[R-pkg-devel] R vignettes

Hello,

I am doing a R CMD check on an R package I have developed. However, I keep
receiving the warning below:

*Files in the 'vignettes' directory but no files in 'inst/doc':*

And

*Files named as vignettes but with no recognized vignette engine:*

I am pretty sure I have the correct YAML header for my vignettes, and also
inst/docs is an older convention for vignettes that's no longer
recommended.

Do you have an idea of what's going wrong? I have attached my YAML header
below as reference.

Sincerely,
Danielle







*title: "title of this vignette"author: "name"output:
markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette title}
%\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*

On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

Hello,

I am doing a R CMD check on an R package I have developed. However, I

keep

receiving the warning below:

*Files in the 'vignettes' directory but no files in 'inst/doc':*

And

*Files named as vignettes but with no recognized vignette engine:*

I am pretty sure I have the correct YAML header for my vignettes, and

also

inst/docs is an older convention for vignettes that's no longer
recommended.

Do you have an idea of what's going wrong? I have attached my YAML header
below as reference.

You may be missing the line

   VignetteBuilder: knitr

in your DESCRIPTION file.  Without that, R won't know how to interpret
your vignette.

It's also a little unusual to use

   %\VignetteEngine{knitr::markdown}

nowadays; the more common engine is knitr::rmarkdown (but I believe both
are still supported).  If you make this change you should also have

   rmarkdown::html_vignette

as the output format.

Finally, since a recent update of knitr, you need to make sure that
package holding the output format (i.e. markdown currently, rmarkdown if
you make the change above) is declared as a Suggested package in your
DESCRIPTION file.

Duncan Murdoch

Sincerely,
Danielle







*title: "title of this vignette"author: "name"output:
markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette title}
%\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new error:

*trying to use CRAN without setting a mirror

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Suggests: knitr, rmarkdown*

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
 ? %\VignetteIndexEntry{title}
 ? %\VignetteEngine{knitr::rmarkdown}
 ? %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <murdoch.duncan at gmail.com 
<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in 'inst/doc':*
     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette engine:*
     >
     > I am pretty sure I have the correct YAML header for my vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no longer
     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

     ? ?VignetteBuilder: knitr

    in your DESCRIPTION file.? Without that, R won't know how to interpret
    your vignette.

    It's also a little unusual to use

     ? ?%\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I believe
    both
    are still supported).? If you make this change you should also have

     ? ?rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure that
    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in your
    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >? %\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}? %\VignetteEncoding{UTF-8}*
     >

-- 
Ph.D. Student
Bioinformatics and?Computational?Biology
University of Minnesota

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new error:

*trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in
one of your functions?  Normally you shouldn't do that.

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to
cli::col_ed, or try to import col_ed from cli?

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Do you really have a data subdir in your package? You shouldn't have the
LazyData line without one.

Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
   %\VignetteIndexEntry{title}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <murdoch.duncan at gmail.com
<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in 'inst/doc':*
     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette engine:*
     >
     > I am pretty sure I have the correct YAML header for my vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no longer
     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

        VignetteBuilder: knitr

    in your DESCRIPTION file.  Without that, R won't know how to

interpret

    your vignette.

    It's also a little unusual to use

        %\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I believe
    both
    are still supported).  If you make this change you should also have

        rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure that
    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in your
    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
     >

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

Hi Duncan,

I really appreciate your response. Unfortunately, I am still receiving the
error below.

If anyone has ideas, I'd appreciate it!

This is the only online forum I can find that discusses the error, but I
have not found it helpful: https://github.com/r-lib/cli/issues/94




*   ERROR: package installation failedError: 'col_ed' is not an exported
object from 'namespace:cli'Execution halted*

On Wed, Apr 28, 2021 at 7:32 PM Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new error:

*trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in
one of your functions?  Normally you shouldn't do that.

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to
cli::col_ed, or try to import col_ed from cli?

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Do you really have a data subdir in your package? You shouldn't have the
LazyData line without one.

Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
   %\VignetteIndexEntry{title}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <murdoch.duncan at gmail.com
<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in 'inst/doc':*
     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette engine:*
     >
     > I am pretty sure I have the correct YAML header for my vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no longer
     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

        VignetteBuilder: knitr

    in your DESCRIPTION file.  Without that, R won't know how to

interpret

    your vignette.

    It's also a little unusual to use

        %\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I believe
    both
    are still supported).  If you make this change you should also have

        rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure that
    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in your
    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
     >

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

        [[alternative HTML version deleted]]

If you could share a reproducible example with us, and/or you could
show the full output, then we could probably help you better.

Gabor

On Thu, Apr 29, 2021 at 6:29 PM Danielle Maeser <maese005 at umn.edu> wrote:

Hi Duncan,

I really appreciate your response. Unfortunately, I am still receiving

the

error below.

If anyone has ideas, I'd appreciate it!

This is the only online forum I can find that discusses the error, but I
have not found it helpful: https://github.com/r-lib/cli/issues/94




*   ERROR: package installation failedError: 'col_ed' is not an exported
object from 'namespace:cli'Execution halted*

On Wed, Apr 28, 2021 at 7:32 PM Duncan Murdoch <murdoch.duncan at gmail.com

wrote:

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new

error:

*trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in
one of your functions?  Normally you shouldn't do that.

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to
cli::col_ed, or try to import col_ed from cli?

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Do you really have a data subdir in your package? You shouldn't have

the

LazyData line without one.

Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
   %\VignetteIndexEntry{title}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <

murdoch.duncan at gmail.com

<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in

'inst/doc':*

     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette

engine:*

     >
     > I am pretty sure I have the correct YAML header for my

vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no

longer

     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

        VignetteBuilder: knitr

    in your DESCRIPTION file.  Without that, R won't know how to

interpret

    your vignette.

    It's also a little unusual to use

        %\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I

believe

    both
    are still supported).  If you make this change you should also

have

        rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure

that

    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in

your

    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >

%\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
     >

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

        [[alternative HTML version deleted]]

Hi Gabor,

My full output is below:
   Error: object 'col_ed' is not exported by 'namespace:cli'
   Execution halted
   ERROR: lazy loading failed for package 'packagename'
         -----------------------------------
   ERROR: package installation failed

Error: 'col_ed' is not an exported object from 'namespace:cli'
Execution halted

Exited with status 1.

Unfortunately, I can't share a full reproducible example since this package is also included in a manuscript for publication.

I don't export any objects named 'col_ed' so I am quite perplexed by this error message.

I'd appreciate any advice!

Danielle

On Thu, Apr 29, 2021 at 11:42 AM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

If you could share a reproducible example with us, and/or you could
show the full output, then we could probably help you better.

Gabor

On Thu, Apr 29, 2021 at 6:29 PM Danielle Maeser <maese005 at umn.edu> wrote:

Hi Duncan,

I really appreciate your response. Unfortunately, I am still receiving the
error below.

If anyone has ideas, I'd appreciate it!

This is the only online forum I can find that discusses the error, but I
have not found it helpful: https://github.com/r-lib/cli/issues/94




*   ERROR: package installation failedError: 'col_ed' is not an exported
object from 'namespace:cli'Execution halted*

On Wed, Apr 28, 2021 at 7:32 PM Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new error:

*trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in
one of your functions?  Normally you shouldn't do that.

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to
cli::col_ed, or try to import col_ed from cli?

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Do you really have a data subdir in your package? You shouldn't have the
LazyData line without one.

Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
   %\VignetteIndexEntry{title}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <murdoch.duncan at gmail.com
<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in 'inst/doc':*
     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette engine:*
     >
     > I am pretty sure I have the correct YAML header for my vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no longer
     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

        VignetteBuilder: knitr

    in your DESCRIPTION file.  Without that, R won't know how to

interpret

    your vignette.

    It's also a little unusual to use

        %\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I believe
    both
    are still supported).  If you make this change you should also have

        rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure that
    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in your
    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >  %\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
     >

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

        [[alternative HTML version deleted]]

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

Hi Gabor,

My full output is below:
*? ?Error: object 'col_ed' is not exported by 'namespace:cli'
 ? ?Execution halted
 ? ?ERROR: lazy loading failed for package 'packagename'
 ? ? ? ? ?-----------------------------------
 ? ?ERROR: package installation failed

Error: 'col_ed' is not an exported object from 'namespace:cli'
Execution halted

Exited with status 1.*
*
*
Unfortunately, I can't share a full reproducible example since this 
package is also included in a manuscript for publication.

I don't export any objects named 'col_ed' so I am quite perplexed?by 
this error message.

Hi Duncan,

I really appreciate your response. Unfortunately, I am still receiving the
error below.

If anyone has ideas, I'd appreciate it!

This is the only online forum I can find that discusses the error, but I
have not found it helpful: https://github.com/r-lib/cli/issues/94




*   ERROR: package installation failedError: 'col_ed' is not an exported
object from 'namespace:cli'Execution halted*

On Wed, Apr 28, 2021 at 7:32 PM Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

On 28/04/2021 4:41 p.m., Danielle Maeser wrote:

Hi Duncan,

Thank you for your feedback!

Unfortunately, when I made the changes recommended I have a new error:

*trying to use CRAN without setting a mirror

That would be a result of your code.  Do you call install.packages() in
one of your functions?  Normally you shouldn't do that.

*

And:
*Error: 'col_ed' is not an exported object from 'namespace:cli'*

Similarly, something in your code or NAMESPACE file.  Do you refer to
cli::col_ed, or try to import col_ed from cli?

*
*
My description file includes:
*VignetteBuilder: knitr
Depends: R (>= 4.0), knitr
License: GPL-2
Encoding: UTF-8
Roxygen: list(rmarkdown = TRUE)
RoxygenNote: 7.1.1
LazyData: true

Do you really have a data subdir in your package? You shouldn't have the
LazyData line without one.

Suggests: knitr, rmarkdown*

You shouldn't list knitr in both Depends and Suggests.

Duncan Murdoch

*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
   %\VignetteIndexEntry{title}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}*
*
*
I'd appreciate any advice!

Danielle

On Wed, Apr 28, 2021 at 2:27 PM Duncan Murdoch <

murdoch.duncan at gmail.com

<mailto:murdoch.duncan at gmail.com>> wrote:

    On 28/04/2021 2:44 p.m., Danielle Maeser wrote:

     > Hello,
     >
     > I am doing a R CMD check on an R package I have developed.

    However, I keep

     > receiving the warning below:
     >
     > *Files in the 'vignettes' directory but no files in 'inst/doc':*
     >
     > And
     >
     > *Files named as vignettes but with no recognized vignette

engine:*

     >
     > I am pretty sure I have the correct YAML header for my

vignettes,

    and also

     > inst/docs is an older convention for vignettes that's no longer
     > recommended.
     >
     > Do you have an idea of what's going wrong? I have attached my

    YAML header

     > below as reference.

    You may be missing the line

        VignetteBuilder: knitr

    in your DESCRIPTION file.  Without that, R won't know how to

interpret

    your vignette.

    It's also a little unusual to use

        %\VignetteEngine{knitr::markdown}

    nowadays; the more common engine is knitr::rmarkdown (but I believe
    both
    are still supported).  If you make this change you should also have

        rmarkdown::html_vignette

    as the output format.

    Finally, since a recent update of knitr, you need to make sure that
    package holding the output format (i.e. markdown currently,
    rmarkdown if
    you make the change above) is declared as a Suggested package in

your

    DESCRIPTION file.

    Duncan Murdoch

     >
     > Sincerely,
     > Danielle
     >
     >
     >
     >
     >
     >
     >
     > *title: "title of this vignette"author: "name"output:
     > markdown::html_vignettevignette: >

%\VignetteIndexEntry{vignette

    title}

     > %\VignetteEngine{knitr::markdown}  %\VignetteEncoding{UTF-8}*
     >

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

--
Ph.D. Student
Bioinformatics and Computational Biology
University of Minnesota

        [[alternative HTML version deleted]]