'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 $.02
/Henrik
On Wed, Mar 11, 2020 at 8:13 AM Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>
> Uwe Ligges answered you yesterday on this question.
>
> Duncan Murdoch
>
> On 11/03/2020 7:39 a.m., fpaloma...@correo.ugr.es wrote:
> > Hi,
> >
> > I dont know how to fix this problem:
> > https://win-builder.r-project.org/VK8P07E1QHFA/
> >
> > The error is:
> >
> > Error in UseMethod("fit") :
> > no applicable method for 'fit' applied to an object of class
> > "model_sslr"
> >
> > I check with my platform Windows 10 Home and I dont have problems
> >
> > The code used is:
> >
> > #' fit
> > #' @title fit object
> > #' @param object object
> > #' @param ... other parameters to be passed
> > #' @export
> > fit <- function(object, ...){
> > UseMethod("fit")
> > }
> >
> > #' @title Fit with formula and data
> > #' @description Funtion to fit through the formula
> > #' @param object is the model
> > #' @param formula is the formula
> > #' @param data is the total data train
> > #' @param ... unused in this case
> > #' @importFrom rlang quos
> > #' @export fit.model_sslr
> > #' @export
> > fit.model_sslr <- function(object, formula = NULL, data = NULL, ...) {
> >
> > dots <- quos(...)
> >
> >
> > if (all(c("x", "y") %in% names(dots)))
> > rlang::abort("`fit.model_sslr()` is for the formula methods. Use
> > `fit_xy()` instead.")
> >
> > fit_form_interface <- check_form_interface(formula, data)
> >
> > x_and_y <- get_x_y(formula, data)
> >
> > eval_env <- rlang::env()
> > eval_env$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, fpaloma...@correo.ugr.es escribió:
> >> 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, lig...@statistik.tu-dortmund.de escribió:
> >>> 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 Jesús Palomares Alabarce
> >>> <fpaloma...@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
> >>>
> >>> ______________________________________________
> >>> R-package-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> ______________________________________________
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
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