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

withCallingHandlers({

[...] 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. [...]

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]]

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

Is it correct that you are proposing something that allows us to do:

registerDefaultConditionHandlers(
 packageStartupMessage = function(c) {
   ## Do something with condition 'c'
   ...
   ## Suppress futher processing
   invokeRestart("muffleMessage")
 }
)

at the core, which avoids having us to wrap up calls in
withCallingHandlers() at top-level calls, e.g.

withCallingHandlers({

 library("foobar"),
}, packageStartupMessage = function(c) {
 ## Do something with condition 'c'
 ...
 ## Suppress futher processing
 invokeRestart("muffleMessage")
})

?

Then, if I read this correctly, I'd say, this would be a very useful
addition to base R.  This will provide a core framework that opens up
for several neat extensions, e.g. the one that Marcel suggests - some
people prefer a message/warning on misspelled package names, while
others might want to see if it can be automatically installed, and so
on.  And, it will (=should) be all in the hands of the end user to
control this, i.e. various packages should not override this similar
to how we don't expect them to override other personal R settings we
have.

With this in place, it's not hard to imagine a third-party package
that provides useful handlers that users can pick from, e.g.

 buttlr::i_am_a("first_time_r_user")

to get extra information for some of the common warnings and errors,
which is in the same spirit as your idea on:

[...] 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. [...]

I also think such a framework could replace some of the "legacy
handlers" we currently have in place, e.g. R options 'warn',
'warnPartialMatchArgs', '...', and even 'error', and give more
granular control over those use cases.  For instance, instead of a
warning or a partial argument match, I might want to produce an error
unless it comes from one particular package, say, which is something
that is a bit tricky to do today.

/Henrik

PS. Somewhat related to this, standardizing muffling and signaling of
conditions could be worth looking into as well.  For instance, being
able to resignal an error 'e' with a *generic* signalCondition(e)
instead of having to know that you should call stop(e) for 'error'
conditions and maybe another function if the error is of another
class.

On Fri, Jun 21, 2019 at 8:55 AM Marcel Ramos
<Marcel.Ramos at roswellpark.org> wrote:

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]]