Re: [Rd] [External] Missing function Rf_findFun3
On Sat, 7 Sep 2019, Laurent Gautier wrote: > Hi, > > > The function `Rf_findFun3` is declared in > `$(R CMD CONFIG HOME)/lib/R/include/Rinternals.h` > but appears to be missing from R's shared library (R.so). > > Is this an oversight? No. This is not part of the API supported for use in packages. Best, luke > > Best, > > Laurent > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [External] Missing function Rf_findFun3
I am not using the C API from a package but with an embedded R. Why have it declared in the include/ if it cannot be accessed then? Best, Laurent On Sun, Sep 8, 2019, 8:27 AM Tierney, Luke wrote: > On Sat, 7 Sep 2019, Laurent Gautier wrote: > > > Hi, > > > > > > The function `Rf_findFun3` is declared in > > `$(R CMD CONFIG HOME)/lib/R/include/Rinternals.h` > > but appears to be missing from R's shared library (R.so). > > > > Is this an oversight? > > No. This is not part of the API supported for use in packages. > > Best, > > luke > > > > > Best, > > > > Laurent > > > > [[alternative HTML version deleted]] > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > Luke Tierney > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: 319-335-3386 > Department of Statistics andFax: 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: luke-tier...@uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error: package or namespace load failed for ‘utils
Hi,
When starting an embedded R I encounter the following issue under certain
conditions:
```
Error: package or namespace load failed for ‘utils’ in if (.identC(class1,
class2) || .identC(class2, "ANY")) TRUE else {:
missing value where TRUE/FALSE needed
```
(more such errors for grDevices, graphics, and stats)
And in the end:
```
Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found
2: package ‘grDevices’ in options("defaultPackages") was not found
3: package ‘graphics’ in options("defaultPackages") was not found
4: package ‘stats’ in options("defaultPackages") was not found
```
While the embedded R appears functional, no package can be loaded.
The erorr message from R (`missing value where TRUE/FALSE needed`) suggests
that R should be able to catch the underlying issue (I am yet to find what
it is) earlier and with this make the task of troubleshooting easier.
Best,
Laurent
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
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Re: [Rd] Error: package or namespace load failed for ‘utils
Look at section 6.1 of the R Installation and Admin manual.
6.1 Default packages
The set of packages loaded on startup is by default
> getOption("defaultPackages")
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
(plus, of course, *base*) and this can be changed by setting the option in
startup code (e.g. in ~/.Rprofile). It is initially set to the value of the
environment variable R_DEFAULT_PACKAGES if set (as a comma-separated list).
Setting R_DEFAULT_PACKAGES=NULL ensures that only package *base* is loaded.
Changing the set of default packages is normally used to reduce the set for
speed when scripting: in particular not using *methods*will reduce the
start-up time by a factor of up to two. But it can also be used to
customize R, e.g. for class use. Rscript also checks the environment
variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
R_DEFAULT_PACKAGES.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Sun, Sep 8, 2019 at 8:42 AM Laurent Gautier wrote:
> Hi,
>
> When starting an embedded R I encounter the following issue under certain
> conditions:
>
> ```
> Error: package or namespace load failed for ‘utils’ in if (.identC(class1,
> class2) || .identC(class2, "ANY")) TRUE else {:
> missing value where TRUE/FALSE needed
> ```
> (more such errors for grDevices, graphics, and stats)
>
> And in the end:
>
> ```
> Warning messages:
> 1: package ‘utils’ in options("defaultPackages") was not found
> 2: package ‘grDevices’ in options("defaultPackages") was not found
> 3: package ‘graphics’ in options("defaultPackages") was not found
> 4: package ‘stats’ in options("defaultPackages") was not found
> ```
>
> While the embedded R appears functional, no package can be loaded.
>
> The erorr message from R (`missing value where TRUE/FALSE needed`) suggests
> that R should be able to catch the underlying issue (I am yet to find what
> it is) earlier and with this make the task of troubleshooting easier.
>
> Best,
>
>
> Laurent
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
[[alternative HTML version deleted]]
__
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Re: [Rd] Error: package or namespace load failed for ‘utils
Hi,
Thanks, but I am unsure this helps.
The point I am making is that an R error (about a missing value where a
boolean would be expected), originating from the package methods, is not
informative. This is indicating that a core R function involved in the
loading of an R packages may receive invalid arguments, and rather than the
current situation I believe that such invalid arguments should be
identified earlier with a more meaningful error message (as in an error
message leading to the root of the issue) produced.
L.
Le dim. 8 sept. 2019 à 12:58, William Dunlap a écrit :
> Look at section 6.1 of the R Installation and Admin manual.
>
> 6.1 Default packages
>
> The set of packages loaded on startup is by default
>
> > getOption("defaultPackages")
> [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
>
> (plus, of course, *base*) and this can be changed by setting the option
> in startup code (e.g. in ~/.Rprofile). It is initially set to the value
> of the environment variable R_DEFAULT_PACKAGES if set (as a
> comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only
> package *base* is loaded.
>
> Changing the set of default packages is normally used to reduce the set
> for speed when scripting: in particular not using *methods*will reduce
> the start-up time by a factor of up to two. But it can also be used to
> customize R, e.g. for class use. Rscript also checks the environment
> variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
> R_DEFAULT_PACKAGES.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Sun, Sep 8, 2019 at 8:42 AM Laurent Gautier wrote:
>
>> Hi,
>>
>> When starting an embedded R I encounter the following issue under certain
>> conditions:
>>
>> ```
>> Error: package or namespace load failed for ‘utils’ in if (.identC(class1,
>> class2) || .identC(class2, "ANY")) TRUE else {:
>> missing value where TRUE/FALSE needed
>> ```
>> (more such errors for grDevices, graphics, and stats)
>>
>> And in the end:
>>
>> ```
>> Warning messages:
>> 1: package ‘utils’ in options("defaultPackages") was not found
>> 2: package ‘grDevices’ in options("defaultPackages") was not found
>> 3: package ‘graphics’ in options("defaultPackages") was not found
>> 4: package ‘stats’ in options("defaultPackages") was not found
>> ```
>>
>> While the embedded R appears functional, no package can be loaded.
>>
>> The erorr message from R (`missing value where TRUE/FALSE needed`)
>> suggests
>> that R should be able to catch the underlying issue (I am yet to find what
>> it is) earlier and with this make the task of troubleshooting easier.
>>
>> Best,
>>
>>
>> Laurent
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
[[alternative HTML version deleted]]
__
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Re: [Rd] Error: package or namespace load failed for ‘utils
Also, check the settings of R_HOME and/or R_LIBS.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Sun, Sep 8, 2019 at 9:58 AM William Dunlap wrote:
> Look at section 6.1 of the R Installation and Admin manual.
>
> 6.1 Default packages
>
> The set of packages loaded on startup is by default
>
> > getOption("defaultPackages")
> [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
>
> (plus, of course, *base*) and this can be changed by setting the option
> in startup code (e.g. in ~/.Rprofile). It is initially set to the value
> of the environment variable R_DEFAULT_PACKAGES if set (as a
> comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only
> package *base* is loaded.
>
> Changing the set of default packages is normally used to reduce the set
> for speed when scripting: in particular not using *methods*will reduce
> the start-up time by a factor of up to two. But it can also be used to
> customize R, e.g. for class use. Rscript also checks the environment
> variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
> R_DEFAULT_PACKAGES.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Sun, Sep 8, 2019 at 8:42 AM Laurent Gautier wrote:
>
>> Hi,
>>
>> When starting an embedded R I encounter the following issue under certain
>> conditions:
>>
>> ```
>> Error: package or namespace load failed for ‘utils’ in if (.identC(class1,
>> class2) || .identC(class2, "ANY")) TRUE else {:
>> missing value where TRUE/FALSE needed
>> ```
>> (more such errors for grDevices, graphics, and stats)
>>
>> And in the end:
>>
>> ```
>> Warning messages:
>> 1: package ‘utils’ in options("defaultPackages") was not found
>> 2: package ‘grDevices’ in options("defaultPackages") was not found
>> 3: package ‘graphics’ in options("defaultPackages") was not found
>> 4: package ‘stats’ in options("defaultPackages") was not found
>> ```
>>
>> While the embedded R appears functional, no package can be loaded.
>>
>> The erorr message from R (`missing value where TRUE/FALSE needed`)
>> suggests
>> that R should be able to catch the underlying issue (I am yet to find what
>> it is) earlier and with this make the task of troubleshooting easier.
>>
>> Best,
>>
>>
>> Laurent
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
[[alternative HTML version deleted]]
__
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Re: [Rd] Error: package or namespace load failed for ‘utils
R_HOME is not the issue, and I believe that R_LIBS is not involved with
packages such as "datasets", "utils", etc...
I suspect that the issue is around dynamic loading of C libraries, as
depending on the way the R shared library is called the issue is absent or
present, but the error reporting from R makes tracking this easy.
Le dim. 8 sept. 2019 à 13:22, William Dunlap a écrit :
> Also, check the settings of R_HOME and/or R_LIBS.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Sun, Sep 8, 2019 at 9:58 AM William Dunlap wrote:
>
>> Look at section 6.1 of the R Installation and Admin manual.
>>
>> 6.1 Default packages
>>
>> The set of packages loaded on startup is by default
>>
>> > getOption("defaultPackages")
>> [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
>>
>> (plus, of course, *base*) and this can be changed by setting the option
>> in startup code (e.g. in ~/.Rprofile). It is initially set to the value
>> of the environment variable R_DEFAULT_PACKAGES if set (as a
>> comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only
>> package *base* is loaded.
>>
>> Changing the set of default packages is normally used to reduce the set
>> for speed when scripting: in particular not using *methods*will reduce
>> the start-up time by a factor of up to two. But it can also be used to
>> customize R, e.g. for class use. Rscript also checks the environment
>> variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
>> R_DEFAULT_PACKAGES.
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>>
>> On Sun, Sep 8, 2019 at 8:42 AM Laurent Gautier
>> wrote:
>>
>>> Hi,
>>>
>>> When starting an embedded R I encounter the following issue under certain
>>> conditions:
>>>
>>> ```
>>> Error: package or namespace load failed for ‘utils’ in if
>>> (.identC(class1,
>>> class2) || .identC(class2, "ANY")) TRUE else {:
>>> missing value where TRUE/FALSE needed
>>> ```
>>> (more such errors for grDevices, graphics, and stats)
>>>
>>> And in the end:
>>>
>>> ```
>>> Warning messages:
>>> 1: package ‘utils’ in options("defaultPackages") was not found
>>> 2: package ‘grDevices’ in options("defaultPackages") was not found
>>> 3: package ‘graphics’ in options("defaultPackages") was not found
>>> 4: package ‘stats’ in options("defaultPackages") was not found
>>> ```
>>>
>>> While the embedded R appears functional, no package can be loaded.
>>>
>>> The erorr message from R (`missing value where TRUE/FALSE needed`)
>>> suggests
>>> that R should be able to catch the underlying issue (I am yet to find
>>> what
>>> it is) earlier and with this make the task of troubleshooting easier.
>>>
>>> Best,
>>>
>>>
>>> Laurent
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
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Re: [Rd] install_github and survival
You got the same error 2 years ago. It seems some data files are missing. https://github.com/therneau/survival/issues/12 F. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [External] Missing function Rf_findFun3
On Sun, 8 Sep 2019, Laurent Gautier wrote: > I am not using the C API from a package but with an embedded R. Same rules apply. > Why have it declared in the include/ if it cannot be accessed then? Rinternals.h is used by R internally, as the name suggests. Only a small fraction of the things declared there are part of the API. Would it be better to separate out the things that are in the API into a separate header? Probably. Would doing this be a good use of our limited time resources? Probably not. Would doing this prevent people from using things they shouldn't? Not likely. Best, luke > > Best, > > Laurent > > On Sun, Sep 8, 2019, 8:27 AM Tierney, Luke wrote: > On Sat, 7 Sep 2019, Laurent Gautier wrote: > > > Hi, > > > > > > The function `Rf_findFun3` is declared in > > `$(R CMD CONFIG HOME)/lib/R/include/Rinternals.h` > > but appears to be missing from R's shared library (R.so). > > > > Is this an oversight? > > No. This is not part of the API supported for use in packages. > > Best, > > luke > > > > > Best, > > > > Laurent > > > > [[alternative HTML version deleted]] > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > Luke Tierney > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: > 319-335-3386 > Department of Statistics and Fax: > 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: > luke-tier...@uiowa.edu > Iowa City, IA 52242 WWW: > http://www.stat.uiowa.edu > > > -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
