* using log directory ‘/srv/hornik/tmp/CRAN/catregs.Rcheck’ * using R Under development (unstable) (2024-06-05 r86695) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.5 (2) Debian flang-new version 18.1.5 (2) * running under: Debian GNU/Linux trixie/sid * 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 ... [3s/3s] 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) 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 Packages suggested but not available for checking: 'countreg', 'margins' * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘catregs’ can be installed ... [3s/3s] 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 ... [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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s/5s] 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 ... [0s/0s] 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 ... [1s/1s] 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 ... [0s/0s] ERROR Running examples in ‘catregs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compare.margins > ### Title: Compares two marginal effects (MEMs or AMEs). Estimate of > ### uncertainty is from a simulated draw from a normal distribution. > ### Aliases: compare.margins > > ### ** Examples > > data("essUK") > m1 <- glm(safe ~ religious + minority*female + age,data=essUK,family="binomial") > ma1 <- summary(margins::margins(m1,variables="female",at=list(minority=0))) Error in loadNamespace(x) : there is no package called ‘margins’ Calls: summary ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [21s/21s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘compare.margins.Rmd’ using rmarkdown Quitting from lines 16-24 [unnamed-chunk-1] (compare.margins.Rmd) Error: processing vignette 'compare.margins.Rmd' failed with diagnostics: there is no package called 'margins' --- failed re-building ‘compare.margins.Rmd’ --- re-building ‘count.fit.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/catregs.Rcheck/vign_test/catregs/vignettes/count.fit_files/figure-html/unnamed-chunk-1-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17508 bytes Input file size = 17610 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13750 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13750 Output IDAT size = 13750 bytes (3758 bytes decrease) Output file size = 13828 bytes (3782 bytes = 21.48% decrease) ** Processing: /srv/hornik/tmp/CRAN/catregs.Rcheck/vign_test/catregs/vignettes/count.fit_files/figure-html/unnamed-chunk-1-2.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8948 bytes Input file size = 9818 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8472 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8472 Output IDAT size = 8472 bytes (476 bytes decrease) Output file size = 8550 bytes (1268 bytes = 12.92% decrease) --- finished re-building ‘count.fit.Rmd’ --- re-building ‘daign.Rmd’ using rmarkdown --- finished re-building ‘daign.Rmd’ --- re-building ‘first.diff.fitted.Rmd’ using rmarkdown --- finished re-building ‘first.diff.fitted.Rmd’ --- re-building ‘list.coef.Rmd’ using rmarkdown --- finished re-building ‘list.coef.Rmd’ --- re-building ‘lr.test.Rmd’ using rmarkdown --- finished re-building ‘lr.test.Rmd’ --- re-building ‘margins.dat.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/catregs.Rcheck/vign_test/catregs/vignettes/margins.dat_files/figure-html/unnamed-chunk-1-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24630 bytes Input file size = 24744 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18412 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18412 Output IDAT size = 18412 bytes (6218 bytes decrease) Output file size = 18490 bytes (6254 bytes = 25.27% decrease) --- finished re-building ‘margins.dat.Rmd’ --- re-building ‘margins.dat.clogit.Rmd’ using rmarkdown --- finished re-building ‘margins.dat.clogit.Rmd’ --- re-building ‘margins.des.Rmd’ using rmarkdown --- finished re-building ‘margins.des.Rmd’ --- re-building ‘rubins.rule.Rmd’ using rmarkdown --- finished re-building ‘rubins.rule.Rmd’ --- re-building ‘second.diff.fitted.Rmd’ using rmarkdown --- finished re-building ‘second.diff.fitted.Rmd’ SUMMARY: processing the following file failed: ‘compare.margins.Rmd’ Error: Vignette re-building failed. Execution halted * 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: 2 ERRORs, 4 NOTEs