* using log directory ‘/srv/hornik/tmp/CRAN/MicrobiomeSurv.Rcheck’ * using R Under development (unstable) (2023-09-23 r85215) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘MicrobiomeSurv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MicrobiomeSurv’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Thi Huyen Nguyen ’ New submission Possibly misspelled words in DESCRIPTION: Microbiome (4:35) SPLS (14:113) microbiome (11:38, 11:97, 12:113, 13:76, 16:128) * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... WARNING Found the following file with a non-portable file name: Rcodes test w3.R These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘MicrobiomeSurv’ can be installed ... [3s/3s] WARNING Found the following significant warnings: Note: possible error in 'try(Temp = Lasoelascox(Survival = Survival[ind.s[i, ': unused argument (Temp = Lasoelascox(Survival = Survival[ind.s[i, ]], Censor = Censor[ind.s[i, ]], Micro.mat[, ind.mi[i, ]], Prognostic = data.frame(perPrognostic), Plots = FALSE, Mean = TRUE, Quantile = Quantile, Standardize = TRUE, Alpha = 1, Fold = 4, nlambda = 100)) Warning: /srv/hornik/tmp/CRAN/MicrobiomeSurv.Rcheck/00_pkg_src/MicrobiomeSurv/man/CVLasoelascox.Rd:41: unexpected '}', expecting '{' See ‘/srv/hornik/tmp/CRAN/MicrobiomeSurv.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 package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘Rcodes test w3.R’ ‘Week3_otu.xlsx’ ‘Week3_response.xlsx’ ‘data_zero_per_group_otu_w3.xlsx’ ‘fam_info_w3.xlsx’ ‘fam_shan_trim_w3.xlsx’ ‘metadata_taxonomy.csv’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘ggplot2’ ‘glmnet’ ‘gplots’ ‘lmtest’ ‘methods’ ‘microbiome’ ‘pls’ ‘superpc’ ‘survival’ package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s/5s] NOTE CVLasoelascox: no visible global function definition for ‘cv.glmnet’ CVLasoelascox: no visible global function definition for ‘coef’ CVMSpecificCoxPh: no visible global function definition for ‘p.adjust’ CVMSpecificCoxPh: no visible global function definition for ‘new’ CVMajorityvotes: no visible global function definition for ‘p.adjust’ CVMajorityvotes: no visible binding for global variable ‘quantile’ CVMajorityvotes: no visible global function definition for ‘new’ CVPcaPls: no visible global function definition for ‘p.adjust’ CVPcaPls: no visible global function definition for ‘median’ CVPcaPls: no visible global function definition for ‘new’ CVSITaxa: no visible global function definition for ‘new’ CoxPHUni: no visible global function definition for ‘p.adjust’ DistHR: no visible global function definition for ‘p.adjust’ DistHR: no visible binding for global variable ‘Method’ DistHR: possible error in try(Temp = Lasoelascox(Survival = Survival[ind.s[i, ]], Censor = Censor[ind.s[i, ]], Micro.mat[, ind.mi[i, ]], Prognostic = data.frame(perPrognostic), Plots = FALSE, Mean = TRUE, Quantile = Quantile, Standardize = TRUE, Alpha = 1, Fold = 4, nlambda = 100), silent = TRUE): unused argument (Temp = Lasoelascox(Survival = Survival[ind.s[i, ]], Censor = Censor[ind.s[i, ]], Micro.mat[, ind.mi[i, ]], Prognostic = data.frame(perPrognostic), Plots = FALSE, Mean = TRUE, Quantile = Quantile, Standardize = TRUE, Alpha = 1, Fold = 4, nlambda = 100)) DistHR: no visible global function definition for ‘new’ EstimateHR: no visible global function definition for ‘survfit’ EstimateHR: no visible global function definition for ‘ggsurvplot’ EstimateHR: no visible global function definition for ‘ggplot’ EstimateHR: no visible global function definition for ‘aes’ EstimateHR: no visible global function definition for ‘geom_boxplot’ EstimateHR: no visible global function definition for ‘ggtitle’ EstimateHR: no visible global function definition for ‘ylab’ EstimateHR: no visible global function definition for ‘xlab’ EstimateHR: no visible global function definition for ‘theme_bw’ EstimateHR: no visible global function definition for ‘theme’ EstimateHR: no visible global function definition for ‘element_blank’ EstimateHR: no visible global function definition for ‘element_text’ EstimateHR: no visible global function definition for ‘coxph’ Lasoelascox: no visible global function definition for ‘quantile’ Lasoelascox: no visible global function definition for ‘coef’ Lasoelascox: no visible global function definition for ‘par’ Lasoelascox: no visible global function definition for ‘lines’ Lasoelascox: no visible global function definition for ‘abline’ MSpecificCoxPh: no visible global function definition for ‘p.adjust’ MSpecificCoxPh: no visible global function definition for ‘new’ Majorityvotes: no visible global function definition for ‘par’ Majorityvotes: no visible global function definition for ‘points’ Majorityvotes: no visible global function definition for ‘axis’ Majorityvotes: no visible global function definition for ‘box’ Majorityvotes: no visible global function definition for ‘legend’ MiFreq: no visible global function definition for ‘barplot’ MiFreq: no visible global function definition for ‘rainbow’ MiFreq: no visible binding for global variable ‘N’ QuantileAnalysis: no visible global function definition for ‘p.adjust’ QuantileAnalysis: no visible global function definition for ‘axis’ SITaxa: no visible global function definition for ‘p.adjust’ SummaryData: no visible global function definition for ‘%>%’ SummaryData: no visible global function definition for ‘group_by’ SummaryData: no visible global function definition for ‘across’ SurvPcaClass: no visible global function definition for ‘p.adjust’ SurvPlsClass: no visible global function definition for ‘p.adjust’ Top1Uni: no visible global function definition for ‘survfit’ Top1Uni: no visible global function definition for ‘ggsurvplot’ Top1Uni: no visible global function definition for ‘survdiff’ ZerosPerGroup: no visible global function definition for ‘ggplot’ ZerosPerGroup: no visible global function definition for ‘aes’ ZerosPerGroup: no visible binding for global variable ‘n’ ZerosPerGroup: no visible binding for global variable ‘pp’ ZerosPerGroup: no visible binding for global variable ‘Treatment’ ZerosPerGroup: no visible global function definition for ‘geom_point’ ZerosPerGroup: no visible global function definition for ‘facet_grid’ ZerosPerGroup: no visible global function definition for ‘theme’ ZerosPerGroup: no visible global function definition for ‘element_blank’ ZerosPerGroup: no visible global function definition for ‘element_text’ ZerosPerGroup: no visible global function definition for ‘scale_color_manual’ ZerosPerGroup: no visible global function definition for ‘guide_legend’ ZerosPerGroup: no visible global function definition for ‘xlab’ ZerosPerGroup: no visible global function definition for ‘ylab’ f.pca: no visible global function definition for ‘princomp’ plot,cvle-missing: no visible global function definition for ‘hasArg’ plot,cvle-missing: no visible binding for global variable ‘boxplot’ plot,cvmm-ANY: no visible global function definition for ‘hasArg’ plot,cvmm-ANY: no visible binding for global variable ‘boxplot’ plot,cvmv-ANY: no visible global function definition for ‘hasArg’ plot,cvmv-ANY: no visible global function definition for ‘par’ plot,cvmv-ANY: no visible global function definition for ‘lines’ plot,cvmv-ANY: no visible global function definition for ‘abline’ plot,cvmv-ANY: no visible binding for global variable ‘boxplot’ plot,cvpp-missing: no visible global function definition for ‘hasArg’ plot,cvpp-missing: no visible binding for global variable ‘boxplot’ plot,cvsit-missing: no visible global function definition for ‘hasArg’ plot,cvsit-missing: no visible binding for global variable ‘boxplot’ plot,ms-ANY: no visible global function definition for ‘qnorm’ plot,ms-ANY: no visible global function definition for ‘par’ plot,ms-ANY: no visible global function definition for ‘barplot’ plot,ms-ANY: no visible global function definition for ‘rainbow’ plot,ms-ANY: no visible global function definition for ‘arrows’ plot,ms-ANY: no visible global function definition for ‘abline’ plot,perm-ANY: no visible global function definition for ‘na.exclude’ plot,perm-ANY: no visible global function definition for ‘hasArg’ plot,perm-ANY: no visible global function definition for ‘density’ plot,perm-ANY: no visible global function definition for ‘abline’ plot,perm-ANY: no visible global function definition for ‘quantile’ plot,perm-ANY: no visible global function definition for ‘median’ summary,cvle: no visible global function definition for ‘quantile’ summary,cvmm: no visible global function definition for ‘median’ summary,cvmm: no visible global function definition for ‘quantile’ summary,cvmv: no visible global function definition for ‘quantile’ summary,cvpp: no visible global function definition for ‘quantile’ summary,cvsit : : no visible global function definition for ‘median’ summary,cvsit : : no visible global function definition for ‘quantile’ summary,ms: no visible global function definition for ‘qnorm’ summary,perm: no visible global function definition for ‘quantile’ Undefined global functions or variables: %>% Method N Treatment abline across aes arrows axis barplot box boxplot coef coxph cv.glmnet density element_blank element_text facet_grid geom_boxplot geom_point ggplot ggsurvplot ggtitle group_by guide_legend hasArg legend lines median n na.exclude new p.adjust par points pp princomp qnorm quantile rainbow scale_color_manual survdiff survfit theme theme_bw xlab ylab Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "arrows", "axis", "barplot", "box", "boxplot", "legend", "lines", "par", "points") importFrom("methods", "hasArg", "new") importFrom("stats", "coef", "density", "median", "na.exclude", "p.adjust", "princomp", "qnorm", "quantile") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). Found if() conditions comparing class() to string: File ‘MicrobiomeSurv/R/CVSITaxa.R’: if (class(Object) != "cvmm") ... File ‘MicrobiomeSurv/R/Majorityvotes.R’: if (class(Result) != "ms") ... File ‘MicrobiomeSurv/R/MiFreq.R’: if (class(Object) != "cvle") ... File ‘MicrobiomeSurv/R/cvle-class.R’: if (class(x) != "cvle") ... File ‘MicrobiomeSurv/R/cvmv-class.R’: if (class(x) != "cvmv") ... File ‘MicrobiomeSurv/R/cvsit-class.R’: if (class(x) != "cvsit") ... File ‘MicrobiomeSurv/R/perm-class.R’: if (class(x) != "perm") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] WARNING prepare_Rd: ./man/CVLasoelascox.Rd:41: unexpected '}', expecting '{' * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'Top1Uni.Rd': \examples lines wider than 100 characters: summary_fam_shan_w3 = CoxPHUni(Survival = surv_fam_shan_w3$Survival, Censor = surv_fam_shan_w3$Censor, These lines will be truncated in the PDF manual. * checking Rd cross-references ... WARNING Unknown packages ‘Microbiome’, ‘microbiomeSurv’ in Rd xrefs Missing link or links in documentation object 'EstimateHR.Rd': ‘[MicrobiomeSurv]{Lasoelacox}’ Missing link or links in documentation object 'MiFreq.Rd': ‘[MicrobiomeSurv]{CVLasoelacox}’ Missing link or links in documentation object 'cvle-class.Rd': ‘[MicrobiomeSurv]{CVLasoelacox}’ ‘[MicrobiomeSurv]{Lasoelacox}’ Missing link or links in documentation object 'cvmm-class.Rd': ‘[MicrobiomeSurv]{CVMspecificCoxPh}’ Missing link or links in documentation object 'perm-class.Rd': ‘[MicrobiomeSurv]{Lasoelacox}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘IntermediatePCA’ ‘IntermediatePLS’ ‘Week3_otu’ ‘Week3_response’ ‘f.pca’ ‘metadata_taxonomy’ ‘plot’ ‘summary’ Undocumented data sets: ‘Week3_otu’ ‘Week3_response’ ‘metadata_taxonomy’ 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 ... WARNING Functions or methods with usage in documentation object 'hello' but not in code: ‘hello’ * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'CVLasoelascox' ‘Mean’ ‘Quantile’ Undocumented arguments in documentation object 'MSpecificCoxPh' ‘Method’ 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': 7: unexpected symbol 289: rownames(fam_shan_trim_w3) = names_fam_shan_trim_w3 290: Using the ^ ** will not attempt to run examples * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 8 WARNINGs, 4 NOTEs