail.com> wrote:



Hello Package Maintainer,

We would like to bring to your attention that your package is failing in
devel across all platforms. This is very problematic. Please investigate
the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/


If you have further questions or concerns please reach out on the
bioc-devel@r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team







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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Zhigang Li 
Hi There,

It seems that the error says :
"
** byte-compile and prepare package for lazy loading

Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'

"

But we checked and the package "MatrixExtra" still has the function
"crossprod". And in the NAMESPACE file, there is a row for
"importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
error happened. And there was no error for the previous version. Would you
mind providing some advice? Thanks.

Regards,
Zhigang
https://sites.google.com/view/zlab


On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <
> bioconductorcoret...@gmail.com> wrote:
>
>> Hello Package Maintainer,
>>
>> We would like to bring to your attention that your package is failing in
>> devel across all platforms. This is very problematic. Please investigate
>> the issues and fix the package to avoid deprecation.
>>
>> https://bioconductor.org/checkResults/devel/bioc-LATEST/
>> 
>>
>> If you have further questions or concerns please reach out on the
>> bioc-devel@r-project.org
>>
>> We appreciate your quick attention to this matter
>>
>> Cheers,
>> On behalf of the Bioconductor Core Team
>>
>

[[alternative HTML version deleted]]

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