R devel - Sep 2019 - 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]]

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 <lgautier at gmail.com>
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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
	[[alternative HTML version deleted]]

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 ? 12:58, William Dunlap <wdunlap at tibco.com> a
?crit :
> 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 <lgautier at
gmail.com> 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
	[[alternative HTML version deleted]]

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 <wdunlap at tibco.com>
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 <lgautier at
gmail.com> 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
	[[alternative HTML version deleted]]

In case a search engine leads someone with the same issue here, I am
documenting the point I reached:

I can reproduce the issue with a small example when forcing R to not load
any package at startup time (using an Renviron file):
```
package <- "utils"
lib.loc <- "<fill this according to your R install>"
ns <- loadNamespace(package, lib.loc)
```

The code path goes through `registerS3methods(nsInfo$S3methods, package,
env)` and there to:

```
if (methods::is(genfun, "genericFunction"))
```

The evaluation of `methods::is` reaches the line triggering the error as
`.identC(class1, class2)` and `.identC(class2, "ANY")` both return
`NA` and
`NA || NA` is not defined:

```
> if (NA || NA) { cat("here\n") }
Error in if (NA || NA) { : missing value where TRUE/FALSE needed
```

As I understand it `.identC()` should never return `NA`, and if the case
this would mean that R itself is an unstable state (something at the C
level that should not have happened has happened) but this was not caught
earlier.

	[[alternative HTML version deleted]]

>>>>> Laurent Gautier writes:
> In case a search engine leads someone with the same issue here, I am
> documenting the point I reached:
> I can reproduce the issue with a small example when forcing R to not load
> any package at startup time (using an Renviron file):
> ```
> package <- "utils"
> lib.loc <- "<fill this according to your R install>"
> ns <- loadNamespace(package, lib.loc)
> ```
I cannot reproduce this using current R-devel or R-patched.  After
starting with R_DEFAULT_PACKAGES=NULL,

R> search()
[1] ".GlobalEnv"   "Autoloads"    "package:base"
R> loadedNamespaces()
[1] "compiler" "tools"    "base"    
R> package <- "utils"
R> lib.loc <- file.path(R.home(), "library")
R> ns <- loadNamespace(package, lib.loc)
R> loadedNamespaces()
[1] "compiler" "tools"    "utils"   
"base"

-k
> The code path goes through `registerS3methods(nsInfo$S3methods, package,
> env)` and there to:
> ```
> if (methods::is(genfun, "genericFunction"))
> ```
> The evaluation of `methods::is` reaches the line triggering the error as
> `.identC(class1, class2)` and `.identC(class2, "ANY")` both
return `NA` and
> `NA || NA` is not defined:
> ```
>> if (NA || NA) { cat("here\n") }
> Error in if (NA || NA) { : missing value where TRUE/FALSE needed
> ```
> As I understand it `.identC()` should never return `NA`, and if the case
> this would mean that R itself is an unstable state (something at the C
> level that should not have happened has happened) but this was not caught
> earlier.
> 	[[alternative HTML version deleted]]
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> Laurent Gautier 
>>>>>     on Sun, 15 Sep 2019 15:01:09 -0400 writes:
    > In case a search engine leads someone with the same issue
    > here, I am documenting the point I reached:

    > I can reproduce the issue with a small example when
    > forcing R to not load any package at startup time (using
    > an Renviron file): ``` package <- "utils" lib.loc <-
    > "<fill this according to your R install>" ns <-
    > loadNamespace(package, lib.loc) ```

    > The code path goes through
    > `registerS3methods(nsInfo$S3methods, package, env)` and
    > there to:

    > ``` if (methods::is(genfun, "genericFunction")) ```

    > The evaluation of `methods::is` reaches the line
    > triggering the error as `.identC(class1, class2)` and
    > `.identC(class2, "ANY")` both return `NA` and `NA || NA`
    > is not defined:

    > ```
    >> if (NA || NA) { cat("here\n") }
    > Error in if (NA || NA) { : missing value where TRUE/FALSE
    > needed ```

    > As I understand it `.identC()` should never return `NA`,

that understanding is correct, it should return TRUE or FALSE,
nothing else.

    > and if the case this would mean that R itself is an
    > unstable state (something at the C level that should not
    > have happened has happened) but this was not caught
    > earlier.

yes.. something like that...
My current diagnosis would be that something in your embedding of R happened
in a way that "broke R entirely" ...
but note that I know almost nothing about embedding R.

Martin