[R-pkg-devel] Fwd: Re: [CRAN-pretest-archived] CRAN submission SSLR 0.9.0
ip@iom@res m@iii@g oii correo@ugr@es
ip@iom@res m@iii@g oii correo@ugr@es
Wed Mar 11 15:39:39 CET 2020
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 using 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, ligges using 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
>> <fpalomares using 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: SSLR_0.9.0.tar.gz
Type: application/x-gzip
Size: 286448 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20200311/211233bb/attachment.bin>
More information about the R-package-devel
mailing list