Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Dirk Eddelbuettel 


On 16 May 2024 at 05:34, Duncan Murdoch wrote:
| I forget now, but presumably the thinking at the time was that Suggested 
| packages would always be available for building and checking vignettes.

Yes. I argued for years (cf https://dirk.eddelbuettel.com/blog/2017/03/22/
from seven (!!) years ago) and CRAN is slowly moving away from that implicit
'always there' guarantee to prefering explicit enumerations -- and now even
tests via the NoSuggests flavour.

As Uwe stated in this thread, having the vignette dependencies both in
Suggests as well as in the VignetteHeader should do. And it is the Right
Thing (TM) to do.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Sebastian Meyer 

Am 16.05.24 um 11:34 schrieb Duncan Murdoch:

On 2024-05-16 4:15 a.m., Sebastian Meyer wrote:

Am 15.05.24 um 00:09 schrieb Lluís Revilla:

Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle 
installed.
I don't know if it is possible to use a vignette output conditionally 
with

knitr: In any case it seems that it would be a requirement (Imports, or
Depends).


Yes, I'd consider the package providing the vignette output format for
the rmarkdown engine, here BiocStyle, as a strong dependency of that
vignette.


It is documented in WRE as a soft dependency of the package: "As Sweave 
is the only engine supplied with the R distribution, the package 
providing any other engine must be specified in the ‘VignetteBuilder’ 
field of the package DESCRIPTION file, and also specified in the 
‘Suggests’, ‘Imports’ or ‘Depends’ field (since its namespace must be 
available to build or check your package)."


I forget now, but presumably the thinking at the time was that Suggested 
packages would always be available for building and checking vignettes.


With most soft dependencies, it's up to the package writer to handle the 
possibility that it is missing, but here, I think it has to be the check 
code that does it, skipping the vignette test if the builder is missing.


Yes, re-building vignettes is skipped when a VignetteBuilder package is 
unavailable.


In the present case, the VignetteBuilder package that provides the 
engine is knitr and BiocStyle is used for an alternative rmarkdown 
output format. Not sure if the latter should be declared as an 
additional VignetteBuilder even if it does not provide the vignette 
engine, but you are right that it comes very close.




Alternatively, it could be required to be a hard dependency, but that 
seems too strong:  most package users don't need to rebuild vignettes.


Agreed. Declaring it as part of the vignette's \VignetteDepends is what 
I'd do to solve the check issue.


Sebastian Meyer



Duncan Murdoch


  The error from the additional "noSuggests" check

() shows it
cannot be rebuild if BiocStyle is unavailable.

The 'StepReg' vignette could use a metadata line to declare strong
vignette dependencies, for example:

  %\VignetteDepends{StepReg, BiocStyle, kableExtra}

(I haven't checked if this list is complete.)

This avoids spurious check errors in incomplete setups, such as when
mass-checking packages (e.g., reverse dependencies) without some of the
suggested packages being installed.

Best,

Sebastian Meyer



However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from 
rmarkdown

if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  
wrote:



Hi everyone,

I recently developed an R package called 'StepReg' and used the
Bioconductor R package 'BiocStyle' in my vignettes, as shown below:

output:
    BiocStyle::html_document:
  toc_float: true
    BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
included a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
  knitr,
  testthat,
  BiocStyle,
  kableExtra

You may find all those information here:
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on
https://win-builder.r-project.org/upload.aspx. However, an error 
message

occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
 'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (
https://cran.r-project.org/web/packages/StepReg/index.html), I
successfully uploaded it to CRAN without including 'biocViews:' in the
DESCRIPTION file two months ago. However, I'm encountering difficulties
this time. Any insights or suggestions on resolving this issue would be
greatly appreciated.

Thanks,
Junhui

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Uwe Ligges 



On 16.05.2024 10:15, Sebastian Meyer wrote:

Am 15.05.24 um 00:09 schrieb Lluís Revilla:

Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally 
with

knitr: In any case it seems that it would be a requirement (Imports, or
Depends).


Yes, I'd consider the package providing the vignette output format for 
the rmarkdown engine, here BiocStyle, as a strong dependency of that 
vignette. The error from the additional "noSuggests" check 
() shows it 
cannot be rebuild if BiocStyle is unavailable.


The 'StepReg' vignette could use a metadata line to declare strong 
vignette dependencies, for example:


     %\VignetteDepends{StepReg, BiocStyle, kableExtra}


Indeed, having it listed in Suggests plus the \VignetteDepends 
declaration should suffice.


Best,
Uwe Ligges





(I haven't checked if this list is complete.)

This avoids spurious check errors in incomplete setups, such as when 
mass-checking packages (e.g., reverse dependencies) without some of the 
suggested packages being installed.


Best,

 Sebastian Meyer



However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from 
rmarkdown

if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  
wrote:



Hi everyone,

I recently developed an R package called 'StepReg' and used the
Bioconductor R package 'BiocStyle' in my vignettes, as shown below:

output:
   BiocStyle::html_document:
 toc_float: true
   BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
included a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
 knitr,
 testthat,
 BiocStyle,
 kableExtra

You may find all those information here:
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on
https://win-builder.r-project.org/upload.aspx. However, an error message
occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
    'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (
https://cran.r-project.org/web/packages/StepReg/index.html), I
successfully uploaded it to CRAN without including 'biocViews:' in the
DESCRIPTION file two months ago. However, I'm encountering difficulties
this time. Any insights or suggestions on resolving this issue would be
greatly appreciated.

Thanks,
Junhui

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Duncan Murdoch 

On 2024-05-16 4:15 a.m., Sebastian Meyer wrote:

Am 15.05.24 um 00:09 schrieb Lluís Revilla:

Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with
knitr: In any case it seems that it would be a requirement (Imports, or
Depends).


Yes, I'd consider the package providing the vignette output format for
the rmarkdown engine, here BiocStyle, as a strong dependency of that
vignette.


It is documented in WRE as a soft dependency of the package: "As Sweave 
is the only engine supplied with the R distribution, the package 
providing any other engine must be specified in the ‘VignetteBuilder’ 
field of the package DESCRIPTION file, and also specified in the 
‘Suggests’, ‘Imports’ or ‘Depends’ field (since its namespace must be 
available to build or check your package)."


I forget now, but presumably the thinking at the time was that Suggested 
packages would always be available for building and checking vignettes.


With most soft dependencies, it's up to the package writer to handle the 
possibility that it is missing, but here, I think it has to be the check 
code that does it, skipping the vignette test if the builder is missing.


Alternatively, it could be required to be a hard dependency, but that 
seems too strong:  most package users don't need to rebuild vignettes.


Duncan Murdoch


 The error from the additional "noSuggests" check

() shows it
cannot be rebuild if BiocStyle is unavailable.

The 'StepReg' vignette could use a metadata line to declare strong
vignette dependencies, for example:

  %\VignetteDepends{StepReg, BiocStyle, kableExtra}

(I haven't checked if this list is complete.)

This avoids spurious check errors in incomplete setups, such as when
mass-checking packages (e.g., reverse dependencies) without some of the
suggested packages being installed.

Best,

Sebastian Meyer



However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown
if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  wrote:


Hi everyone,

I recently developed an R package called 'StepReg' and used the
Bioconductor R package 'BiocStyle' in my vignettes, as shown below:

output:
BiocStyle::html_document:
  toc_float: true
BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
included a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
  knitr,
  testthat,
  BiocStyle,
  kableExtra

You may find all those information here:
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on
https://win-builder.r-project.org/upload.aspx. However, an error message
occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
 'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (
https://cran.r-project.org/web/packages/StepReg/index.html), I
successfully uploaded it to CRAN without including 'biocViews:' in the
DESCRIPTION file two months ago. However, I'm encountering difficulties
this time. Any insights or suggestions on resolving this issue would be
greatly appreciated.

Thanks,
Junhui

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Sebastian Meyer 

Am 15.05.24 um 00:09 schrieb Lluís Revilla:

Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with
knitr: In any case it seems that it would be a requirement (Imports, or
Depends).


Yes, I'd consider the package providing the vignette output format for 
the rmarkdown engine, here BiocStyle, as a strong dependency of that 
vignette. The error from the additional "noSuggests" check 
() shows it 
cannot be rebuild if BiocStyle is unavailable.


The 'StepReg' vignette could use a metadata line to declare strong 
vignette dependencies, for example:


%\VignetteDepends{StepReg, BiocStyle, kableExtra}

(I haven't checked if this list is complete.)

This avoids spurious check errors in incomplete setups, such as when 
mass-checking packages (e.g., reverse dependencies) without some of the 
suggested packages being installed.


Best,

Sebastian Meyer



However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown
if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  wrote:


Hi everyone,

I recently developed an R package called 'StepReg' and used the
Bioconductor R package 'BiocStyle' in my vignettes, as shown below:

output:
   BiocStyle::html_document:
 toc_float: true
   BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
included a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
 knitr,
 testthat,
 BiocStyle,
 kableExtra

You may find all those information here:
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on
https://win-builder.r-project.org/upload.aspx. However, an error message
occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (
https://cran.r-project.org/web/packages/StepReg/index.html), I
successfully uploaded it to CRAN without including 'biocViews:' in the
DESCRIPTION file two months ago. However, I'm encountering difficulties
this time. Any insights or suggestions on resolving this issue would be
greatly appreciated.

Thanks,
Junhui

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-15 Thread Li, Junhui 
Hi Llu�s,

Thanks for your input. I believe it is ok to use a vignette output 
conditionally with knitr. However,  what confuses me is that I was able to 
successfully upload StepReg version 1.5.0 to CRAN with BiocStyle listed in the 
Suggests field. It seems that there is some issues with CRAN check.

Best,
Junhui
From: Llu�s Revilla 
Date: Tuesday, May 14, 2024 at 18:09
To: Li, Junhui 
Cc: r-package-devel@r-project.org 
Subject: Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages
Hi Junhui,

There is a separate log for checking if your package works without suggested 
packages: in the StepReg results
The noSuggests title leads to: 
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with 
knitr: In any case it seems that it would be a requirement (Imports, or 
Depends).

However, it is best to not use the Bioconductor style for a package in CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown if I 
recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Llu�s


On Tue, 14 May 2024 at 22:48, Li, Junhui 
mailto:junhui.l...@umassmed.edu>> wrote:
Hi everyone,

I recently developed an R package called 'StepReg' and used the Bioconductor R 
package 'BiocStyle' in my vignettes, as shown below:

output:
  BiocStyle::html_document:
toc_float: true
  BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included 
a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
knitr,
testthat,
BiocStyle,
kableExtra

You may find all those information here: 
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on 
https://win-builder.r-project.org/upload.aspx. However, an error message 
occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
   'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), 
I successfully uploaded it to CRAN without including 'biocViews:' in the 
DESCRIPTION file two months ago. However, I'm encountering difficulties this 
time. Any insights or suggestions on resolving this issue would be greatly 
appreciated.

Thanks,
Junhui

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-14 Thread Lluís Revilla 
Hi Junhui,

There is a separate log for checking if your package works without
suggested packages: in the StepReg results
The noSuggests title leads to:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out
Where you can see that it fails if a user don't have BiocStyle installed.
I don't know if it is possible to use a vignette output conditionally with
knitr: In any case it seems that it would be a requirement (Imports, or
Depends).

However, it is best to not use the Bioconductor style for a package in
CRAN.
You could use the *_vignette or *_document format directly (from rmarkdown
if I recall correctly).
You will remove a dependency and avoid this problem entirely.

Best,

Lluís


On Tue, 14 May 2024 at 22:48, Li, Junhui  wrote:

> Hi everyone,
>
> I recently developed an R package called 'StepReg' and used the
> Bioconductor R package 'BiocStyle' in my vignettes, as shown below:
>
> output:
>   BiocStyle::html_document:
> toc_float: true
>   BiocStyle::pdf_document: default
>
> In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and
> included a new line 'biocViews:', as follows:
>
> VignetteBuilder: knitr
> biocViews:
> Suggests:
> knitr,
> testthat,
> BiocStyle,
> kableExtra
>
> You may find all those information here:
> https://github.com/JunhuiLi1017/StepReg/tree/dev
>
> There were no error messages when checking with 'R CMD check' and on
> https://win-builder.r-project.org/upload.aspx. However, an error message
> occurred when I attempted to upload it to CRAN:
>
> * checking re-building of vignette outputs ... ERROR
> Error(s) in re-building vignettes:
> --- re-building 'StepReg.Rmd' using rmarkdown
> Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
> there is no package called 'BiocStyle'
> --- failed re-building 'StepReg.Rmd'
>
> SUMMARY: processing the following file failed:
>'StepReg.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
> For version 1.5.0 (
> https://cran.r-project.org/web/packages/StepReg/index.html), I
> successfully uploaded it to CRAN without including 'biocViews:' in the
> DESCRIPTION file two months ago. However, I'm encountering difficulties
> this time. Any insights or suggestions on resolving this issue would be
> greatly appreciated.
>
> Thanks,
> Junhui
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-14 Thread Li, Junhui 
Hi everyone,

I recently developed an R package called 'StepReg' and used the Bioconductor R 
package 'BiocStyle' in my vignettes, as shown below:

output:
  BiocStyle::html_document:
toc_float: true
  BiocStyle::pdf_document: default

In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included 
a new line 'biocViews:', as follows:

VignetteBuilder: knitr
biocViews:
Suggests:
knitr,
testthat,
BiocStyle,
kableExtra

You may find all those information here: 
https://github.com/JunhuiLi1017/StepReg/tree/dev

There were no error messages when checking with 'R CMD check' and on 
https://win-builder.r-project.org/upload.aspx. However, an error message 
occurred when I attempted to upload it to CRAN:

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'

SUMMARY: processing the following file failed:
   'StepReg.Rmd'

Error: Vignette re-building failed.
Execution halted

For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), 
I successfully uploaded it to CRAN without including 'biocViews:' in the 
DESCRIPTION file two months ago. However, I'm encountering difficulties this 
time. Any insights or suggestions on resolving this issue would be greatly 
appreciated.

Thanks,
Junhui

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