[R-pkg-devel] Fwd: Re: [CRAN-pretest-archived] CRAN submission SSLR 0.9.0
'fpalomares', it's not clear if you can reproduce this locally or not, but make sure you can reproduce it locally. I could using: R CMD check --as-cran SSLR_0.9.0.tar.gz with R 3.6.3 on Ubuntu 18.04. In other words, this is neither a problem with the CRAN incoming checks nor win-builder. Yes, I agree, at a first glance, this looks odd because:
library(SSLR) fit
function (object, ...)
{
UseMethod("fit")
}
<environment: namespace:SSLR>
methods("fit")
[1] fit,onlearn-method fit.model_sslr
see '?methods' for accessing help and source code
Neither
$ Rscript -e 'example("COREG", package = "SSLR")'
nor
example("COREG", package = "SSLR")
in an interactive session produce the error.
For troubleshooting, I'd added a:
print(methods("fit"))
before
m <- COREG(max.iter = 2) %>% fit(class ~ ., data = train)
I'd also try rewriting that without %>%, e.g. something like
a <- COREG(max.iter = 2)
b <- fit(class ~ a, data = train)
to see if that makes a difference.
My $.02
/Henrik
On Wed, Mar 11, 2020 at 8:13 AM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
Uwe Ligges answered you yesterday on this question. Duncan Murdoch On 11/03/2020 7:39 a.m., fpalomares at correo.ugr.es wrote:
Hi, I dont know how to fix this problem: https://win-builder.r-project.org/VK8P07E1QHFA/ The error is: Error in UseMethod("fit") : no applicable method for 'fit' applied to an object of class "model_sslr" I check with my platform Windows 10 Home and I dont have problems The code used is: #' fit #' @title fit object #' @param object object #' @param ... other parameters to be passed #' @export fit <- function(object, ...){ UseMethod("fit") } #' @title Fit with formula and data #' @description Funtion to fit through the formula #' @param object is the model #' @param formula is the formula #' @param data is the total data train #' @param ... unused in this case #' @importFrom rlang quos #' @export fit.model_sslr #' @export fit.model_sslr <- function(object, formula = NULL, data = NULL, ...) { dots <- quos(...) if (all(c("x", "y") %in% names(dots))) rlang::abort("`fit.model_sslr()` is for the formula methods. Use `fit_xy()` instead.") fit_form_interface <- check_form_interface(formula, data) x_and_y <- get_x_y(formula, data) eval_env <- rlang::env() eval_env$x <- x_and_y$x eval_env$y <- x_and_y$y fit_interface <- check_xy_interface(eval_env$x, eval_env$y) elapsed <- system.time(model <- object$fit_function(eval_env$x, eval_env$y)) new_model_sslr_fitted(model,class(model),object$args,colnames(eval_env$x),elapsed,formula) } In my NAMESPACE we have this: # Generated by roxygen2: do not edit by hand S3method(fit,model_sslr) S3method(fit_x_u,model_sslr) S3method(fit_xy,model_sslr) S3method(predict,OneNN) S3method(predict,model_sslr_fitted) S3method(predict,snnrceG) export(COREG) export(EMLeastSquaresClassifierSSLR) export(EMNearestMeanClassifierSSLR) export(EntropyRegularizedLogisticRegressionSSLR) export(LaplacianSVMSSLR) export(LinearTSVMSSLR) export(MCNearestMeanClassifierSSLR) export(SSLRDecisionTree) export(SSLRRandomForest) export(TSVMSSLR) export(USMLeastSquaresClassifierSSLR) export(WellSVMSSLR) export(coBC) export(coBCCombine) export(coBCG) export(democratic) export(democraticCombine) export(democraticG) export(fit) export(fit.model_sslr) export(fit_x_u) export(fit_x_u.model_sslr) export(fit_xy) export(fit_xy.model_sslr) export(newDecisionTree) export(oneNN) export(selfTraining) export(selfTrainingG) export(setred) export(setredG) export(snnrce) export(train_generic) export(triTraining) export(triTrainingCombine) export(triTrainingG) exportClasses(nullOrNumericOrCharacter) exportMethods(predict) exportMethods(predict_inputs) import(stats) importFrom(RANN,nn2) importFrom(RSSL,EMLeastSquaresClassifier) importFrom(RSSL,EMNearestMeanClassifier) importFrom(RSSL,EntropyRegularizedLogisticRegression) importFrom(RSSL,LaplacianSVM) importFrom(RSSL,LinearTSVM) importFrom(RSSL,MCNearestMeanClassifier) importFrom(RSSL,TSVM) importFrom(RSSL,USMLeastSquaresClassifier) importFrom(RSSL,WellSVM) importFrom(dplyr,as_tibble) importFrom(dplyr,tibble) importFrom(foreach,"%dopar%") importFrom(magrittr,"%>%") importFrom(methods,new) importFrom(parsnip,nearest_neighbor) importFrom(parsnip,set_engine) importFrom(plyr,is.formula) importFrom(purrr,map) importFrom(rlang,quos) importFrom(stats,predict) importFrom(utils,tail) useDynLib(SSLR) We have: S3method(fit,model_sslr) ... export(fit) export(fit.model_sslr) I don't know why the problem appears when everything is exported. I attach the built .tar Thanks. El 2020-03-10 17:28, fpalomares at correo.ugr.es escribi?:
Hi, I thiks its weird:
The error is: no applicable method for 'fit' applied to an object of
class "model_sslr"
In the code:
#' fit
#'
#' @title fit object
#' @param object object
#' @param ... other parameters to be passed
#' @rdname fit
#' @export fit
fit <- function(object, ...){
UseMethod("fit")
}
And:
#' @title Fit with formula and data
#' @description Funtion to fit through the formula
#' @param object is the model
#' @param formula is the formula
#' @param data is the total data train
#' @param ... unused in this case
#' @importFrom rlang quos
#' @rdname fit
#' @export
#' @export fit.model_sslr
fit.model_sslr <- function(object, formula = NULL, data = NULL, ...) {
dots <- quos(...)
if (all(c("x", "y") %in% names(dots)))
rlang::abort("`fit.model_sslr()` is for the formula methods. Use
`fit_xy()` instead.")
fit_form_interface <- check_form_interface(formula, data)
x_and_y <- get_x_y(formula, data)
eval_env <- rlang::env()
eval_env$x <- x_and_y$x
eval_env$y <- x_and_y$y
fit_interface <- check_xy_interface(eval_env$x, eval_env$y)
elapsed <- system.time(model <- object$fit_function(eval_env$x,
eval_env$y))
new_model_sslr_fitted(model,class(model),object$args,colnames(eval_env$x),elapsed,formula)
}
Thanks
El 2020-03-10 16:19, ligges at statistik.tu-dortmund.de escribi?:
Dear maintainer, package SSLR_0.9.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows: <https://win-builder.r-project.org/incoming_pretest/SSLR_0.9.0_20200310_160158/Windows/00check.log> Status: 2 ERRORs, 1 WARNING, 1 NOTE Debian: <https://win-builder.r-project.org/incoming_pretest/SSLR_0.9.0_20200310_160158/Debian/00check.log> Status: 1 ERROR, 1 WARNING, 1 NOTE Please fix all problems and resubmit a fixed version via the webform. If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list: <https://stat.ethz.ch/mailman/listinfo/r-package-devel> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain. More details are given in the directory: <https://win-builder.r-project.org/incoming_pretest/SSLR_0.9.0_20200310_160158/> The files will be removed after roughly 7 days. No strong reverse dependencies to be checked. Best regards, CRAN teams' auto-check service Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility, Result: NOTE Maintainer: 'Francisco Jes??s Palomares Alabarce <fpalomares at correo.ugr.es>' New submission Possibly mis-spelled words in DESCRIPTION: SSLR (23:14) VM (27:37) Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/RSSL/RSSL.pdf From: inst/doc/introduction.html inst/doc/models.html Status: 200 Message: OK CRAN URL not in canonical form The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname Found the following (possibly) invalid file URI: URI: www.cs.ucr.edu/~eamonn/time_series_data/ From: man/coffee.Rd The Description field should not start with the package name, 'This package' or similar. Flavor: r-devel-windows-ix86+x86_64 Check: running examples for arch 'i386', Result: ERROR Running examples in 'SSLR-Ex.R' failed The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: COREG
> ### Title: General Interface for COREG model
> ### Aliases: COREG
>
> ### ** Examples
>
> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.3.0 -- v ggplot2 3.3.0 v purrr 0.3.3 v tibble 2.1.3 v dplyr 0.8.5 v tidyr 1.0.2 v stringr 1.4.0 v readr 1.3.1 v forcats 0.5.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag()
> library(tidymodels)
-- Attaching packages -------------------------------------- tidymodels 0.1.0 -- v broom 0.5.5 v rsample 0.0.5 v dials 0.0.4 v tune 0.0.1 v infer 0.5.1 v workflows 0.1.0 v parsnip 0.0.5 v yardstick 0.0.5 v recipes 0.1.9 -- Conflicts ----------------------------------------- tidymodels_conflicts() -- x scales::discard() masks purrr::discard() x dplyr::filter() masks stats::filter() x recipes::fixed() masks stringr::fixed() x dplyr::lag() masks stats::lag() x dials::margin() masks ggplot2::margin() x yardstick::spec() masks readr::spec() x recipes::step() masks stats::step() x recipes::yj_trans() masks scales::yj_trans()
> library(SSLR) > > data <- na.omit(airquality) > #data <- na.omit(airquality) > > cls <- which(colnames(data) == "Ozone") > > colnames(data)[cls]<- "class" > > set.seed(1) > train.index <- sample(nrow(data), round(0.7 * nrow(data))) > train <- data[ train.index,] > test <- data[-train.index,] > > > #% LABELED > labeled.index <- sample(nrow(train), round(0.2 * nrow(train))) > train[-labeled.index,cls] <- NA > > m <- COREG(max.iter = 2) %>% fit(class ~ ., data = train)
Error in UseMethod("fit") :
no applicable method for 'fit' applied to an object of class
"model_sslr"
Calls: %>% ... _fseq -> freduce -> withVisible -> <Anonymous> -> fit
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'x64', Result: ERROR
Running examples in 'SSLR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: COREG
> ### Title: General Interface for COREG model
> ### Aliases: COREG
>
> ### ** Examples
>
> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.3.0 -- v ggplot2 3.3.0 v purrr 0.3.3 v tibble 2.1.3 v dplyr 0.8.5 v tidyr 1.0.2 v stringr 1.4.0 v readr 1.3.1 v forcats 0.5.0 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag()
> library(tidymodels)
-- Attaching packages -------------------------------------- tidymodels 0.1.0 -- v broom 0.5.5 v rsample 0.0.5 v dials 0.0.4 v tune 0.0.1 v infer 0.5.1 v workflows 0.1.0 v parsnip 0.0.5 v yardstick 0.0.5 v recipes 0.1.9 -- Conflicts ----------------------------------------- tidymodels_conflicts() -- x scales::discard() masks purrr::discard() x dplyr::filter() masks stats::filter() x recipes::fixed() masks stringr::fixed() x dplyr::lag() masks stats::lag() x dials::margin() masks ggplot2::margin() x yardstick::spec() masks readr::spec() x recipes::step() masks stats::step() x recipes::yj_trans() masks scales::yj_trans()
> library(SSLR) > > data <- na.omit(airquality) > #data <- na.omit(airquality) > > cls <- which(colnames(data) == "Ozone") > > colnames(data)[cls]<- "class" > > set.seed(1) > train.index <- sample(nrow(data), round(0.7 * nrow(data))) > train <- data[ train.index,] > test <- data[-train.index,] > > > #% LABELED > labeled.index <- sample(nrow(train), round(0.2 * nrow(train))) > train[-labeled.index,cls] <- NA > > m <- COREG(max.iter = 2) %>% fit(class ~ ., data = train)
Error in UseMethod("fit") :
no applicable method for 'fit' applied to an object of class
"model_sslr"
Calls: %>% ... _fseq -> freduce -> withVisible -> <Anonymous> -> fit
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'classification.Rmd' using rmarkdown
Quitting from lines 58-60 (classification.Rmd)
Error: processing vignette 'classification.Rmd' failed with
diagnostics:
no applicable method for 'fit' applied to an object of class
"model_sslr"
--- failed re-building 'classification.Rmd'
--- re-building 'fit.Rmd' using rmarkdown
--- finished re-building 'fit.Rmd'
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'
--- re-building 'models.Rmd' using rmarkdown
--- finished re-building 'models.Rmd'
--- re-building 'regression.Rmd' using rmarkdown
Quitting from lines 51-53 (regression.Rmd)
Error: processing vignette 'regression.Rmd' failed with diagnostics:
no applicable method for 'fit' applied to an object of class
"model_sslr"
--- failed re-building 'regression.Rmd'
SUMMARY: processing the following files failed:
'classification.Rmd' 'regression.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: ERROR
Running examples in 'SSLR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: COREG
> ### Title: General Interface for COREG model
> ### Aliases: COREG
>
> ### ** Examples
>
> library(tidyverse)
?????? Attaching packages ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidyverse 1.3.0 ?????? ??? ggplot2 3.3.0 ??? purrr 0.3.3 ??? tibble 2.1.3 ??? dplyr 0.8.5 ??? tidyr 1.0.2 ??? stringr 1.4.0 ??? readr 1.3.1 ??? forcats 0.5.0 ?????? Conflicts ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidyverse_conflicts() ?????? ??? dplyr::filter() masks stats::filter() ??? dplyr::lag() masks stats::lag()
> library(tidymodels)
?????? Attaching packages ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidymodels 0.1.0 ?????? ??? broom 0.5.5 ??? rsample 0.0.5 ??? dials 0.0.4 ??? tune 0.0.1 ??? infer 0.5.1 ??? workflows 0.1.0 ??? parsnip 0.0.5 ??? yardstick 0.0.5 ??? recipes 0.1.9 ?????? Conflicts ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? tidymodels_conflicts() ?????? ??? scales::discard() masks purrr::discard() ??? dplyr::filter() masks stats::filter() ??? recipes::fixed() masks stringr::fixed() ??? dplyr::lag() masks stats::lag() ??? dials::margin() masks ggplot2::margin() ??? yardstick::spec() masks readr::spec() ??? recipes::step() masks stats::step() ??? recipes::yj_trans() masks scales::yj_trans()
> library(SSLR) > > data <- na.omit(airquality) > #data <- na.omit(airquality) > > cls <- which(colnames(data) == "Ozone") > > colnames(data)[cls]<- "class" > > set.seed(1) > train.index <- sample(nrow(data), round(0.7 * nrow(data))) > train <- data[ train.index,] > test <- data[-train.index,] > > > #% LABELED > labeled.index <- sample(nrow(train), round(0.2 * nrow(train))) > train[-labeled.index,cls] <- NA > > m <- COREG(max.iter = 2) %>% fit(class ~ ., data = train)
Error in UseMethod("fit") :
no applicable method for 'fit' applied to an object of class
"model_sslr"
Calls: %>% ... _fseq -> freduce -> withVisible -> <Anonymous> -> fit
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
...
--- re-building 'classification.Rmd' using rmarkdown
Quitting from lines 58-60 (classification.Rmd)
Error: processing vignette 'classification.Rmd' failed with
diagnostics:
no applicable method for 'fit' applied to an object of class
"model_sslr"
--- failed re-building 'classification.Rmd'
--- re-building 'fit.Rmd' using rmarkdown
--- finished re-building 'fit.Rmd'
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'
--- re-building 'models.Rmd' using rmarkdown
--- finished re-building 'models.Rmd'
--- re-building 'regression.Rmd' using rmarkdown
Quitting from lines 51-53 (regression.Rmd)
Error: processing vignette 'regression.Rmd' failed with diagnostics:
no applicable method for 'fit' applied to an object of class
"model_sslr"
--- failed re-building 'regression.Rmd'
SUMMARY: processing the following files failed:
'classification.Rmd' 'regression.Rmd'
Error: Vignette re-building failed.
Execution halted
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