* using log directory 'd:/RCompile/CRANincoming/R-devel/scR.Rcheck' * using R Under development (unstable) (2024-11-24 r87369 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'scR/DESCRIPTION' ... OK * this is package 'scR' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Perry Carter ' New submission Non-FOSS package license (`use_mit_license()`) Possibly misspelled words in DESCRIPTION: VCD (2:17) scR (10:18) Package has a VignetteBuilder field but no prebuilt vignette index. Size of tarball: 60910967 bytes * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scR' can be installed ... WARNING Found the following significant warnings: Note: possible error in 'layout(yaxis = list(title = ""), ': unused arguments (yaxis = list(title = ""), legend = list(orientation = "")) See 'd:/RCompile/CRANincoming/R-devel/scR.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'. * checking installed package size ... INFO installed size is 77.3Mb sub-directories of 1Mb or more: data 77.2Mb * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_mit_license()` Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE acc_sim: no visible binding for global variable 'nsample' acc_sim: no visible binding for global variable 'dat' acc_sim: no visible global function definition for 'rbinom' acc_sim: no visible binding for global variable 'eta' acc_sim: no visible binding for global variable 'outcome' acc_sim: no visible global function definition for '%>%' acc_sim: no visible global function definition for 'select' acc_sim: no visible global function definition for 'all_of' acc_sim: no visible global function definition for 'model' acc_sim: no visible global function definition for 'predict' acc_sim: no visible global function definition for 'precision' acc_sim: no visible global function definition for 'recall' acc_sim: no visible global function definition for 'F_meas' acc_sim: no visible binding for global variable 'power' acc_sim: no visible binding for global variable 'powersims' acc_sim: no visible binding for global variable 'effect_size' acc_sim: no visible global function definition for 'rnorm' acc_sim: no visible global function definition for 'lm' acc_sim: no visible binding for global variable 'alpha' estimate_accuracy: no visible global function definition for 'model.frame' estimate_accuracy: no visible global function definition for 'detectCores' estimate_accuracy: no visible global function definition for 'makeCluster' estimate_accuracy: no visible global function definition for 'clusterExport' estimate_accuracy: no visible global function definition for 'clusterEvalQ' estimate_accuracy: no visible global function definition for 'pblapply' estimate_accuracy: no visible global function definition for 'stopCluster' estimate_accuracy: no visible global function definition for 'bind_rows' estimate_accuracy: no visible global function definition for '%>%' estimate_accuracy: no visible global function definition for 'group_by' estimate_accuracy: no visible binding for global variable 'n' estimate_accuracy: no visible global function definition for 'summarise' estimate_accuracy: no visible binding for global variable 'accuracy' estimate_accuracy: no visible binding for global variable 'prec' estimate_accuracy: no visible binding for global variable 'rec' estimate_accuracy: no visible binding for global variable 'fscore' estimate_accuracy: no visible global function definition for 'quantile' estimate_accuracy: no visible binding for global variable 'pwr' gendata: no visible global function definition for 'runif' gendata: no visible global function definition for 'predict' getpac: no visible global function definition for '%>%' getpac: no visible global function definition for 'group_by' getpac: no visible binding for global variable 'n' getpac: no visible global function definition for 'summarise' getpac: no visible binding for global variable 'accuracy' getpac: no visible binding for global variable 'prec' getpac: no visible binding for global variable 'rec' getpac: no visible binding for global variable 'fscore' getpac: no visible global function definition for 'quantile' getpac: no visible binding for global variable 'pwr' plot_accuracy: no visible global function definition for '%>%' plot_accuracy: no visible global function definition for 'select' plot_accuracy: no visible binding for global variable 'n' plot_accuracy: no visible global function definition for 'all_of' plot_accuracy: no visible global function definition for 'pivot_longer' plot_accuracy: no visible binding for global variable 'Accuracy' plot_accuracy: no visible binding for global variable 'Power' plot_accuracy: no visible global function definition for 'ggplot' plot_accuracy: no visible binding for global variable '.' plot_accuracy: no visible global function definition for 'aes' plot_accuracy: no visible binding for global variable 'Value' plot_accuracy: no visible binding for global variable 'Metric' plot_accuracy: no visible global function definition for 'geom_line' plot_accuracy: no visible global function definition for 'plot_ly' plot_accuracy: no visible global function definition for 'layout' risk_bounds: no visible binding for global variable 'm' risk_bounds: no visible binding for global variable 'l' risk_bounds: no visible global function definition for 'rnorm' risk_bounds: no visible global function definition for 'bind_rows' risk_bounds: no visible global function definition for 'model' risk_bounds: no visible global function definition for 'predict' simvcd: no visible global function definition for 'detectCores' simvcd: no visible global function definition for 'makeCluster' simvcd: no visible global function definition for 'clusterExport' simvcd: no visible global function definition for 'clusterEvalQ' simvcd: no visible global function definition for 'pbsapply' simvcd: no visible global function definition for 'res2stopCluster' simvcd: no visible global function definition for 'optim' Undefined global functions or variables: %>% . Accuracy F_meas Metric Power Value accuracy aes all_of alpha bind_rows clusterEvalQ clusterExport dat detectCores effect_size eta fscore geom_line ggplot group_by l layout lm m makeCluster model model.frame n nsample optim outcome pblapply pbsapply pivot_longer plot_ly power powersims prec precision predict pwr quantile rbinom rec recall res2stopCluster rnorm runif select stopCluster summarise Consider adding importFrom("graphics", "layout") importFrom("stats", "lm", "model.frame", "optim", "power", "predict", "quantile", "rbinom", "rnorm", "runif") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'estimate_accuracy.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] results <- estimate_accuracy(two_year_recid ~ race + sex + age + juv_fel_count + juv_misd_count + priors_count + charge_degree..misd.fe ... [TRUNCATED] Rd file 'gendata.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] formula <- two_year_recid ~ race + sex + age + juv_fel_count + juv_misd_count + priors_count + charge_degree..misd.fel.,mylogit Rd file 'getpac.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] results <- estimate_accuracy(two_year_recid ~ race + sex + age + juv_fel_count + juv_misd_count + priors_count + charge_degree..misd.fe ... [TRUNCATED] Rd file 'plot_accuracy.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] results <- estimate_accuracy(two_year_recid ~ race + sex + age + juv_fel_count + juv_misd_count + priors_count + charge_degree..misd.fe ... [TRUNCATED] Rd file 'risk_bounds.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] Rd file 'scb.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] scb(epsilon=0.05,delta=0.05,eta=0.05,theor=F,model=mylogit,dim=7,m=100,k=100,maxn=500,predictfn = mypred) Rd file 'simvcd.Rd': \examples lines wider than 100 characters: out <- factor(ifelse(out>0.5,1,0),levels=c("0","1")) #Important - must specify levels to account for possibility of all observations be ... [TRUNCATED] vcd <- simvcd(model=mylogit,dim=7,m=100,k=100,maxn=500,predictfn = mypred) #Takes about 20 minutes to run on mid-range test machine (In ... [TRUNCATED] These lines will be truncated in the PDF manual. * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plot_accuracy.Rd: ggplot2, plotly Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented data sets: 'br' 'data' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'simvcd.Rd' 'maxn' 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. * checking Rd contents ... OK * checking for unstated dependencies in examples ... ERROR Warning: parse error in file 'lines': 120: unexpected ',' 63: } 64: formula <- two_year_recid ~ race + sex + age + juv_fel_count + juv_misd_count + priors_count + charge_degree..misd.fel., ^ ** will not attempt to run examples * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [30s] OK * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress brdat.RData 90Kb 39Kb xz poly.RData 77.1Mb 2.7Mb xz * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'DTMs_en.rdata' 'app1_1.png' 'app1_2.jpeg' 'app1_3.jpeg' 'app2_1.jpeg' 'app2_2.jpeg' 'app2_3.jpeg' 'congress_rollcalls.csv' 'distributions.Rmd' 'dw-nominate.Rmd' 'isis_tweets.Rmd' 'recidivism.Rmd' 'response_en.rdata' 'training_set_en.rdata' * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... WARNING Directory 'inst/doc' does not exist. Package vignettes without corresponding single PDF/HTML: 'distributions.Rmd' 'dw-nominate.Rmd' 'isis_tweets.Rmd' 'recidivism.Rmd' * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'distributions.Rmd' using rmarkdown Quitting from lines 50-56 [unnamed-chunk-4] (distributions.Rmd) Error: processing vignette 'distributions.Rmd' failed with diagnostics: 'br' is not an exported object from 'namespace:scR' --- failed re-building 'distributions.Rmd' --- re-building 'dw-nominate.Rmd' using rmarkdown Quitting from lines 35-37 [unnamed-chunk-3] (dw-nominate.Rmd) Error: processing vignette 'dw-nominate.Rmd' failed with diagnostics: 96 simultaneous processes spawned --- failed re-building 'dw-nominate.Rmd' --- re-building 'isis_tweets.Rmd' using rmarkdown Quitting from lines 18-27 [unnamed-chunk-2] (isis_tweets.Rmd) Error: processing vignette 'isis_tweets.Rmd' failed with diagnostics: there is no package called 'glmnet' --- failed re-building 'isis_tweets.Rmd' --- re-building 'recidivism.Rmd' using rmarkdown Quitting from lines 38-41 [unnamed-chunk-3] (recidivism.Rmd) Error: processing vignette 'recidivism.Rmd' failed with diagnostics: there is no package called 'randomForest' --- failed re-building 'recidivism.Rmd' SUMMARY: processing the following files failed: 'distributions.Rmd' 'dw-nominate.Rmd' 'isis_tweets.Rmd' 'recidivism.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [22s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 7 WARNINGs, 5 NOTEs