[R-pkg-devel] Fwd: Re: [CRAN-pretest-archived] CRAN submission SSLR 0.9.0
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Wed Mar 11 16:12:56 CET 2020
Uwe Ligges answered you yesterday on this question.
Duncan Murdoch
On 11/03/2020 7:39 a.m., fpalomares using 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 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
>>>
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