* using log directory 'd:/RCompile/CRANincoming/R-devel/catregs.Rcheck' * using R Under development (unstable) (2024-06-05 r86695 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'catregs/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'catregs' version '0.2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'The package maintainer ' New submission Possibly misspelled words in DESCRIPTION: AMEs (7:580) Boca (7:1458) CRC (7:1474) Doan (7:1385) MEMs (7:588) Melamed (7:1373) Rotan (7:1463) clmm (7:1903) coef (7:393) dat (7:223, 7:1667) des (7:210, 7:1654) diagn (7:684) glmer (7:1780, 7:1837) lme (7:1775, 7:1832) lr (7:314) nb (7:1843) nonparametric (7:899) rubins (7:599) Suggests or Enhances not in mainstream repositories: countreg, margins The Title field should be in title case. Current version is: 'Post-estimation functions for Generalized Linear Mixed Models' In title case that is: 'Post-Estimation Functions for Generalized Linear Mixed Models' DESCRIPTION fields with placeholder content: Maintainer: The package maintainer * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: 'countreg' * 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 'catregs' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 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 Found if() conditions comparing class() to string: File 'catregs/R/functions.R': if (class(X.mod) == "numeric") ... File 'catregs/R/functions.R': if (class(X.mod) == "numeric") ... File 'catregs/R/functions.R': if (class(X.mod) == "numeric") ... File 'catregs/R/functions.R': if (class(X.mod) == "numeric") ... File 'catregs/R/functions.R': if (class(mod) == "polr") ... File 'catregs/R/functions.R': if (class(mod) == "vglm") ... File 'catregs/R/functions.R': if (class(mod) == "clmm" & cum.probs == "no") ... File 'catregs/R/functions.R': if (class(mod) == "clmm" & cum.probs == "no") ... File 'catregs/R/functions.R': if (class(mod) == "clogistic") ... File 'catregs/R/functions.R': if (class(mod) == "mlogit") ... Use inherits() (or maybe is()) instead. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'diagn.Rd': \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'first.diff.fitted.Rd': \usage lines wider than 90 characters: first.diff.fitted(mod,design.matrix,compare,alpha=.05,rounded=3,bootstrap="no",num.sample=1000,prop.sample=.9,data,seed=1234,cum.probs= ... [TRUNCATED] \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'list.coef.Rd': \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'lr.test.Rd': \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) m0 <- glm(alcB ~woman + parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'margins.dat.Rd': \usage lines wider than 90 characters: margins.dat(mod,des,alpha=.05,rounded=3,cumulate="no",pscl.data=data,num.sample=1000,prop.sample=.9,seed=1234) \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'margins.dat.clogit.Rd': \usage lines wider than 90 characters: margins.dat.clogit(mod,design.matrix,run.boot="no",num.sample=1000,prop.sample=.9,alpha=.05,seed=1234,rounded=3) Rd file 'margins.des.Rd': \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) Rd file 'second.diff.fitted.Rd': \usage lines wider than 90 characters: second.diff.fitted(mod,design.matrix,compare,alpha=.05,rounded=3,bootstrap="no",num.sample=1000,prop.sample=.9,data,seed=1234,cum.probs ... [TRUNCATED] \examples lines wider than 100 characters: m1 <- glm(alcB ~woman*parrole + age + race2 + race3 + race4 + income + ed1 + ed2 + ed3 + ed4,family="binomial",data=Mize19AH) second.diff.fitted(m1,des2,compare=c(4,2,3,1),rounded=5) # [Pr(Drink | Mothers) - Pr(Drink | Childless Women)] - [Pr(Drink | Fathers) - ... [TRUNCATED] # Note that this is reported as the "Second Difference" in Table 3 of Mize (2019: 104, "Best Practices for Estimating, Interpreting, an ... [TRUNCATED] These lines will be truncated in the PDF manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [16s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed margins.dat.clogit 12.23 0.25 12.49 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [25s] OK * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 5 NOTEs