* using log directory 'd:/Rcompile/CRANpkg/local/3.4/ClinReport.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'ClinReport/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ClinReport' version '0.9.1.12' * package encoding: UTF-8 * 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 'ClinReport' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * 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 ... 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 ... [14s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'ClinReport-Ex.R' failed The error most likely occurred in: > ### Name: report.quali > ### Title: Descriptive "qualitative" statistics (frequencies and > ### percentages) reporting > ### Aliases: report.quali > > ### ** Examples > > > > data(data) > > # No explicative variable changing y labels (option y.levels.label) > report.quali(data=data,y="y_logistic", + y.label="Clinical cure",y.levels.label="Levels") Levels Statistics Clinical cure 1 0 n (column %) 186(46.97%) 2 1 n (column %) 200(50.51%) 3 Missing n(%) 10(2.53%) > > # 1 explicative variable (option x1: levels in columns) > report.quali(data=data,y="y_logistic",x1="GROUP",y.levels.label="Clinical cure") Clinical cure Statistics A B C 1 0 n (column %) 79(43.89%) 60(50.00%) 47(48.96%) 2 1 n (column %) 97(53.89%) 59(49.17%) 44(45.83%) 3 Missing n(%) 4(2.22%) 1(0.83%) 5(5.21%) > > # 2 explicative variables (x1, levels in columns, option x2, levels in rows), > # spcacing the results (option at.row) > report.quali(data=data,y="y_logistic",x1="GROUP", + x2="TIMEPOINT",y.levels.label="Clinical cure",x2.label="Days",at.row="Days") Days Clinical cure Statistics A B C 1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%) 2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%) 3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%) 4 5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%) 6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%) 7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%) 8 9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%) 10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%) 11 D2 Missing n(%) 0(0%) 0(0%) 0(0%) 12 13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%) 14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%) 15 D3 Missing n(%) 0(0%) 0(0%) 0(0%) 16 17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%) 18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%) 19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%) 20 21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%) 22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%) 23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%) > > # 2 explicative variables with row percentages (option percent.col=F) > report.quali(data=data,y="y_logistic",x1="GROUP", + x2="TIMEPOINT",percent.col=FALSE,x2.label="Days",y.levels.label="Clinical cure") Days Clinical cure Statistics A B C 1 D0 0 n (row %) 11(37.93%) 11(37.93%) 7(24.14%) 2 D0 1 n (row %) 18(54.55%) 8(24.24%) 7(21.21%) 3 D0 Missing n(%) 1(25.00%) 1(25.00%) 2(50.00%) 4 D1 0 n (row %) 7(25.00%) 13(46.43%) 8(28.57%) 5 D1 1 n (row %) 21(60.00%) 7(20.00%) 7(20.00%) 6 D1 Missing n(%) 2(66.67%) 0(0%) 1(33.33%) 7 D2 0 n (row %) 18(50.00%) 7(19.44%) 11(30.56%) 8 D2 1 n (row %) 12(40.00%) 13(43.33%) 5(16.67%) 9 D2 Missing n(%) 0 0 0 10 D3 0 n (row %) 11(39.29%) 10(35.71%) 7(25.00%) 11 D3 1 n (row %) 19(50.00%) 10(26.32%) 9(23.68%) 12 D3 Missing n(%) 0 0 0 13 D4 0 n (row %) 18(50.00%) 12(33.33%) 6(16.67%) 14 D4 1 n (row %) 12(42.86%) 8(28.57%) 8(28.57%) 15 D4 Missing n(%) 0(0%) 0(0%) 2(100.00%) 16 D5 0 n (row %) 14(48.28%) 7(24.14%) 8(27.59%) 17 D5 1 n (row %) 15(41.67%) 13(36.11%) 8(22.22%) 18 D5 Missing n(%) 1(100.00%) 0(0%) 0(0%) > > # Add Total number of subjects in headers (option subjid="SUBJID") > report.quali(data=data,y="y_logistic",x1="GROUP", + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID") TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17) 1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%) 2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%) 3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%) 4 5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%) 6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%) 7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%) 8 9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%) 10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%) 11 D2 Missing n(%) 0(0%) 0(0%) 0(0%) 12 13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%) 14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%) 15 D3 Missing n(%) 0(0%) 0(0%) 0(0%) 16 17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%) 18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%) 19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%) 20 21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%) 22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%) 23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%) > > # Round percentages to 1 digit (option round=1) > report.quali(data=data,y="y_logistic",x1="GROUP", + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1) TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17) 1 D0 0 n (column %) 11(36.7%) 11(55.0%) 7(43.8%) 2 D0 1 n (column %) 18(60.0%) 8(40.0%) 7(43.8%) 3 D0 Missing n(%) 1(3.3%) 1(5.0%) 2(12.5%) 4 5 D1 0 n (column %) 7(23.3%) 13(65.0%) 8(50.0%) 6 D1 1 n (column %) 21(70.0%) 7(35.0%) 7(43.8%) 7 D1 Missing n(%) 2(6.7%) 0(0.0%) 1(6.2%) 8 9 D2 0 n (column %) 18(60.0%) 7(35.0%) 11(68.8%) 10 D2 1 n (column %) 12(40.0%) 13(65.0%) 5(31.2%) 11 D2 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%) 12 13 D3 0 n (column %) 11(36.7%) 10(50.0%) 7(43.8%) 14 D3 1 n (column %) 19(63.3%) 10(50.0%) 9(56.2%) 15 D3 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%) 16 17 D4 0 n (column %) 18(60.0%) 12(60.0%) 6(37.5%) 18 D4 1 n (column %) 12(40.0%) 8(40.0%) 8(50.0%) 19 D4 Missing n(%) 0(0.0%) 0(0.0%) 2(12.5%) 20 21 D5 0 n (column %) 14(46.7%) 7(35.0%) 8(50.0%) 22 D5 1 n (column %) 15(50.0%) 13(65.0%) 8(50.0%) 23 D5 Missing n(%) 1(3.3%) 0(0.0%) 0(0.0%) > > > # Qualitative statistics with a response with more than one levels > tab=report.quali(data=data,y="y_poisson",x1="GROUP", + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1) data[,'y_poisson']has been transformed into a factor Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? Calls: report.quali -> check.x -> as.factor -> factor -> sort.list Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [51s] OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR