[jira] [Commented] (SPARK-22281) Handle R method breaking signature changes
[ https://issues.apache.org/jira/browse/SPARK-22281?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16214760#comment-16214760 ] Apache Spark commented on SPARK-22281: -- User 'felixcheung' has created a pull request for this issue: https://github.com/apache/spark/pull/19557 > Handle R method breaking signature changes > -- > > Key: SPARK-22281 > URL: https://issues.apache.org/jira/browse/SPARK-22281 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.2.1, 2.3.0 >Reporter: Felix Cheung > > cAs discussed here > http://apache-spark-developers-list.1001551.n3.nabble.com/VOTE-Spark-2-1-2-RC2-tt22540.html#a22555 > this WARNING on R-devel > * checking for code/documentation mismatches ... WARNING > Codoc mismatches from documentation object 'attach': > attach > Code: function(what, pos = 2L, name = deparse(substitute(what), > backtick = FALSE), warn.conflicts = TRUE) > Docs: function(what, pos = 2L, name = deparse(substitute(what)), > warn.conflicts = TRUE) > Mismatches in argument default values: > Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: > deparse(substitute(what)) > Codoc mismatches from documentation object 'glm': > glm > Code: function(formula, family = gaussian, data, weights, subset, > na.action, start = NULL, etastart, mustart, offset, > control = list(...), model = TRUE, method = "glm.fit", > x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = > NULL, ...) > Docs: function(formula, family = gaussian, data, weights, subset, > na.action, start = NULL, etastart, mustart, offset, > control = list(...), model = TRUE, method = "glm.fit", > x = FALSE, y = TRUE, contrasts = NULL, ...) > Argument names in code not in docs: > singular.ok > Mismatches in argument names: > Position: 16 Code: singular.ok Docs: contrasts > Position: 17 Code: contrasts Docs: ... > Checked the latest release R 3.4.1 and the signature change wasn't there. > This likely indicated an upcoming change in the next R release that could > incur this new warning when we attempt to publish the package. > Not sure what we can do now since we work with multiple versions of R and > they will have different signatures then. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-22281) Handle R method breaking signature changes
[ https://issues.apache.org/jira/browse/SPARK-22281?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16214751#comment-16214751 ] Felix Cheung commented on SPARK-22281: -- ok, I have a solution for both. it turns out the fix for glm is quite a bit different from attach, so I added the error above. in short, with glm it's pulling in the function definition (ie. "usage") from the stats::glm function. Since this is "compiled in" when we build the source package into the .Rd, when/if it changes at runtime or in CRAN check it won't match the latest signature. > Handle R method breaking signature changes > -- > > Key: SPARK-22281 > URL: https://issues.apache.org/jira/browse/SPARK-22281 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.2.1, 2.3.0 >Reporter: Felix Cheung > > cAs discussed here > http://apache-spark-developers-list.1001551.n3.nabble.com/VOTE-Spark-2-1-2-RC2-tt22540.html#a22555 > this WARNING on R-devel > * checking for code/documentation mismatches ... WARNING > Codoc mismatches from documentation object 'attach': > attach > Code: function(what, pos = 2L, name = deparse(substitute(what), > backtick = FALSE), warn.conflicts = TRUE) > Docs: function(what, pos = 2L, name = deparse(substitute(what)), > warn.conflicts = TRUE) > Mismatches in argument default values: > Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: > deparse(substitute(what)) > Codoc mismatches from documentation object 'glm': > glm > Code: function(formula, family = gaussian, data, weights, subset, > na.action, start = NULL, etastart, mustart, offset, > control = list(...), model = TRUE, method = "glm.fit", > x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = > NULL, ...) > Docs: function(formula, family = gaussian, data, weights, subset, > na.action, start = NULL, etastart, mustart, offset, > control = list(...), model = TRUE, method = "glm.fit", > x = FALSE, y = TRUE, contrasts = NULL, ...) > Argument names in code not in docs: > singular.ok > Mismatches in argument names: > Position: 16 Code: singular.ok Docs: contrasts > Position: 17 Code: contrasts Docs: ... > Checked the latest release R 3.4.1 and the signature change wasn't there. > This likely indicated an upcoming change in the next R release that could > incur this new warning when we attempt to publish the package. > Not sure what we can do now since we work with multiple versions of R and > they will have different signatures then. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-22281) Handle R method breaking signature changes
[ https://issues.apache.org/jira/browse/SPARK-22281?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16214663#comment-16214663 ] Shivaram Venkataraman commented on SPARK-22281: --- Thanks for looking into this [~felixcheung] Is there anyway we can remove the `usage` entry as well from the Rdoc ? This might also be something to raise with the roxygen project for a more long term solution > Handle R method breaking signature changes > -- > > Key: SPARK-22281 > URL: https://issues.apache.org/jira/browse/SPARK-22281 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.2.1, 2.3.0 >Reporter: Felix Cheung > > cAs discussed here > http://apache-spark-developers-list.1001551.n3.nabble.com/VOTE-Spark-2-1-2-RC2-tt22540.html#a22555 > this WARNING on R-devel > * checking for code/documentation mismatches ... WARNING > Codoc mismatches from documentation object 'attach': > attach > Code: function(what, pos = 2L, name = deparse(substitute(what), > backtick = FALSE), warn.conflicts = TRUE) > Docs: function(what, pos = 2L, name = deparse(substitute(what)), > warn.conflicts = TRUE) > Mismatches in argument default values: > Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: > deparse(substitute(what)) > Checked the latest release R 3.4.1 and the signature change wasn't there. > This likely indicated an upcoming change in the next R release that could > incur this new warning when we attempt to publish the package. > Not sure what we can do now since we work with multiple versions of R and > they will have different signatures then. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-22281) Handle R method breaking signature changes
[
https://issues.apache.org/jira/browse/SPARK-22281?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16214431#comment-16214431
]
Felix Cheung commented on SPARK-22281:
--
tried a few things. If we remove the
{code}
@param
{code}
then cran checks fail with
{code}
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'attach'
‘what’ ‘pos’ ‘name’ ‘warn.conflicts’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
{code}
if we change the method signature to
{code}
setMethod("attach",
signature(what = "SparkDataFrame"),
function(what, ...) {
{code}
Then it fails to install
{code}
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
methods can add arguments to the generic ‘attach’ only if '...' is an
argument to the generic
Error : unable to load R code in package ‘SparkR’
ERROR: lazy loading failed for package ‘SparkR’
{code}
> Handle R method breaking signature changes
> --
>
> Key: SPARK-22281
> URL: https://issues.apache.org/jira/browse/SPARK-22281
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.2.1, 2.3.0
>Reporter: Felix Cheung
>
> cAs discussed here
> http://apache-spark-developers-list.1001551.n3.nabble.com/VOTE-Spark-2-1-2-RC2-tt22540.html#a22555
> this WARNING on R-devel
> * checking for code/documentation mismatches ... WARNING
> Codoc mismatches from documentation object 'attach':
> attach
> Code: function(what, pos = 2L, name = deparse(substitute(what),
> backtick = FALSE), warn.conflicts = TRUE)
> Docs: function(what, pos = 2L, name = deparse(substitute(what)),
> warn.conflicts = TRUE)
> Mismatches in argument default values:
> Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs:
> deparse(substitute(what))
> Checked the latest release R 3.4.1 and the signature change wasn't there.
> This likely indicated an upcoming change in the next R release that could
> incur this new warning when we attempt to publish the package.
> Not sure what we can do now since we work with multiple versions of R and
> they will have different signatures then.
--
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[jira] [Commented] (SPARK-22281) Handle R method breaking signature changes
[ https://issues.apache.org/jira/browse/SPARK-22281?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16205313#comment-16205313 ] Felix Cheung commented on SPARK-22281: -- And here for all r-devel WARN https://cran.r-project.org/web/checks/check_results_SparkR.html > Handle R method breaking signature changes > -- > > Key: SPARK-22281 > URL: https://issues.apache.org/jira/browse/SPARK-22281 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0, 2.21 >Reporter: Felix Cheung > > As discussed here > http://apache-spark-developers-list.1001551.n3.nabble.com/VOTE-Spark-2-1-2-RC2-tt22540.html#a22555 > this WARNING on R-devel > * checking for code/documentation mismatches ... WARNING > Codoc mismatches from documentation object 'attach': > attach > Code: function(what, pos = 2L, name = deparse(substitute(what), > backtick = FALSE), warn.conflicts = TRUE) > Docs: function(what, pos = 2L, name = deparse(substitute(what)), > warn.conflicts = TRUE) > Mismatches in argument default values: > Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: > deparse(substitute(what)) > Checked the latest release R 3.4.1 and the signature change wasn't there. > This likely indicated an upcoming change in the next R release that could > insur this new warning when we attempt to publish the package. > Not sure what we can do now since we work with multiple versions of R and > they will have different signatures then. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
