Re: [R-pkg-devel] API client package failing due to API authentication

2023-10-26 Thread Cole Johanson 
Thank you. I did forget to re-document. I appreciate the help!

On Thu, Oct 26, 2023 at 12:30 PM Ivan Krylov  wrote:

> В Thu, 26 Oct 2023 11:14:15 -0400
> Cole Johanson  пишет:
>
> > I have wrapped the examples with the roxygen2 tag *\dontrun*, but it
> > is still attempting to run the examples.
>
> Judging by the latest commit at
> <
> https://github.com/cole-johanson/smartsheetr/commit/5e4f8fb23b1f9d91c5941d9f116f7f076d785d8f
> >,
> you forgot to run roxygen2::roxygenise() to regenerate the man/*.Rd
> files (which is what R cares about). Your use of the Rd tag \dontrun{}
> is otherwise fine and should prevent the code from being run.
>
> I am not sure whether it's acceptable to \dontrun{} every possible test
> and example, but if the code useless without a valid API key, so be it.
> Maybe you could write your examples in
> if(nzchar(getenv('SMARTSHEET_API_TOKEN'))) withAutoprint({ ... })
> instead to make it possible to run
>
> SMARTSHEET_API_TOKEN=YOURTOKEN R CMD check shartsheetr*.tar.gz
>
> ...and have all the tests run, the way your CI is currently set up.
>
> --
> Best regards,
> Ivan
>

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Re: [R-pkg-devel] API client package failing due to API authentication

2023-10-26 Thread Dirk Eddelbuettel 


On 26 October 2023 at 11:14, Cole Johanson wrote:
| My package https://github.com/cole-johanson/smartsheetr requires an
| environment variable, the API access token, to run most of the functions.
| The steps for setting this are documented in the README, but my package is
| being auto-rejected by CRAN for failing the examples.
| 
| I have wrapped the examples with the roxygen2 tag *\dontrun*, but it is
| still attempting to run the examples.
| 
| Should I report this as a false positive, or is there a step I am missing?

You should not attempt to run the examples when they could fail e.g. when no
API key is present as it the case for CRAN.

Dirk

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

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Re: [R-pkg-devel] API client package failing due to API authentication

2023-10-26 Thread Ivan Krylov 
В Thu, 26 Oct 2023 11:14:15 -0400
Cole Johanson  пишет:

> I have wrapped the examples with the roxygen2 tag *\dontrun*, but it
> is still attempting to run the examples.

Judging by the latest commit at
,
you forgot to run roxygen2::roxygenise() to regenerate the man/*.Rd
files (which is what R cares about). Your use of the Rd tag \dontrun{}
is otherwise fine and should prevent the code from being run.

I am not sure whether it's acceptable to \dontrun{} every possible test
and example, but if the code useless without a valid API key, so be it.
Maybe you could write your examples in
if(nzchar(getenv('SMARTSHEET_API_TOKEN'))) withAutoprint({ ... })
instead to make it possible to run

SMARTSHEET_API_TOKEN=YOURTOKEN R CMD check shartsheetr*.tar.gz

...and have all the tests run, the way your CI is currently set up.

-- 
Best regards,
Ivan

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[R-pkg-devel] API client package failing due to API authentication

2023-10-26 Thread Cole Johanson 
Hello,

My package https://github.com/cole-johanson/smartsheetr requires an
environment variable, the API access token, to run most of the functions.
The steps for setting this are documented in the README, but my package is
being auto-rejected by CRAN for failing the examples.

I have wrapped the examples with the roxygen2 tag *\dontrun*, but it is
still attempting to run the examples.

Should I report this as a false positive, or is there a step I am missing?

Thank you!

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Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

2023-10-26 Thread Plamen Mirazchiyski 
I apologize for misreading Ivan's first email. I now installed from the 
tar.gz source file, everything worked as expected.


Thank you both for the thorough explanations.

Best,
Plamen

On 10/26/23 16:20, Ivan Krylov wrote:

В Thu, 26 Oct 2023 15:43:54 +0200
Plamen Mirazchiyski  пишет:


If I understand Ivan's email, my package should work on R 4.3.1, but
what about newer versions?


The source package (the .tar.gz file obtained using R CMD build) will
keep working fine on both R 4.3 and R 4.4.

The binary package (the .zip file obtained using R CMD INSTALL --build
and produced on Win-Builder) is only guaranteed to work with the R
version that was used to build the binary package.

This is the reason why https://CRAN.R-project.org/package=RALSA offers
a single download of the source package...


Package source: RALSA_1.3.5.tar.gz


...but multiple, separate downloads of binary versions of the package,
for R-4.4, R-4.3, and R-4.2:


Windows binaries:   r-devel: RALSA_1.3.5.zip, r-release:
RALSA_1.3.5.zip, r-oldrel: RALSA_1.3.5.zip




--
==
Plamen Mirazchiyski, PhD
International Educational Research and Evaluation Institute
24 Tehnološki park
SI-1000 Ljubljana
Slovenia
tel.: +386 51 303 817
email: plamen.mirazchiy...@ineri.org

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Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

2023-10-26 Thread Ivan Krylov 
В Thu, 26 Oct 2023 15:43:54 +0200
Plamen Mirazchiyski  пишет:

> If I understand Ivan's email, my package should work on R 4.3.1, but 
> what about newer versions?

The source package (the .tar.gz file obtained using R CMD build) will
keep working fine on both R 4.3 and R 4.4.

The binary package (the .zip file obtained using R CMD INSTALL --build
and produced on Win-Builder) is only guaranteed to work with the R
version that was used to build the binary package.

This is the reason why https://CRAN.R-project.org/package=RALSA offers
a single download of the source package...

>> Package source:  RALSA_1.3.5.tar.gz

...but multiple, separate downloads of binary versions of the package,
for R-4.4, R-4.3, and R-4.2:

>> Windows binaries:r-devel: RALSA_1.3.5.zip, r-release:
>> RALSA_1.3.5.zip, r-oldrel: RALSA_1.3.5.zip

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

2023-10-26 Thread Duncan Murdoch 
There are two kinds of builds:  source builds (producing the .tar.gz 
file) and binary builds (producing the .zip file on Windows).  Binary 
builds are specific to R minor versions:  if you build on R version 
x.y.z, you can't expect the package to work if either x or y changes.


Source builds should work on other R versions, though sometimes moving 
to earlier versions will cause problems (because the format of files in 
the .tar.gz file may have changed), or your package relies on features 
that weren't present earlier.  Generally .tar.gz files will work on 
later versions (though changes in R might break it).


So if you did a binary build on R 4.4.x and tested it on R 4.3.1, it's 
not at all surprising that it failed.  If you did a source build on R 
4.4.x and it failed on R 4.3.1, that's more surprising.


Duncan Murdoch

On 26/10/2023 9:43 a.m., Plamen Mirazchiyski wrote:

Thank you very much for your responses Duncan and Ivan.

I do not call .Internal(crossprod( ... )) directly. I use crossprod()
just once in the entire package, the actual line of code is

unname(obj = crossprod(x = sweep(x = as.matrix(replicated.averages),
MARGIN = 2, mean.replicate.averages, FUN = "-"))*des.scale.fac)

I followed Ivan's advice, built a binary package from source in R 4.3.1
on Windows 10, then tested it on another Windows 10 machine with R
4.3.1. The problem did not occur et all.

If I understand Ivan's email, my package should work on R 4.3.1, but
what about newer versions? I checked some packages that were released
today, e.g. abn, these were built by CRAN "using R Under development
(unstable) (2023-10-24 r85407 ucrt)". Does this mean mine will fail on
the current released version (4.3.1) if built by CRAN. As far as I see
from the R Developer Page (https://developer.r-project.org), there is a
new version (4.3.2) scheduled for October 31, 2023. Should I better wait
until then?

Best,
Plamen

On 10/25/23 21:26, Ivan Krylov wrote:

В Wed, 25 Oct 2023 21:02:00 +0200
Plamen Mirazchiyski  пишет:


Today I was preparing a new version for the RALSA package. I have
built a Windows package using "devtools::check_win_devel()".



The machine has R 4.3.1, the latest official release. After I load the
test RALSA package, R displays a message saying "Package RALSA built
under R version 4.4.0"


Can you use R CMD build to make a .tar.gz source package and then
install that on the Windows 10 machine running R 4.3.1? There is
convenience and a lot of added value in both Win-Builder and devtools,
but it shouldn't be necessary to rely on 96 CRAN packages and an online
service just to build a package.

crossprod(x,y) has indeed been recently changed from
.Internal(crossprod(x, y)) to .Primitive("crossprod"). This makes it
possible for a binary package prepared using R-devel (with a call to
.Primitive('crossprod')) to misbehave on a released version of R (which
does have .Internal(crossprod(...)) but not .Primitive('crossprod')).

Installing from source will avoid this problem. So will building the
binary package using R-4.3.1 to run it on a different machine with
R-4.3.1.







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Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

2023-10-26 Thread Plamen Mirazchiyski 

Thank you very much for your responses Duncan and Ivan.

I do not call .Internal(crossprod( ... )) directly. I use crossprod() 
just once in the entire package, the actual line of code is


unname(obj = crossprod(x = sweep(x = as.matrix(replicated.averages), 
MARGIN = 2, mean.replicate.averages, FUN = "-"))*des.scale.fac)


I followed Ivan's advice, built a binary package from source in R 4.3.1 
on Windows 10, then tested it on another Windows 10 machine with R 
4.3.1. The problem did not occur et all.


If I understand Ivan's email, my package should work on R 4.3.1, but 
what about newer versions? I checked some packages that were released 
today, e.g. abn, these were built by CRAN "using R Under development 
(unstable) (2023-10-24 r85407 ucrt)". Does this mean mine will fail on 
the current released version (4.3.1) if built by CRAN. As far as I see 
from the R Developer Page (https://developer.r-project.org), there is a 
new version (4.3.2) scheduled for October 31, 2023. Should I better wait 
until then?


Best,
Plamen

On 10/25/23 21:26, Ivan Krylov wrote:

В Wed, 25 Oct 2023 21:02:00 +0200
Plamen Mirazchiyski  пишет:


Today I was preparing a new version for the RALSA package. I have
built a Windows package using "devtools::check_win_devel()".



The machine has R 4.3.1, the latest official release. After I load the
test RALSA package, R displays a message saying "Package RALSA built
under R version 4.4.0"


Can you use R CMD build to make a .tar.gz source package and then
install that on the Windows 10 machine running R 4.3.1? There is
convenience and a lot of added value in both Win-Builder and devtools,
but it shouldn't be necessary to rely on 96 CRAN packages and an online
service just to build a package.

crossprod(x,y) has indeed been recently changed from
.Internal(crossprod(x, y)) to .Primitive("crossprod"). This makes it
possible for a binary package prepared using R-devel (with a call to
.Primitive('crossprod')) to misbehave on a released version of R (which
does have .Internal(crossprod(...)) but not .Primitive('crossprod')).

Installing from source will avoid this problem. So will building the
binary package using R-4.3.1 to run it on a different machine with
R-4.3.1.





--
==
Plamen Mirazchiyski, PhD
International Educational Research and Evaluation Institute
24 Tehnološki park
SI-1000 Ljubljana
Slovenia
tel.: +386 51 303 817
email: plamen.mirazchiy...@ineri.org

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