R devel - Jun 2019 - [External] Suggested Patch: Library returns matching installed packages when typo present

Dear R-core devs,

I hope this email finds you well.

Please see the proposed patch to R-devel below:

Scenario:

When loading a package using `library`, a package may not be found if the cases
are not matching:

```
> library(ORG.Hs.eg.db)
 Error in library(ORG.Hs.eg.db) :
  there is no package called 'ORG.Hs.eg.db'
```


Suggested Patch:

Returns a message matching what `install.packages` returns in such situations:

```
> library("ORG.Hs.eg.db")
 Error in library("ORG.Hs.eg.db") :
   there is no package called 'ORG.Hs.eg.db'
 In addition: Warning message:
 Perhaps you meant 'org.Hs.eg.db' ?
```

This patch will be helpful with 'fat-finger' typos. It will match a
package
called with `library` against installed packages.


svn diff:

Index: src/library/base/R/library.R
==================================================================---
src/library/base/R/library.R    (revision 76727)
+++ src/library/base/R/library.R    (working copy)
@@ -300,8 +300,13 @@
         pkgpath <- find.package(package, lib.loc, quiet = TRUE,
                                     verbose = verbose)
             if(length(pkgpath) == 0L) {
-                if(length(lib.loc) && !logical.return)
+                if(length(lib.loc) && !logical.return) {
+                    allpkgs <- .packages(TRUE, lib.loc)
+                    if (!is.na(w <- match(tolower(package),
tolower(allpkgs))))
+                        warning(sprintf("Perhaps you meant %s ?",
+                            sQuote(allpkgs[w])), call. = FALSE, domain = NA)
                     stop(packageNotFoundError(package, lib.loc, sys.call()))
+                }
                 txt <- if(length(lib.loc))
                     gettextf("there is no package called %s",
sQuote(package))
                 else


Thank you!

Best regards,

Marcel



--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
	[[alternative HTML version deleted]]

Thanks for the suggestion. However I don't think it is the right way
to go. I also don't care for what install.packages() does. Signaling a
warning and then an error means someone has to catch both the error
and the warning, or suppress the warning, in order to handle the error
programmatically.

Now that library() signals a structured error there are other options.
One possibility, at least as an interim, is to define a
conditionMessage method, e.g. as

conditionMessage.packageNotFoundError <- function(c) {
     lib.loc <- c$lib.loc
     msg <- c$message
     package <- c$package
     if(length(lib.loc)) {
         allpkgs <- .packages(TRUE, lib.loc)
         if (!is.na(w <- match(tolower(package), tolower(allpkgs)))) {
             msg2 <- sprintf("Perhaps you meant %s ?",
sQuote(allpkgs[w]))
             return(paste(msg, msg2, sep = "\n"))
         }
     }
     msg
}

This is something you can do yourself, though it is generally not a
good idea to define a method when you don't own either the generic or
the class.

Something that would be useful and is being considered is having a
mechanism for registering default condition handlers. This would allow
the condition to be re-signaled with a custom class and then having
a custom conditionMessage method is less likely to cause conflicts.

Also worth looking into is establishing a restart around the error
signal.  This would allow an IDE, for example, to provide a dialog for
choosing the alternate package and retrying without the need to call
library() again. This is currently done in loadNamespace() but not yet
in library(). Can have downsides as well -- if the library() call is
in a notebook, for example, then you do want to fix the call ...  It
is arguably more useful in loadNamespace since that can get called
implicitly inside a longer computation that you don't necessarily want
to start over.

Best,

luke

On Fri, 21 Jun 2019, Marcel Ramos wrote:
> Dear R-core devs,
>
> I hope this email finds you well.
>
> Please see the proposed patch to R-devel below:
>
> Scenario:
>
> When loading a package using `library`, a package may not be found if the
cases are not matching:
>
> ```
>> library(ORG.Hs.eg.db)
> Error in library(ORG.Hs.eg.db) :
>  there is no package called 'ORG.Hs.eg.db'
> ```
>
>
> Suggested Patch:
>
> Returns a message matching what `install.packages` returns in such
situations:
>
> ```
>> library("ORG.Hs.eg.db")
> Error in library("ORG.Hs.eg.db") :
>   there is no package called 'ORG.Hs.eg.db'
> In addition: Warning message:
> Perhaps you meant 'org.Hs.eg.db' ?
> ```
>
> This patch will be helpful with 'fat-finger' typos. It will match a
package
> called with `library` against installed packages.
>
>
> svn diff:
>
> Index: src/library/base/R/library.R
> ==================================================================> ---
src/library/base/R/library.R    (revision 76727)
> +++ src/library/base/R/library.R    (working copy)
> @@ -300,8 +300,13 @@
>         pkgpath <- find.package(package, lib.loc, quiet = TRUE,
>                                     verbose = verbose)
>             if(length(pkgpath) == 0L) {
> -                if(length(lib.loc) && !logical.return)
> +                if(length(lib.loc) && !logical.return) {
> +                    allpkgs <- .packages(TRUE, lib.loc)
> +                    if (!is.na(w <- match(tolower(package),
tolower(allpkgs))))
> +                        warning(sprintf("Perhaps you meant %s
?",
> +                            sQuote(allpkgs[w])), call. = FALSE, domain =
NA)
>                     stop(packageNotFoundError(package, lib.loc,
sys.call()))
> +                }
>                 txt <- if(length(lib.loc))
>                     gettextf("there is no package called %s",
sQuote(package))
>                 else
>
>
> Thank you!
>
> Best regards,
>
> Marcel
>
>
>
> --
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Care Center
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at 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-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

Hi Luke,

Thank you for your response.

On 6/21/19 10:56 AM, Tierney, Luke wrote:

Thanks for the suggestion. However I don't think it is the right way
to go. I also don't care for what install.packages() does. Signaling a
warning and then an error means someone has to catch both the error
and the warning, or suppress the warning, in order to handle the error
programmatically.

I do care for what install.packages() does because it's preferable
to have consistency in the user interface.

I see that the proposed patch does return both an error and a warning
but as far as I understand it, library()'s main/intended use is interactive
and
there are other functions available for programmatic use cases.



Now that library() signals a structured error there are other options.
One possibility, at least as an interim, is to define a
conditionMessage method, e.g. as

conditionMessage.packageNotFoundError <- function(c) {
     lib.loc <- c$lib.loc
     msg <- c$message
     package <- c$package
     if(length(lib.loc)) {
         allpkgs <- .packages(TRUE, lib.loc)
         if (!is.na(w <- match(tolower(package), tolower(allpkgs)))) {
             msg2 <- sprintf("Perhaps you meant %s ?",
sQuote(allpkgs[w]))
             return(paste(msg, msg2, sep = "\n"))
         }
     }
     msg
}

This is something you can do yourself, though it is generally not a
good idea to define a method when you don't own either the generic or
the class.

Something that would be useful and is being considered is having a
mechanism for registering default condition handlers. This would allow
the condition to be re-signaled with a custom class and then having
a custom conditionMessage method is less likely to cause conflicts.

I'd argue that this is quite useful especially for new users and that
creating
condition handlers may involve more than what is needed for interactive use.


Best,

Marcel



Also worth looking into is establishing a restart around the error
signal.  This would allow an IDE, for example, to provide a dialog for
choosing the alternate package and retrying without the need to call
library() again. This is currently done in loadNamespace() but not yet
in library(). Can have downsides as well -- if the library() call is
in a notebook, for example, then you do want to fix the call ...  It
is arguably more useful in loadNamespace since that can get called
implicitly inside a longer computation that you don't necessarily want
to start over.

Best,

luke

On Fri, 21 Jun 2019, Marcel Ramos wrote:



Dear R-core devs,

I hope this email finds you well.

Please see the proposed patch to R-devel below:

Scenario:

When loading a package using `library`, a package may not be found if the cases
are not matching:

```


library(ORG.Hs.eg.db)


Error in library(ORG.Hs.eg.db) :
 there is no package called 'ORG.Hs.eg.db'
```


Suggested Patch:

Returns a message matching what `install.packages` returns in such situations:

```


library("ORG.Hs.eg.db")


Error in library("ORG.Hs.eg.db") :
  there is no package called 'ORG.Hs.eg.db'
In addition: Warning message:
Perhaps you meant 'org.Hs.eg.db' ?
```

This patch will be helpful with 'fat-finger' typos. It will match a
package
called with `library` against installed packages.


svn diff:

Index: src/library/base/R/library.R
==================================================================---
src/library/base/R/library.R    (revision 76727)
+++ src/library/base/R/library.R    (working copy)
@@ -300,8 +300,13 @@
        pkgpath <- find.package(package, lib.loc, quiet = TRUE,
                                    verbose = verbose)
            if(length(pkgpath) == 0L) {
-                if(length(lib.loc) && !logical.return)
+                if(length(lib.loc) && !logical.return) {
+                    allpkgs <- .packages(TRUE, lib.loc)
+                    if (!is.na(w <- match(tolower(package),
tolower(allpkgs))))
+                        warning(sprintf("Perhaps you meant %s ?",
+                            sQuote(allpkgs[w])), call. = FALSE, domain = NA)
                    stop(packageNotFoundError(package, lib.loc, sys.call()))
+                }
                txt <- if(length(lib.loc))
                    gettextf("there is no package called %s",
sQuote(package))
                else


Thank you!

Best regards,

Marcel



--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
        [[alternative HTML version deleted]]

______________________________________________
R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel







This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited.  If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
	[[alternative HTML version deleted]]