Re: [R-pkg-devel] CRAN policy on binary submission
Dear Hugh, this question was asked earlier on this list: http://r.789695.n4.nabble.com/executable-files-R-package-td4390488.html See especially the answer of Duncan Murdoch. Best, Mark Op di 9 jan. 2018 om 03:26 schreef Hugh Parsonage : > On https://cran.r-project.org/ , it says > > > Note that we generally do not accept submissions of precompiled binaries > due to security reasons > > I note it says 'generally', not 'always'. Are there any packages on > CRAN which were submitted as precompiled binaries? Under what > circumstances would CRAN accept binaries? > > > Hugh > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] CRAN policy on binary submission
On https://cran.r-project.org/ , it says > Note that we generally do not accept submissions of precompiled binaries due > to security reasons I note it says 'generally', not 'always'. Are there any packages on CRAN which were submitted as precompiled binaries? Under what circumstances would CRAN accept binaries? Hugh __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Fixed for messages
Just to complete the record, the suggested fixes did indeed fix things, and as
I said Henrik provided a clear explanation of why the results are different in
R-devel.
Thanks again,
-Roy
> On Jan 8, 2018, at 9:28 AM, Roy Mendelssohn - NOAA Federal
> wrote:
>
> Thanks. What I have at the top of my Vignette is:
>
>> output:
>> rmarkdown::html_vignette: default
>>
>> vignette: >
>> %\VignetteIndexEntry{Usingxtractomatic}
>> %\VignetteEngine{knitr::rmarkdown}
>> \usepackage[utf8]{inputenc}
>> ---
>>
>
> It is based on the template in RStudio when you choose a vignette as the
> file. I have added rmarkdown as well as webshot to my suggests, and sent to
> win-builder-devel, will see what happens.
>
> Thanks,
>
> -Roy
>
>
>
>> On Jan 8, 2018, at 9:17 AM, Thierry Onkelinx
>> wrote:
>>
>> Dear Roy,
>>
>> Make sure that in DESCRIPTION you have at least
>>
>> Suggests: knitr, rmarkdown
>> VignetteBuilder: knitr
>>
>> The vignette requires
>>
>> %\VignetteEngine{knitr::rmarkdown}
>>
>> webshot is used by rmarkdown or knitr to convert dynamic HTML output
>> to a static image when the output is not HTML. Are you using pdf as
>> output format for the vignette? Consider using
>> rmarkdown::html_vignette.
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkel...@inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be
>>
>> ///
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data. ~ John Tukey
>> ///
>>
>>
>>
>>
>> 2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
>> :
>>> Thanks Henrik:
>>>
>>> I am a little slow, I want to make certain I do this correctly. I already
>>> have knitr in my Suggests, and the message is:
>>>
>> knitr::rmarkdown
>>>
>>> So do I put in my Suggests list rmarkdown or knitr::rmarkdown
>>>
>>> And most importantly, thanks for the explanation about what is happening
>>> with R-devel. Of the responses I have seen, it is the first one (at least
>>> to me) that is clear what is going on to cause the errors, and how to
>>> approach correcting them.
>>>
>>> -Roy
>>>
>>>
>>>
>>>
>>>
On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson
wrote:
On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
wrote:
> Hi All:
>
> In tesitng a package on winbuild-devel (but not on release) I get the
> following errors or warnings:
>
>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>> The vignette engine knitr::rmarkdown is not available, because the
>> rmarkdown package is not installed. Please install it.
>>
>
> There was an email about this a few days ago, but then, as now, it is
> not clear to me specifically what I need to do where so that I don't get
> this warning. Do I need to include rmarkdown in the Suggests,
Yes, add it to Suggests.
or do I need to do something specific in the Vignette. Or is this
just a question that winbuild hasn't installed it yet in the
development version and I can ignore it for now?
>
> Also I am getting this error (again only in the development version):
>
>> Error: processing vignette 'Usingxtractomatic.Rmd' failed with
>> diagnostics:
>> there is no package called 'webshot'
>>
>
>
>
> Now I don't explicitly use a package called 'webshot', but the lines
> referenced in the error message are:
>
>> require("DT")
>> DT::datatable(searchResult)
>>
>
> where "searchResult" is just a list. DT itself does not explicitly
> import "webshot" either.
It most likely depend on 'webshot' indirectly through some of your
package dependencies. So, add this one too to Suggests.
As far as I understand it, the new R-devel tests basically tests your
package with the minimal setup of packages (a "sandboxed" .libPaths())
inferred from you DESCRIPTION (by excluding Suggests of the packages
you depend on, which is where I think 'webshot' lives).
/Henrik
>
> I would like to submit this package, but I don't want to submit with any
> errors or warn
Re: [R-pkg-devel] Fixed for messages
Thanks. What I have at the top of my Vignette is:
> output:
> rmarkdown::html_vignette: default
>
> vignette: >
> %\VignetteIndexEntry{Usingxtractomatic}
> %\VignetteEngine{knitr::rmarkdown}
> \usepackage[utf8]{inputenc}
> ---
>
It is based on the template in RStudio when you choose a vignette as the file.
I have added rmarkdown as well as webshot to my suggests, and sent to
win-builder-devel, will see what happens.
Thanks,
-Roy
> On Jan 8, 2018, at 9:17 AM, Thierry Onkelinx wrote:
>
> Dear Roy,
>
> Make sure that in DESCRIPTION you have at least
>
> Suggests: knitr, rmarkdown
> VignetteBuilder: knitr
>
> The vignette requires
>
> %\VignetteEngine{knitr::rmarkdown}
>
> webshot is used by rmarkdown or knitr to convert dynamic HTML output
> to a static image when the output is not HTML. Are you using pdf as
> output format for the vignette? Consider using
> rmarkdown::html_vignette.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
> ///
> To call in the statistician after the experiment is done may be no
> more than asking him to perform a post-mortem examination: he may be
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does
> not ensure that a reasonable answer can be extracted from a given body
> of data. ~ John Tukey
> ///
>
>
>
>
> 2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
> :
>> Thanks Henrik:
>>
>> I am a little slow, I want to make certain I do this correctly. I already
>> have knitr in my Suggests, and the message is:
>>
> knitr::rmarkdown
>>
>> So do I put in my Suggests list rmarkdown or knitr::rmarkdown
>>
>> And most importantly, thanks for the explanation about what is happening
>> with R-devel. Of the responses I have seen, it is the first one (at least
>> to me) that is clear what is going on to cause the errors, and how to
>> approach correcting them.
>>
>> -Roy
>>
>>
>>
>>
>>
>>> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson
>>> wrote:
>>>
>>> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
>>> wrote:
Hi All:
In tesitng a package on winbuild-devel (but not on release) I get the
following errors or warnings:
> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
> The vignette engine knitr::rmarkdown is not available, because the
> rmarkdown package is not installed. Please install it.
>
There was an email about this a few days ago, but then, as now, it is
not clear to me specifically what I need to do where so that I don't get
this warning. Do I need to include rmarkdown in the Suggests,
>>>
>>> Yes, add it to Suggests.
>>>
>>> or do I need to do something specific in the Vignette. Or is this
>>> just a question that winbuild hasn't installed it yet in the
>>> development version and I can ignore it for now?
Also I am getting this error (again only in the development version):
> Error: processing vignette 'Usingxtractomatic.Rmd' failed with
> diagnostics:
> there is no package called 'webshot'
>
Now I don't explicitly use a package called 'webshot', but the lines
referenced in the error message are:
> require("DT")
> DT::datatable(searchResult)
>
where "searchResult" is just a list. DT itself does not explicitly
import "webshot" either.
>>>
>>> It most likely depend on 'webshot' indirectly through some of your
>>> package dependencies. So, add this one too to Suggests.
>>>
>>> As far as I understand it, the new R-devel tests basically tests your
>>> package with the minimal setup of packages (a "sandboxed" .libPaths())
>>> inferred from you DESCRIPTION (by excluding Suggests of the packages
>>> you depend on, which is where I think 'webshot' lives).
>>>
>>> /Henrik
>>>
I would like to submit this package, but I don't want to submit with any
errors or warnings. Again, I only get these on winbuild-devel.
Thanks for any help.
-Roy
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Scien
Re: [R-pkg-devel] Fixed for messages
Dear Roy,
Make sure that in DESCRIPTION you have at least
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
The vignette requires
%\VignetteEngine{knitr::rmarkdown}
webshot is used by rmarkdown or knitr to convert dynamic HTML output
to a static image when the output is not HTML. Are you using pdf as
output format for the vignette? Consider using
rmarkdown::html_vignette.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///
2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
:
> Thanks Henrik:
>
> I am a little slow, I want to make certain I do this correctly. I already
> have knitr in my Suggests, and the message is:
>
knitr::rmarkdown
>
> So do I put in my Suggests list rmarkdown or knitr::rmarkdown
>
> And most importantly, thanks for the explanation about what is happening
> with R-devel. Of the responses I have seen, it is the first one (at least
> to me) that is clear what is going on to cause the errors, and how to
> approach correcting them.
>
> -Roy
>
>
>
>
>
>> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson
>> wrote:
>>
>> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
>> wrote:
>>> Hi All:
>>>
>>> In tesitng a package on winbuild-devel (but not on release) I get the
>>> following errors or warnings:
>>>
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the
rmarkdown package is not installed. Please install it.
>>>
>>> There was an email about this a few days ago, but then, as now, it is
>>> not clear to me specifically what I need to do where so that I don't get
>>> this warning. Do I need to include rmarkdown in the Suggests,
>>
>> Yes, add it to Suggests.
>>
>> or do I need to do something specific in the Vignette. Or is this
>> just a question that winbuild hasn't installed it yet in the
>> development version and I can ignore it for now?
>>>
>>> Also I am getting this error (again only in the development version):
>>>
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
there is no package called 'webshot'
>>>
>>>
>>>
>>> Now I don't explicitly use a package called 'webshot', but the lines
>>> referenced in the error message are:
>>>
require("DT")
DT::datatable(searchResult)
>>>
>>> where "searchResult" is just a list. DT itself does not explicitly import
>>> "webshot" either.
>>
>> It most likely depend on 'webshot' indirectly through some of your
>> package dependencies. So, add this one too to Suggests.
>>
>> As far as I understand it, the new R-devel tests basically tests your
>> package with the minimal setup of packages (a "sandboxed" .libPaths())
>> inferred from you DESCRIPTION (by excluding Suggests of the packages
>> you depend on, which is where I think 'webshot' lives).
>>
>> /Henrik
>>
>>>
>>> I would like to submit this package, but I don't want to submit with any
>>> errors or warnings. Again, I only get these on winbuild-devel.
>>>
>>> Thanks for any help.
>>>
>>> -Roy
>>>
>>>
>>>
>>>
>>> **
>>> "The contents of this message do not reflect any position of the U.S.
>>> Government or NOAA."
>>> **
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> ***Note new street address***
>>> 110 McAllister Way
>>> Santa Cruz, CA 95060
>>> Phone: (831)-420-3666
>>> Fax: (831) 420-3980
>>> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>>>
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected"
>>> "the arc of the moral universe is long, but it bends toward justice" -MLK
>>> Jr.
>>>
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> R
Re: [R-pkg-devel] Fixed for messages
Thanks Henrik:
I am a little slow, I want to make certain I do this correctly. I already
have knitr in my Suggests, and the message is:
>>> knitr::rmarkdown
So do I put in my Suggests list rmarkdown or knitr::rmarkdown
And most importantly, thanks for the explanation about what is happening with
R-devel. Of the responses I have seen, it is the first one (at least to me)
that is clear what is going on to cause the errors, and how to approach
correcting them.
-Roy
> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson
> wrote:
>
> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
> wrote:
>> Hi All:
>>
>> In tesitng a package on winbuild-devel (but not on release) I get the
>> following errors or warnings:
>>
>>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>>> The vignette engine knitr::rmarkdown is not available, because the
>>> rmarkdown package is not installed. Please install it.
>>>
>>
>> There was an email about this a few days ago, but then, as now, it is not
>> clear to me specifically what I need to do where so that I don't get this
>> warning. Do I need to include rmarkdown in the Suggests,
>
> Yes, add it to Suggests.
>
> or do I need to do something specific in the Vignette. Or is this
> just a question that winbuild hasn't installed it yet in the
> development version and I can ignore it for now?
>>
>> Also I am getting this error (again only in the development version):
>>
>>> Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
>>> there is no package called 'webshot'
>>>
>>
>>
>>
>> Now I don't explicitly use a package called 'webshot', but the lines
>> referenced in the error message are:
>>
>>> require("DT")
>>> DT::datatable(searchResult)
>>>
>>
>> where "searchResult" is just a list. DT itself does not explicitly import
>> "webshot" either.
>
> It most likely depend on 'webshot' indirectly through some of your
> package dependencies. So, add this one too to Suggests.
>
> As far as I understand it, the new R-devel tests basically tests your
> package with the minimal setup of packages (a "sandboxed" .libPaths())
> inferred from you DESCRIPTION (by excluding Suggests of the packages
> you depend on, which is where I think 'webshot' lives).
>
> /Henrik
>
>>
>> I would like to submit this package, but I don't want to submit with any
>> errors or warnings. Again, I only get these on winbuild-devel.
>>
>> Thanks for any help.
>>
>> -Roy
>>
>>
>>
>>
>> **
>> "The contents of this message do not reflect any position of the U.S.
>> Government or NOAA."
>> **
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new street address***
>> 110 McAllister Way
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>>
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected"
>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Fixed for messages
On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
wrote:
> Hi All:
>
> In tesitng a package on winbuild-devel (but not on release) I get the
> following errors or warnings:
>
>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>> The vignette engine knitr::rmarkdown is not available, because the
>> rmarkdown package is not installed. Please install it.
>>
>
> There was an email about this a few days ago, but then, as now, it is not
> clear to me specifically what I need to do where so that I don't get this
> warning. Do I need to include rmarkdown in the Suggests,
Yes, add it to Suggests.
or do I need to do something specific in the Vignette. Or is this
just a question that winbuild hasn't installed it yet in the
development version and I can ignore it for now?
>
> Also I am getting this error (again only in the development version):
>
>> Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
>> there is no package called 'webshot'
>>
>
>
>
> Now I don't explicitly use a package called 'webshot', but the lines
> referenced in the error message are:
>
>> require("DT")
>> DT::datatable(searchResult)
>>
>
> where "searchResult" is just a list. DT itself does not explicitly import
> "webshot" either.
It most likely depend on 'webshot' indirectly through some of your
package dependencies. So, add this one too to Suggests.
As far as I understand it, the new R-devel tests basically tests your
package with the minimal setup of packages (a "sandboxed" .libPaths())
inferred from you DESCRIPTION (by excluding Suggests of the packages
you depend on, which is where I think 'webshot' lives).
/Henrik
>
> I would like to submit this package, but I don't want to submit with any
> errors or warnings. Again, I only get these on winbuild-devel.
>
> Thanks for any help.
>
> -Roy
>
>
>
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Fixed for messages
Hi All:
In tesitng a package on winbuild-devel (but not on release) I get the
following errors or warnings:
> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
> The vignette engine knitr::rmarkdown is not available, because the
> rmarkdown package is not installed. Please install it.
>
There was an email about this a few days ago, but then, as now, it is not
clear to me specifically what I need to do where so that I don't get this
warning. Do I need to include rmarkdown in the Suggests, or do I need to do
something specific in the Vignette. Or is this just a question that winbuild
hasn't installed it yet in the development version and I can ignore it for now?
Also I am getting this error (again only in the development version):
> Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
> there is no package called 'webshot'
>
Now I don't explicitly use a package called 'webshot', but the lines
referenced in the error message are:
> require("DT")
> DT::datatable(searchResult)
>
where "searchResult" is just a list. DT itself does not explicitly import
"webshot" either.
I would like to submit this package, but I don't want to submit with any
errors or warnings. Again, I only get these on winbuild-devel.
Thanks for any help.
-Roy
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
