Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-07 Thread Martin Maechler 
> Tim Taylor 
> on Thu, 6 Jul 2023 15:11:41 +0100 writes:

> Ah yes ... and reading the as.data.frame help we see (emphasis mine):
> "... Direct calls to as.data.frame.() are still possible (*base 
> package!*), for 12 atomic base classes, but will deprecated ..."

> So it does seem that a lot of these warnings are triggered by base R and 
> updating this code may be a work in progress.


> A little tangential (but related) to this though is still the fact that 
> we can trigger the warning with:

> lapply(Sys.Date(), as.data.frame)

> so I wonder if the code in base/R/zzz.R 
> 
(https://github.com/wch/r-source/blob/9f1940663f902174034a01197e55fd17c767213a/src/library/base/R/zzz.R#L664-L686)
 
> does need tweaking?

> At this stage this is probably more a question for R-devel though.

Indeed. ... and so I've sent a long reply to you, Enrico,
Vincent *AND* the R-devel mailing list.  In its archives you see it here

 https://stat.ethz.ch/pipermail/r-devel/2023-July/082725.html

With thanks to Vincent, Tim, Enrico, (and Mikael who started
"moving" this to R-devel, see there).

Martin

--
Martin Maechler
ETH Zurich   and   R Core team

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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Tim Taylor 

Ah yes ... and reading the as.data.frame help we see (emphasis mine):

"... Direct calls to as.data.frame.() are still possible (*base 
package!*), for 12 atomic base classes, but will deprecated ..."


So it does seem that a lot of these warnings are triggered by base R and 
updating this code may be a work in progress.



A little tangential (but related) to this though is still the fact that 
we can trigger the warning with:


lapply(Sys.Date(), as.data.frame)

so I wonder if the code in base/R/zzz.R 
(https://github.com/wch/r-source/blob/9f1940663f902174034a01197e55fd17c767213a/src/library/base/R/zzz.R#L664-L686) 
does need tweaking?


At this stage this is probably more a question for R-devel though.

Tim


On 06/07/2023 14:42, Enrico Schumann wrote:

On Thu, 06 Jul 2023, Vincent van Hees writes:


Thanks, in that case the REPLEX for the issue may need to be:


remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
data.frame(time = Sys.time())

  time
1 2023-07-06 14:29:37

data.frame(time = as.POSIXlt(Sys.time()))

  time
1 2023-07-06 14:29:37
Warning message:
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead

Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)


I think it happens because

 data.frame()

calls 'as.data.frame.POSIXlt' (per its S3-class), which
in turn directly calls 'as.data.frame.POSIXct':

 ## as.data.frame.POSIXlt
 function (x, row.names = NULL, optional = FALSE, ...)
 {
 value <- as.data.frame.POSIXct(as.POSIXct(x), row.names,
 optional, ...)
 if (!optional)
 names(value) <- deparse1(substitute(x))
 value
 }
 

Kind regards
 Enrico


Vincent

On Thu, 6 Jul 2023 at 10:41, Tim Taylor 
wrote:


Apologies - I've not had enough caffeine just yet. The reprex below
highlights the issue but I think the code which implemented the change
*may* need tweaking not lapply.

Tim

On 06/07/2023 09:26, Tim Taylor wrote:

This *may* be an issue in lapply.  Let's see what others day. Reprex
below

Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
dat <- Sys.Date()
as.data.frame(dat)
#>  dat
#> 1 2023-07-06
lapply(dat, as.data.frame)
#> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
#> 'as.data.frame.vector()' or 'as.data.frame()' instead
#> [[1]]
#>   X[[i]]
#> 1 2023-07-06

Tim

On 06/07/2023 08:54, Vincent van Hees wrote:

Dear all,

I see the following warning in my package test results:

```
Warning
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead
```

The warning is not always there and I struggle to make it
reproducible. I
have encountered it in both Ubuntu 22.04 and in Windows 11, in both R
4.3.0
and 4.3.1, in both RStudio and in an GitHub Actions environment (example
).
The warning gives the impression that I am doing something that R no
longer
supports. However, I am not using the command as.data.frame.POSIXct()
anywhere directly in my code.

When I dive into the code where the warnings occur I see patterns like:

```
now = Sys.time()
df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
```

(this is a simplification of for example:


https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R

)

Does this mean I am discouraged from putting a vector with POSIXct
values
in a data.frame?
If yes, what would be the recommended work around?

I have been trying to find documentation or online discussions about
this
warning but no luck so far. I see R NEWS
 mentions
updates to POSIXct related objects several times in the past year but
those
seem to be different issues.

Best,

Vincent

 [[alternative HTML version deleted]]

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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Vincent van Hees 
Thanks Dirk,
My plan will then be to revise my package to avoid using POSIXlt when
POSIXct is also sufficient, given that I am storing timestamps in
data.frames a lot. In the few instances where POSIXlt may be necessary I
will avoid storing them in a data.frame.
Vincent

On Thu, 6 Jul 2023 at 15:22, Dirk Eddelbuettel  wrote:

>
> On 6 July 2023 at 08:14, Dirk Eddelbuettel wrote:
> |
> | On 6 July 2023 at 14:31, Vincent van Hees wrote:
> | | Thanks, in that case the REPLEX for the issue may need to be:
> | |
> | | > remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
> | | > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
> | | > data.frame(time = Sys.time())
> | |  time
> | | 1 2023-07-06 14:29:37
> | | > data.frame(time = as.POSIXlt(Sys.time()))
> | |  time
> | | 1 2023-07-06 14:29:37
> | | Warning message:
> | | Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
> | | 'as.data.frame.vector()' or 'as.data.frame()' instead
> | | > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)
> |
> | Does _not_ happen in a plain R session.
> |
> | Does happen when `library(tidyverse)` is executed first. May come from
> | `tibble` or `vectors`, I have a habit of not using those much.
>
> Err, no, wait. I may have confused myself here jumping between R-devel and
> R (release).  Please disregard, and apologies for the noise.
>
> In any event, assigning a POSIXlt (which is an 11-element list) to a single
> column is not a great idiom and we had the POSIXct conversion there for a
> while IIRC.
>
> But assigning a POSIXct to a column should always work, and I would be
> surprised to find a minimally complete reproducible example showing that it
> does not.
>
> Dirk
>
> | Dirk
> |
> | | Vincent
> | |
> | | On Thu, 6 Jul 2023 at 10:41, Tim Taylor <
> tim.tay...@hiddenelephants.co.uk>
> | | wrote:
> | |
> | | > Apologies - I've not had enough caffeine just yet. The reprex below
> | | > highlights the issue but I think the code which implemented the
> change
> | | > *may* need tweaking not lapply.
> | | >
> | | > Tim
> | | >
> | | > On 06/07/2023 09:26, Tim Taylor wrote:
> | | > > This *may* be an issue in lapply.  Let's see what others day.
> Reprex
> | | > > below
> | | > >
> | | > > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
> | | > > dat <- Sys.Date()
> | | > > as.data.frame(dat)
> | | > > #>  dat
> | | > > #> 1 2023-07-06
> | | > > lapply(dat, as.data.frame)
> | | > > #> Warning: Direct call of 'as.data.frame.Date()' is deprecated.
> Use
> | | > > #> 'as.data.frame.vector()' or 'as.data.frame()' instead
> | | > > #> [[1]]
> | | > > #>   X[[i]]
> | | > > #> 1 2023-07-06
> | | > >
> | | > > Tim
> | | > >
> | | > > On 06/07/2023 08:54, Vincent van Hees wrote:
> | | > >> Dear all,
> | | > >>
> | | > >> I see the following warning in my package test results:
> | | > >>
> | | > >> ```
> | | > >> Warning
> | | > >> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
> | | > >> 'as.data.frame.vector()' or 'as.data.frame()' instead
> | | > >> ```
> | | > >>
> | | > >> The warning is not always there and I struggle to make it
> | | > >> reproducible. I
> | | > >> have encountered it in both Ubuntu 22.04 and in Windows 11, in
> both R
> | | > >> 4.3.0
> | | > >> and 4.3.1, in both RStudio and in an GitHub Actions environment
> (example
> | | > >> <
> https://github.com/wadpac/GGIR/actions/runs/5463862340/jobs/9945096566>).
> | | >
> | | > >>
> | | > >> The warning gives the impression that I am doing something that R
> no
> | | > >> longer
> | | > >> supports. However, I am not using the command
> as.data.frame.POSIXct()
> | | > >> anywhere directly in my code.
> | | > >>
> | | > >> When I dive into the code where the warnings occur I see patterns
> like:
> | | > >>
> | | > >> ```
> | | > >> now = Sys.time()
> | | > >> df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
> | | > >> ```
> | | > >>
> | | > >> (this is a simplification of for example:
> | | > >>
> | | >
> https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
> | | > >>
> | | > >> )
> | | > >>
> | | > >> Does this mean I am discouraged from putting a vector with POSIXct
> | | > >> values
> | | > >> in a data.frame?
> | | > >> If yes, what would be the recommended work around?
> | | > >>
> | | > >> I have been trying to find documentation or online discussions
> about
> | | > >> this
> | | > >> warning but no luck so far. I see R NEWS
> | | > >> 
> mentions
> | | > >> updates to POSIXct related objects several times in the past year
> but
> | | > >> those
> | | > >> seem to be different issues.
> | | > >>
> | | > >> Best,
> | | > >>
> | | > >> Vincent
> | | > >>
> | | > >> [[alternative HTML version deleted]]
> | | > >>
> | | > >> __
> | | > >> R-package-devel@r-project.org mailing list
> | | > >> https://stat.e

Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Enrico Schumann 
On Thu, 06 Jul 2023, Vincent van Hees writes:

> Thanks, in that case the REPLEX for the issue may need to be:
>
>> remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
>> Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
>> data.frame(time = Sys.time())
>  time
> 1 2023-07-06 14:29:37
>> data.frame(time = as.POSIXlt(Sys.time()))
>  time
> 1 2023-07-06 14:29:37
> Warning message:
> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
> 'as.data.frame.vector()' or 'as.data.frame()' instead
>> Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)


I think it happens because

data.frame()

calls 'as.data.frame.POSIXlt' (per its S3-class), which
in turn directly calls 'as.data.frame.POSIXct':

## as.data.frame.POSIXlt
function (x, row.names = NULL, optional = FALSE, ...) 
{
value <- as.data.frame.POSIXct(as.POSIXct(x), row.names, 
optional, ...)
if (!optional) 
names(value) <- deparse1(substitute(x))
value
}


Kind regards
Enrico

> Vincent
>
> On Thu, 6 Jul 2023 at 10:41, Tim Taylor 
> wrote:
>
>> Apologies - I've not had enough caffeine just yet. The reprex below
>> highlights the issue but I think the code which implemented the change
>> *may* need tweaking not lapply.
>>
>> Tim
>>
>> On 06/07/2023 09:26, Tim Taylor wrote:
>> > This *may* be an issue in lapply.  Let's see what others day. Reprex
>> > below
>> >
>> > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
>> > dat <- Sys.Date()
>> > as.data.frame(dat)
>> > #>  dat
>> > #> 1 2023-07-06
>> > lapply(dat, as.data.frame)
>> > #> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
>> > #> 'as.data.frame.vector()' or 'as.data.frame()' instead
>> > #> [[1]]
>> > #>   X[[i]]
>> > #> 1 2023-07-06
>> >
>> > Tim
>> >
>> > On 06/07/2023 08:54, Vincent van Hees wrote:
>> >> Dear all,
>> >>
>> >> I see the following warning in my package test results:
>> >>
>> >> ```
>> >> Warning
>> >> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
>> >> 'as.data.frame.vector()' or 'as.data.frame()' instead
>> >> ```
>> >>
>> >> The warning is not always there and I struggle to make it
>> >> reproducible. I
>> >> have encountered it in both Ubuntu 22.04 and in Windows 11, in both R
>> >> 4.3.0
>> >> and 4.3.1, in both RStudio and in an GitHub Actions environment (example
>> >> ).
>>
>> >>
>> >> The warning gives the impression that I am doing something that R no
>> >> longer
>> >> supports. However, I am not using the command as.data.frame.POSIXct()
>> >> anywhere directly in my code.
>> >>
>> >> When I dive into the code where the warnings occur I see patterns like:
>> >>
>> >> ```
>> >> now = Sys.time()
>> >> df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
>> >> ```
>> >>
>> >> (this is a simplification of for example:
>> >>
>> https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
>> >>
>> >> )
>> >>
>> >> Does this mean I am discouraged from putting a vector with POSIXct
>> >> values
>> >> in a data.frame?
>> >> If yes, what would be the recommended work around?
>> >>
>> >> I have been trying to find documentation or online discussions about
>> >> this
>> >> warning but no luck so far. I see R NEWS
>> >>  mentions
>> >> updates to POSIXct related objects several times in the past year but
>> >> those
>> >> seem to be different issues.
>> >>
>> >> Best,
>> >>
>> >> Vincent
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
>> >> __
>> >> 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
>>
>
>   [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
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-- 
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http://enricoschumann.net

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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Dirk Eddelbuettel 


On 6 July 2023 at 08:14, Dirk Eddelbuettel wrote:
| 
| On 6 July 2023 at 14:31, Vincent van Hees wrote:
| | Thanks, in that case the REPLEX for the issue may need to be:
| | 
| | > remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
| | > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
| | > data.frame(time = Sys.time())
| |  time
| | 1 2023-07-06 14:29:37
| | > data.frame(time = as.POSIXlt(Sys.time()))
| |  time
| | 1 2023-07-06 14:29:37
| | Warning message:
| | Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
| | 'as.data.frame.vector()' or 'as.data.frame()' instead
| | > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)
| 
| Does _not_ happen in a plain R session.
| 
| Does happen when `library(tidyverse)` is executed first. May come from
| `tibble` or `vectors`, I have a habit of not using those much. 

Err, no, wait. I may have confused myself here jumping between R-devel and
R (release).  Please disregard, and apologies for the noise.

In any event, assigning a POSIXlt (which is an 11-element list) to a single
column is not a great idiom and we had the POSIXct conversion there for a
while IIRC.

But assigning a POSIXct to a column should always work, and I would be
surprised to find a minimally complete reproducible example showing that it
does not.  

Dirk

| Dirk
|  
| | Vincent
| | 
| | On Thu, 6 Jul 2023 at 10:41, Tim Taylor 
| | wrote:
| | 
| | > Apologies - I've not had enough caffeine just yet. The reprex below
| | > highlights the issue but I think the code which implemented the change
| | > *may* need tweaking not lapply.
| | >
| | > Tim
| | >
| | > On 06/07/2023 09:26, Tim Taylor wrote:
| | > > This *may* be an issue in lapply.  Let's see what others day. Reprex
| | > > below
| | > >
| | > > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
| | > > dat <- Sys.Date()
| | > > as.data.frame(dat)
| | > > #>  dat
| | > > #> 1 2023-07-06
| | > > lapply(dat, as.data.frame)
| | > > #> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
| | > > #> 'as.data.frame.vector()' or 'as.data.frame()' instead
| | > > #> [[1]]
| | > > #>   X[[i]]
| | > > #> 1 2023-07-06
| | > >
| | > > Tim
| | > >
| | > > On 06/07/2023 08:54, Vincent van Hees wrote:
| | > >> Dear all,
| | > >>
| | > >> I see the following warning in my package test results:
| | > >>
| | > >> ```
| | > >> Warning
| | > >> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
| | > >> 'as.data.frame.vector()' or 'as.data.frame()' instead
| | > >> ```
| | > >>
| | > >> The warning is not always there and I struggle to make it
| | > >> reproducible. I
| | > >> have encountered it in both Ubuntu 22.04 and in Windows 11, in both R
| | > >> 4.3.0
| | > >> and 4.3.1, in both RStudio and in an GitHub Actions environment 
(example
| | > >> 
).
| | >
| | > >>
| | > >> The warning gives the impression that I am doing something that R no
| | > >> longer
| | > >> supports. However, I am not using the command as.data.frame.POSIXct()
| | > >> anywhere directly in my code.
| | > >>
| | > >> When I dive into the code where the warnings occur I see patterns like:
| | > >>
| | > >> ```
| | > >> now = Sys.time()
| | > >> df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
| | > >> ```
| | > >>
| | > >> (this is a simplification of for example:
| | > >>
| | > 
https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
| | > >>
| | > >> )
| | > >>
| | > >> Does this mean I am discouraged from putting a vector with POSIXct
| | > >> values
| | > >> in a data.frame?
| | > >> If yes, what would be the recommended work around?
| | > >>
| | > >> I have been trying to find documentation or online discussions about
| | > >> this
| | > >> warning but no luck so far. I see R NEWS
| | > >>  mentions
| | > >> updates to POSIXct related objects several times in the past year but
| | > >> those
| | > >> seem to be different issues.
| | > >>
| | > >> Best,
| | > >>
| | > >> Vincent
| | > >>
| | > >> [[alternative HTML version deleted]]
| | > >>
| | > >> __
| | > >> 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
| | >
| | 
| | [[alternative HTML version deleted]]
| | 
| | __
| | R-package-devel@r-project.org mailing list
| | https://stat.ethz.ch/mailman/listinfo/r-package-devel
| 
| -- 
| dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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

__
R-package-devel

Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Dirk Eddelbuettel 


On 6 July 2023 at 14:31, Vincent van Hees wrote:
| Thanks, in that case the REPLEX for the issue may need to be:
| 
| > remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
| > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
| > data.frame(time = Sys.time())
|  time
| 1 2023-07-06 14:29:37
| > data.frame(time = as.POSIXlt(Sys.time()))
|  time
| 1 2023-07-06 14:29:37
| Warning message:
| Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
| 'as.data.frame.vector()' or 'as.data.frame()' instead
| > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)

Does _not_ happen in a plain R session.

Does happen when `library(tidyverse)` is executed first. May come from
`tibble` or `vectors`, I have a habit of not using those much. 

Dirk
 
| Vincent
| 
| On Thu, 6 Jul 2023 at 10:41, Tim Taylor 
| wrote:
| 
| > Apologies - I've not had enough caffeine just yet. The reprex below
| > highlights the issue but I think the code which implemented the change
| > *may* need tweaking not lapply.
| >
| > Tim
| >
| > On 06/07/2023 09:26, Tim Taylor wrote:
| > > This *may* be an issue in lapply.  Let's see what others day. Reprex
| > > below
| > >
| > > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
| > > dat <- Sys.Date()
| > > as.data.frame(dat)
| > > #>  dat
| > > #> 1 2023-07-06
| > > lapply(dat, as.data.frame)
| > > #> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
| > > #> 'as.data.frame.vector()' or 'as.data.frame()' instead
| > > #> [[1]]
| > > #>   X[[i]]
| > > #> 1 2023-07-06
| > >
| > > Tim
| > >
| > > On 06/07/2023 08:54, Vincent van Hees wrote:
| > >> Dear all,
| > >>
| > >> I see the following warning in my package test results:
| > >>
| > >> ```
| > >> Warning
| > >> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
| > >> 'as.data.frame.vector()' or 'as.data.frame()' instead
| > >> ```
| > >>
| > >> The warning is not always there and I struggle to make it
| > >> reproducible. I
| > >> have encountered it in both Ubuntu 22.04 and in Windows 11, in both R
| > >> 4.3.0
| > >> and 4.3.1, in both RStudio and in an GitHub Actions environment (example
| > >> 
).
| >
| > >>
| > >> The warning gives the impression that I am doing something that R no
| > >> longer
| > >> supports. However, I am not using the command as.data.frame.POSIXct()
| > >> anywhere directly in my code.
| > >>
| > >> When I dive into the code where the warnings occur I see patterns like:
| > >>
| > >> ```
| > >> now = Sys.time()
| > >> df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
| > >> ```
| > >>
| > >> (this is a simplification of for example:
| > >>
| > 
https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
| > >>
| > >> )
| > >>
| > >> Does this mean I am discouraged from putting a vector with POSIXct
| > >> values
| > >> in a data.frame?
| > >> If yes, what would be the recommended work around?
| > >>
| > >> I have been trying to find documentation or online discussions about
| > >> this
| > >> warning but no luck so far. I see R NEWS
| > >>  mentions
| > >> updates to POSIXct related objects several times in the past year but
| > >> those
| > >> seem to be different issues.
| > >>
| > >> Best,
| > >>
| > >> Vincent
| > >>
| > >> [[alternative HTML version deleted]]
| > >>
| > >> __
| > >> 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
| >
| 
|   [[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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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Vincent van Hees 
Thanks, in that case the REPLEX for the issue may need to be:

> remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_")
> Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
> data.frame(time = Sys.time())
 time
1 2023-07-06 14:29:37
> data.frame(time = as.POSIXlt(Sys.time()))
 time
1 2023-07-06 14:29:37
Warning message:
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead
> Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = remember)

Vincent

On Thu, 6 Jul 2023 at 10:41, Tim Taylor 
wrote:

> Apologies - I've not had enough caffeine just yet. The reprex below
> highlights the issue but I think the code which implemented the change
> *may* need tweaking not lapply.
>
> Tim
>
> On 06/07/2023 09:26, Tim Taylor wrote:
> > This *may* be an issue in lapply.  Let's see what others day. Reprex
> > below
> >
> > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
> > dat <- Sys.Date()
> > as.data.frame(dat)
> > #>  dat
> > #> 1 2023-07-06
> > lapply(dat, as.data.frame)
> > #> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
> > #> 'as.data.frame.vector()' or 'as.data.frame()' instead
> > #> [[1]]
> > #>   X[[i]]
> > #> 1 2023-07-06
> >
> > Tim
> >
> > On 06/07/2023 08:54, Vincent van Hees wrote:
> >> Dear all,
> >>
> >> I see the following warning in my package test results:
> >>
> >> ```
> >> Warning
> >> Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
> >> 'as.data.frame.vector()' or 'as.data.frame()' instead
> >> ```
> >>
> >> The warning is not always there and I struggle to make it
> >> reproducible. I
> >> have encountered it in both Ubuntu 22.04 and in Windows 11, in both R
> >> 4.3.0
> >> and 4.3.1, in both RStudio and in an GitHub Actions environment (example
> >> ).
>
> >>
> >> The warning gives the impression that I am doing something that R no
> >> longer
> >> supports. However, I am not using the command as.data.frame.POSIXct()
> >> anywhere directly in my code.
> >>
> >> When I dive into the code where the warnings occur I see patterns like:
> >>
> >> ```
> >> now = Sys.time()
> >> df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
> >> ```
> >>
> >> (this is a simplification of for example:
> >>
> https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
> >>
> >> )
> >>
> >> Does this mean I am discouraged from putting a vector with POSIXct
> >> values
> >> in a data.frame?
> >> If yes, what would be the recommended work around?
> >>
> >> I have been trying to find documentation or online discussions about
> >> this
> >> warning but no luck so far. I see R NEWS
> >>  mentions
> >> updates to POSIXct related objects several times in the past year but
> >> those
> >> seem to be different issues.
> >>
> >> Best,
> >>
> >> Vincent
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> __
> >> 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
>

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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Tim Taylor 
Apologies - I've not had enough caffeine just yet. The reprex below 
highlights the issue but I think the code which implemented the change 
*may* need tweaking not lapply.


Tim

On 06/07/2023 09:26, Tim Taylor wrote:
This *may* be an issue in lapply.  Let's see what others day. Reprex 
below


Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
dat <- Sys.Date()
as.data.frame(dat)
#>  dat
#> 1 2023-07-06
lapply(dat, as.data.frame)
#> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
#> 'as.data.frame.vector()' or 'as.data.frame()' instead
#> [[1]]
#>   X[[i]]
#> 1 2023-07-06

Tim

On 06/07/2023 08:54, Vincent van Hees wrote:

Dear all,

I see the following warning in my package test results:

```
Warning
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead
```

The warning is not always there and I struggle to make it 
reproducible. I
have encountered it in both Ubuntu 22.04 and in Windows 11, in both R 
4.3.0

and 4.3.1, in both RStudio and in an GitHub Actions environment (example
). 

The warning gives the impression that I am doing something that R no 
longer

supports. However, I am not using the command as.data.frame.POSIXct()
anywhere directly in my code.

When I dive into the code where the warnings occur I see patterns like:

```
now = Sys.time()
df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
```

(this is a simplification of for example:
https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R 


)

Does this mean I am discouraged from putting a vector with POSIXct 
values

in a data.frame?
If yes, what would be the recommended work around?

I have been trying to find documentation or online discussions about 
this

warning but no luck so far. I see R NEWS
 mentions
updates to POSIXct related objects several times in the past year but 
those

seem to be different issues.

Best,

Vincent

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Tim Taylor 

This *may* be an issue in lapply.  Let's see what others day. Reprex below

Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE)
dat <- Sys.Date()
as.data.frame(dat)
#>  dat
#> 1 2023-07-06
lapply(dat, as.data.frame)
#> Warning: Direct call of 'as.data.frame.Date()' is deprecated.  Use
#> 'as.data.frame.vector()' or 'as.data.frame()' instead
#> [[1]]
#>   X[[i]]
#> 1 2023-07-06

Tim

On 06/07/2023 08:54, Vincent van Hees wrote:

Dear all,

I see the following warning in my package test results:

```
Warning
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead
```

The warning is not always there and I struggle to make it reproducible. I
have encountered it in both Ubuntu 22.04 and in Windows 11, in both R 4.3.0
and 4.3.1, in both RStudio and in an GitHub Actions environment (example
).
The warning gives the impression that I am doing something that R no longer
supports. However, I am not using the command as.data.frame.POSIXct()
anywhere directly in my code.

When I dive into the code where the warnings occur I see patterns like:

```
now = Sys.time()
df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
```

(this is a simplification of for example:
https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
)

Does this mean I am discouraged from putting a vector with POSIXct values
in a data.frame?
If yes, what would be the recommended work around?

I have been trying to find documentation or online discussions about this
warning but no luck so far. I see R NEWS
 mentions
updates to POSIXct related objects several times in the past year but those
seem to be different issues.

Best,

Vincent

[[alternative HTML version deleted]]

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[R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Vincent van Hees 
Dear all,

I see the following warning in my package test results:

```
Warning
Direct call of 'as.data.frame.POSIXct()' is deprecated.  Use
'as.data.frame.vector()' or 'as.data.frame()' instead
```

The warning is not always there and I struggle to make it reproducible. I
have encountered it in both Ubuntu 22.04 and in Windows 11, in both R 4.3.0
and 4.3.1, in both RStudio and in an GitHub Actions environment (example
).
The warning gives the impression that I am doing something that R no longer
supports. However, I am not using the command as.data.frame.POSIXct()
anywhere directly in my code.

When I dive into the code where the warnings occur I see patterns like:

```
now = Sys.time()
df = data.frame (time = seq(now, now + 10, by =1),  B  = 1:11)
```

(this is a simplification of for example:
https://github.com/wadpac/GGIR/blob/master/tests/testthat/test_read.myacc.csv.R
)

Does this mean I am discouraged from putting a vector with POSIXct values
in a data.frame?
If yes, what would be the recommended work around?

I have been trying to find documentation or online discussions about this
warning but no luck so far. I see R NEWS
 mentions
updates to POSIXct related objects several times in the past year but those
seem to be different issues.

Best,

Vincent

[[alternative HTML version deleted]]

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