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Kurt Hornik

2024-Apr-25 06:07 UTC

[Rd] Question regarding .make_numeric_version with non-character input

>>>>> Herv? Pag?s writes:
> Hi Kurt,
> Is it intended that numeric_version() returns an error by default on
> non-character input in R 4.4.0? 
Dear Herve, yes, that's the intention.
> It seems that I can turn this into a warning by setting
> _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't
> seem to be able to find any of this mentioned in the NEWS file.
That's what I added for smoothing the transition: it will be removed
from the trunk shortly.

Best
-k
> Thanks,
> H.
> On 4/1/24 05:28, Kurt Hornik wrote:
>                         Andrea Gilardi via R-devel writes:
                        >     Thanks: should be fixed now in the trunk.
    >     Best
>     -k
>         Thank you very much Dirk for your kind words and for confirming the
bug.
>         Next week I will open a new issue on Bugzilla adding the related
patch.
        >         Kind regards
        >         Andrea
        >         On 29/03/2024 20:14, Dirk Eddelbuettel wrote:
        >             On 29 March 2024 at 17:56, Andrea Gilardi via R-devel wrote:
>             | Dear all,
>             |
>             | I have a question regarding the R-devel version of
.make_numeric_version() function. As far as I can understand, the current code
(https://github.com/wch/r-source/blob/66b91578dfc85140968f07dd4e72d8cb8a54f4c6/src/library/base/R/version.R#L50-L56)
runs the following steps in case of non-character input:
>             |
>             | 1. It creates a message named msg using gettextf.
>             | 2. Such object is then passed to stop(msg) or warning(msg)
according to the following condition
>             |
>             |
tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_")
!= "false")
>             |
>             | However, I don't understand the previous code since the
output of
Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_") !=
"false" is just a boolean value and tolower() will just return
"true" or "false". Maybe the intended code is
tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_"))
!= "false" ? Or am I missing something?
            >             Yes, agreed -- good catch.  In full, the code is (removing
leading
>             whitespace, and putting it back onto single lines)
            >             msg <- gettextf("invalid non-character version
specification 'x' (type: %s)", typeof(x))
>            
if(tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_")
!= "false"))
>             stop(msg, domain = NA)
>             else
>             warning(msg, domain = NA, immediate. = TRUE)
            >             where msg is constant (but reflecting language settings via
standard i18n)
>             and as you not the parentheses appear wrong.  What was intended
is likely
            >             msg <- gettextf("invalid non-character version
specification 'x' (type: %s)", typeof(x))
>            
if(tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_"))
!= "false")
>             stop(msg, domain = NA)
>             else
>             warning(msg, domain = NA, immediate. = TRUE)
            >             If you use bugzilla before and have a handle, maybe file a bug
report with
>             this as patch at https://bugs.r-project.org/
            >             Dirk
>         ______________________________________________
>         R-devel at r-project.org mailing list
>         https://stat.ethz.ch/mailman/listinfo/r-devel
        >     ______________________________________________
>     R-devel at r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/r-devel
    > -- 
> Herv? Pag?s
> Bioconductor Core Team
> hpages.on.github at gmail.com

Hervé Pagès

2024-Apr-25 07:03 UTC

head link

[Rd] Question regarding .make_numeric_version with non-character input

On 4/24/24 23:07, Kurt Hornik wrote:
>>>>>> Herv? Pag?s writes:
>> Hi Kurt,
>> Is it intended that numeric_version() returns an error by default on
>> non-character input in R 4.4.0?
> Dear Herve, yes, that's the intention.
>
>> It seems that I can turn this into a warning by setting
>> _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't
>> seem to be able to find any of this mentioned in the NEWS file.
> That's what I added for smoothing the transition: it will be removed
> from the trunk shortly.
Thanks for clarifying.? Could this be documented in the NEWS file? This 
is a breaking change (it breaks a couple of Bioconductor packages) and 
people are not going to set this environment variable if they are not 
aware of it.

Thanks again,

H.
>
> Best
> -k
>
>> Thanks,
>> H.
>> On 4/1/24 05:28, Kurt Hornik wrote:
>>                          Andrea Gilardi via R-devel writes:
>                          
>>      Thanks: should be fixed now in the trunk.
>      
>>      Best
>>      -k
>>          Thank you very much Dirk for your kind words and for
confirming the bug.
>>          Next week I will open a new issue on Bugzilla adding the
related patch.
>          
>>          Kind regards
>          
>>          Andrea
>          
>>          On 29/03/2024 20:14, Dirk Eddelbuettel wrote:
>          
>>              On 29 March 2024 at 17:56, Andrea Gilardi via R-devel
wrote:
>>              | Dear all,
>>              |
>>              | I have a question regarding the R-devel version of
.make_numeric_version() function. As far as I can understand, the current code
(https://github.com/wch/r-source/blob/66b91578dfc85140968f07dd4e72d8cb8a54f4c6/src/library/base/R/version.R#L50-L56)
runs the following steps in case of non-character input:
>>              |
>>              | 1. It creates a message named msg using gettextf.
>>              | 2. Such object is then passed to stop(msg) or
warning(msg) according to the following condition
>>              |
>>              |
tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_")
!= "false")
>>              |
>>              | However, I don't understand the previous code since
the output of
Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_") !=
"false" is just a boolean value and tolower() will just return
"true" or "false". Maybe the intended code is
tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_"))
!= "false" ? Or am I missing something?
>              
>>              Yes, agreed -- good catch.  In full, the code is (removing
leading
>>              whitespace, and putting it back onto single lines)
>              
>>              msg <- gettextf("invalid non-character version
specification 'x' (type: %s)", typeof(x))
>>             
if(tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_")
!= "false"))
>>              stop(msg, domain = NA)
>>              else
>>              warning(msg, domain = NA, immediate. = TRUE)
>              
>>              where msg is constant (but reflecting language settings
via standard i18n)
>>              and as you not the parentheses appear wrong.  What was
intended is likely
>              
>>              msg <- gettextf("invalid non-character version
specification 'x' (type: %s)", typeof(x))
>>             
if(tolower(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_"))
!= "false")
>>              stop(msg, domain = NA)
>>              else
>>              warning(msg, domain = NA, immediate. = TRUE)
>              
>>              If you use bugzilla before and have a handle, maybe file a
bug report with
>>              this as patch athttps://bugs.r-project.org/
>              
>>              Dirk
>>          ______________________________________________
>>          R-devel at r-project.org  mailing list
>>          https://stat.ethz.ch/mailman/listinfo/r-devel
>          
>>      ______________________________________________
>>      R-devel at r-project.org  mailing list
>>      https://stat.ethz.ch/mailman/listinfo/r-devel
>      
>> -- 
>> Herv? Pag?s
>> Bioconductor Core Team
>> hpages.on.github at gmail.com
-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com

	[[alternative HTML version deleted]]

Dirk Eddelbuettel

2024-Apr-25 12:22 UTC

head link

[Rd] Question regarding .make_numeric_version with non-character input

Hi Kurt,

On 25 April 2024 at 08:07, Kurt Hornik wrote:
| >>>>> Herv? Pag?s writes:
| 
| > Hi Kurt,
| > Is it intended that numeric_version() returns an error by default on
| > non-character input in R 4.4.0? 
| 
| Dear Herve, yes, that's the intention.
| 
| > It seems that I can turn this into a warning by setting
| > _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't
| > seem to be able to find any of this mentioned in the NEWS file.
| 
| That's what I added for smoothing the transition: it will be removed
| from the trunk shortly.

I would actually be nice to have a more robust variant for non-CRAN
versions. For example I just had to do a local hack to be able to use what
the QuantLib 'rc' 1.34-rc reported (when I then used to R facilities to
condition code and tests on whether I was dealing with code before or after
an API transition).  So as a wishlist: could you envision an extension to
package_version() casting that, say, removes all [a-zA-Z]+ first (if opted
into) ?

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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