Magus // R-cran-epicalc

science/R-cran-epicalc

Epidemiological calculator
Flavor	Version	Run	OSVersion	Arch	License	Restricted	Status
	2.15.1.0	637	4.0	i386	No License	0	fail
License Permissions:
Events

Machine	Type	Time	Message
m4032	info	2026-05-15 01:43:59.376592	Test Started
m4032	fail	2026-05-15 01:47:34.679566	make test returned non-zero: 1
m4032	fail	2026-05-15 01:47:34.750569	Test complete.
Log

[1m===>  Testing for R-cran-epicalc-2.15.1.0[0m
* using log directory '/magus/work/usr/mports/science/R-cran-epicalc/work/epicalc.Rcheck'
* using R version 4.4.0 (2024-04-24)
* using platform: i386-portbld-midnightbsd4.0 (32-bit)
* R was compiled by
    MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)
    GNU Fortran (MidnightBSD Ports Collection) 14.2.0
* running under: MidnightBSD m4032 4.0.4 MidnightBSD 4.0.4 #6 stable/4.0-n13781-2e14c521d0-dirty: Tue Mar 31 20:43:49 EDT 2026     root@m4032:/usr/obj/usr/src/i386.i386/sys/GENERIC i386
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'epicalc/DESCRIPTION' ... OK
* this is package 'epicalc' version '2.15.1.0'
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'epicalc' can be installed ... OK
* checking installed package size ... OK
* checking package 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'foreign' 'survival'
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addMissingRecords: no visible binding for global variable '.data'
adjust: no visible global function definition for 'model.matrix'
adjust: no visible global function definition for
  'aggregate.data.frame'
adjust: no visible global function definition for 'glm'
adjust: no visible global function definition for 'predict.glm'
adjust: no visible global function definition for 'qnorm'
aggregate.numeric : count: no visible global function definition for
  'na.omit'
aggregate.numeric : se: no visible global function definition for 'sd'
aggregate.numeric: no visible global function definition for
  'aggregate.data.frame'
aggregate.plot : p25: no visible global function definition for
  'quantile'
aggregate.plot : p75: no visible global function definition for
  'quantile'
aggregate.plot : se: no visible global function definition for 'sd'
aggregate.plot : se: no visible global function definition for
  'na.omit'
aggregate.plot: no visible global function definition for 'grey.colors'
aggregate.plot : count: no visible global function definition for
  'na.omit'
aggregate.plot: no visible global function definition for 'xtabs'
aggregate.plot: no visible global function definition for
  'barplot.default'
aggregate.plot: no visible global function definition for 'segments'
aggregate.plot: no visible global function definition for 'barplot'
aggregate.plot: no visible global function definition for 'na.omit'
aggregate.plot: no visible global function definition for 'quantile'
aggregate.plot: no visible global function definition for 'title'
alpha: no visible binding for global variable '.data'
alpha: no visible global function definition for 'cor'
alpha: no visible global function definition for 'factanal'
alpha: no visible global function definition for 'na.omit'
alpha: no visible global function definition for 'cov'
alphaBest: no visible binding for global variable '.data'
cc: no visible global function definition for 'fisher.test'
cc: no visible global function definition for 'chisq.test'
cc: no visible global function definition for 'lines'
cc: no visible global function definition for 'points'
cc: no visible global function definition for 'axis'
cc: no visible global function definition for 'text'
cci: no visible global function definition for 'xtabs'
cci: no visible global function definition for 'fisher.test'
cci: no visible global function definition for 'chisq.test'
cci: no visible global function definition for 'qnorm'
cci: no visible global function definition for 'axis'
cci: no visible global function definition for 'mtext'
cci: no visible global function definition for 'title'
ci.binomial: no visible global function definition for 'na.omit'
ci.binomial: no visible global function definition for 'pbinom'
ci.numeric: no visible global function definition for 'na.omit'
ci.numeric: no visible global function definition for 'sd'
ci.numeric: no visible global function definition for 'qt'
ci.poisson: no visible global function definition for 'ppois'
clogistic.display: no visible global function definition for
  'as.formula'
clogistic.display: no visible global function definition for 'qnorm'
codebook: no visible binding for global variable '.data'
codebook: no visible global function definition for 'na.omit'
cox.display: no visible global function definition for 'as.formula'
cox.display: no visible global function definition for 'qnorm'
cs: no visible global function definition for 'qnorm'
cs: no visible global function definition for 'chisq.test'
cs: no visible global function definition for 'fisher.test'
cs: no visible global function definition for 'lines'
cs: no visible global function definition for 'points'
cs: no visible global function definition for 'axis'
cs: no visible global function definition for 'text'
csi: no visible global function definition for 'xtabs'
csi: no visible global function definition for 'addmargins'
csi : newcombe.wilson: no visible global function definition for
  'qnorm'
csi: no visible global function definition for 'qnorm'
csi: no visible global function definition for 'chisq.test'
des: no visible binding for global variable '.data'
des: no visible global function definition for 'glob2rx'
dotplot: no visible global function definition for 'lm'
dotplot: no visible global function definition for 'predict.lm'
dotplot: no visible binding for global variable '.data'
dotplot: no visible global function definition for 'glm'
dotplot: no visible global function definition for 'par'
dotplot: no visible global function definition for 'abline'
dotplot: no visible global function definition for 'axis'
dotplot: no visible global function definition for 'title'
fillin: no visible binding for global variable '.data'
fillin: no visible binding for global variable 'Freq'
followup.plot: no visible global function definition for 'lines'
followup.plot: no visible global function definition for 'text'
graph.casecontrol: no visible global function definition for
  'fisher.test'
graph.casecontrol: no visible global function definition for 'points'
graph.casecontrol: no visible global function definition for 'axis'
graph.casecontrol: no visible global function definition for 'lines'
graph.casecontrol: no visible global function definition for 'arrows'
graph.casecontrol: no visible global function definition for 'text'
graph.casecontrol: no visible global function definition for 'abline'
graph.prospective: no visible global function definition for
  'fisher.test'
graph.prospective: no visible global function definition for 'lines'
graph.prospective: no visible global function definition for 'points'
graph.prospective: no visible global function definition for 'axis'
graph.prospective: no visible global function definition for 'arrows'
graph.prospective: no visible global function definition for 'text'
graph.prospective: no visible global function definition for 'abline'
graph.prospective: no visible global function definition for 'mtext'
idr.display: no visible global function definition for 'qnorm'
idr.display: no visible global function definition for 'as.formula'
idr.display: no visible global function definition for 'glm'
idr.display: no visible binding for global variable 'poisson'
idr.display: no visible global function definition for 'logLik'
kap.ByCategory: no visible global function definition for 'var'
kap.ByCategory: no visible global function definition for 'pnorm'
kap.table: no visible global function definition for 'pnorm'
keepData: no visible binding for global variable '.data'
keepData: no visible global function definition for 'glob2rx'
label.var: no visible binding for global variable '.data'
logistic.display: no visible global function definition for 'qnorm'
logistic.display: no visible global function definition for
  'as.formula'
logistic.display: no visible global function definition for 'glm'
logistic.display: no visible binding for global variable 'binomial'
logistic.display: no visible global function definition for 'logLik'
lroc: no visible global function definition for 'model.frame'
lroc: no visible global function definition for 'xtabs'
lroc: no visible global function definition for 'lines'
lroc: no visible global function definition for 'abline'
lroc: no visible global function definition for 'text'
lrtest: no visible global function definition for 'logLik'
lrtest: no visible global function definition for 'pchisq'
lsNoFunction: no visible global function definition for 'lsf.str'
matchTab: no visible global function definition for
  'aggregate.data.frame'
matchTab: no visible global function definition for 'qnorm'
mhor: no visible global function definition for 'fisher.test'
mhor: no visible global function definition for 'qnorm'
mhor: no visible global function definition for 'pchisq'
mhor: no visible global function definition for 'lines'
mhor: no visible global function definition for 'points'
mhor: no visible global function definition for 'text'
mhor: no visible global function definition for 'axis'
mlogit.display: no visible global function definition for 'pnorm'
mlogit.display: no visible global function definition for 'qnorm'
n.for.2means: no visible global function definition for 'qnorm'
n.for.2p: no visible global function definition for 'qnorm'
n.for.cluster.2means: no visible global function definition for 'qnorm'
n.for.cluster.2p: no visible global function definition for 'qnorm'
n.for.equi.2p: no visible global function definition for 'qnorm'
n.for.lqas: no visible global function definition for 'dhyper'
n.for.lqas: no visible global function definition for 'qnorm'
n.for.noninferior.2p: no visible global function definition for 'qnorm'
n.for.survey: no visible global function definition for 'qnorm'
ordinal.or.display: no visible global function definition for 'pt'
ordinal.or.display: no visible global function definition for 'confint'
pack: no visible binding for global variable '.data'
pack: no visible global function definition for 'ls.str'
poisgof: no visible global function definition for 'pchisq'
power.for.2means: no visible global function definition for 'pnorm'
power.for.2means: no visible global function definition for 'qnorm'
power.for.2means: no visible global function definition for 'dnorm'
power.for.2means: no visible global function definition for 'lines'
power.for.2means: no visible global function definition for 'text'
power.for.2p: no visible global function definition for 'qnorm'
power.for.2p: no visible global function definition for 'pnorm'
print.cci: no visible global function definition for 'addmargins'
print.cci: no visible global function definition for 'fisher.test'
pyramid: no visible global function definition for 'par'
pyramid: no visible global function definition for 'barplot'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'axis'
pyramid: no visible global function definition for 'title'
recode.default: no visible binding for global variable '.data'
recode.is.na: no visible binding for global variable '.data'
regress.display: no visible global function definition for 'qt'
regress.display: no visible global function definition for 'as.formula'
regress.display: no visible global function definition for 'glm'
regress.display: no visible global function definition for 'lm'
regress.display: no visible global function definition for 'logLik'
ren: no visible binding for global variable '.data'
rename: no visible binding for global variable '.data'
rename.default: no visible binding for global variable '.data'
rename.pattern: no visible binding for global variable '.data'
rename.var: no visible binding for global variable '.data'
roc.from.table: no visible global function definition for 'lines'
roc.from.table: no visible global function definition for 'abline'
roc.from.table: no visible global function definition for 'text'
shapiro.qqnorm: no visible global function definition for
  'shapiro.test'
shapiro.qqnorm: no visible global function definition for 'qqnorm'
shapiro.qqnorm: no visible global function definition for 'text'
shapiro.qqnorm: no visible global function definition for 'qqline'
sortBy: no visible binding for global variable '.data'
sortBy: no visible global function definition for 'ls.str'
summ: no visible binding for global variable '.data'
summ: no visible global function definition for 'par'
summ: no visible global function definition for 'axis'
summ: no visible global function definition for 'title'
summ: no visible global function definition for 'abline'
summ: no visible global function definition for 'boxplot'
summ: no visible global function definition for 'na.omit'
summ: no visible global function definition for 'quantile'
summ: no visible global function definition for 'sd'
summ: no visible global function definition for 'median'
tab1: no visible global function definition for 'par'
tab1: no visible global function definition for 'barplot'
tab1: no visible global function definition for 'text'
tab1: no visible global function definition for 'model.matrix'
tableGlm: no visible global function definition for 'na.omit'
tableGlm: no visible global function definition for 'aov'
tableGlm: no visible global function definition for 'as.formula'
tableGlm: no visible global function definition for 'glm'
tableStack: no visible binding for global variable '.data'
tableStack: no visible global function definition for 'cor'
tableStack: no visible global function definition for 'factanal'
tableStack: no visible global function definition for 'na.omit'
tableStack: no visible global function definition for 'median'
tableStack: no visible global function definition for 'sd'
tableStack: no visible global function definition for 'weighted.mean'
tableStack: no visible global function definition for 'shapiro.test'
tableStack: no visible global function definition for 'lm'
tableStack: no visible global function definition for 'bartlett.test'
tableStack: no visible global function definition for 'addmargins'
tableStack: no visible global function definition for 'fisher.test'
tableStack: no visible global function definition for 'chisq.test'
tableStack: no visible global function definition for 'quantile'
tableStack: no visible global function definition for 'kruskal.test'
tableStack: no visible global function definition for 'wilcox.test'
tableStack: no visible global function definition for 'anova'
tableStack: no visible global function definition for 't.test'
tabpct: no visible global function definition for 'addmargins'
tabpct: no visible global function definition for 'mosaicplot'
tally.events: no visible global function definition for 'axis'
tally.events: no visible global function definition for 'lines'
unclassDataframe: no visible binding for global variable '.data'
use: no visible binding for global variable '.data'
use: no visible global function definition for 'read.csv'
zap: no visible global function definition for 'lsf.str'
Undefined global functions or variables:
  .data Freq abline addmargins aggregate.data.frame anova aov arrows
  as.formula axis barplot barplot.default bartlett.test binomial
  boxplot chisq.test confint cor cov dhyper dnorm factanal fisher.test
  glm glob2rx grey.colors kruskal.test lines lm logLik ls.str lsf.str
  median model.frame model.matrix mosaicplot mtext na.omit par pbinom
  pchisq pnorm points poisson ppois predict.glm predict.lm pt qnorm
  qqline qqnorm qt quantile read.csv sd segments shapiro.test t.test
  text title var weighted.mean wilcox.test xtabs
Consider adding
  importFrom("grDevices", "grey.colors")
  importFrom("graphics", "abline", "arrows", "axis", "barplot",
             "barplot.default", "boxplot", "lines", "mosaicplot",
             "mtext", "par", "points", "segments", "text", "title")
  importFrom("stats", "addmargins", "aggregate.data.frame", "anova",
             "aov", "as.formula", "bartlett.test", "binomial",
             "chisq.test", "confint", "cor", "cov", "dhyper", "dnorm",
             "factanal", "fisher.test", "glm", "kruskal.test", "lm",
             "logLik", "median", "model.frame", "model.matrix",
             "na.omit", "pbinom", "pchisq", "pnorm", "poisson", "ppois",
             "predict.glm", "predict.lm", "pt", "qnorm", "qqline",
             "qqnorm", "qt", "quantile", "sd", "shapiro.test", "t.test",
             "var", "weighted.mean", "wilcox.test", "xtabs")
  importFrom("utils", "glob2rx", "ls.str", "lsf.str", "read.csv")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (7) addMissingRecords.rd:27: Invalid email address: 
checkRd: (7) adjust.rd:32: Invalid email address: 
checkRd: (7) aggregate.numeric.rd:38: Invalid email address: 
checkRd: (7) aggregate.plot.rd:52: Invalid email address: 
checkRd: (7) alpha.rd:54: Invalid email address: 
checkRd: (7) auc.rd:18: Invalid email address: 
checkRd: (7) be2ad.rd:21: Invalid email address: 
checkRd: (7) cc.rd:74: Invalid email address: 
checkRd: (7) ci.rd:40: Invalid email address: 
checkRd: (7) codebook.rd:15: Invalid email address: 
checkRd: (7) des.rd:19: Invalid email address: 
checkRd: (7) detachAlllData.rd:14: Invalid email address: 
checkRd: (7) dotplot.rd:36: Invalid email address: 
checkRd: (7) expand.rd:19: Invalid email address: 
checkRd: (7) fillin.rd:18: Invalid email address: 
checkRd: (7) followup.plot.rd:45: Invalid email address: 
checkRd: (7) kap.rd:60: Invalid email address: 
checkRd: (7) keepData.rd:28: Invalid email address: 
checkRd: (7) label.var.rd:25: Invalid email address: 
checkRd: (7) lagVar.rd:20: Invalid email address: 
checkRd: (7) lookup.rd:19: Invalid email address: 
checkRd: (7) lrtest.rd:14: Invalid email address: 
checkRd: (7) lsNoFunction.rd:14: Invalid email address: 
checkRd: (7) markVisits.rd:18: Invalid email address: 
checkRd: (7) matchTab.rd:18: Invalid email address: 
checkRd: (7) merge.lab.rd:20: Invalid email address: 
checkRd: (7) mhor.rd:19: Invalid email address: 
checkRd: (7) poisgof.rd:15: Invalid email address: 
checkRd: (7) power.for.2means.rd:13: Invalid email address: 
checkRd: (7) power.rd:20: Invalid email address: 
checkRd: (7) print.alpha.rd:13: Invalid email address: 
checkRd: (7) print.cci.rd:13: Invalid email address: 
checkRd: (7) print.des.rd:13: Invalid email address: 
checkRd: (7) print.kap.ByCategory.rd:13: Invalid email address: 
checkRd: (7) print.kap.table.rd:13: Invalid email address: 
checkRd: (7) print.lrtest.rd:13: Invalid email address: 
checkRd: (7) print.n.for.2means.rd:13: Invalid email address: 
checkRd: (7) print.n.for.2p.rd:13: Invalid email address: 
checkRd: (7) print.n.for.cluster.2means.rd:13: Invalid email address: 
checkRd: (7) print.n.for.cluster.2p.rd:13: Invalid email address: 
checkRd: (7) print.n.for.equi.2p.rd:13: Invalid email address: 
checkRd: (7) print.n.for.lqas.rd:13: Invalid email address: 
checkRd: (7) print.n.for.noninferior.2p.rd:13: Invalid email address: 
checkRd: (7) print.n.for.survey.rd:13: Invalid email address: 
checkRd: (7) print.power.for.2p.rd:13: Invalid email address: 
checkRd: (7) print.summ.rd:13: Invalid email address: 
checkRd: (7) print.tableStack.rd:13: Invalid email address: 
checkRd: (7) pyramid.rd:37: Invalid email address: 
checkRd: (7) recode.rd:36: Invalid email address: 
checkRd: (7) rename.rd:45: Invalid email address: 
checkRd: (-1) risk.display.rd:63: Escaped LaTeX specials: \$
checkRd: (7) risk.display.rd:75: Invalid email address: 
checkRd: (7) roc.rd:32: Invalid email address: 
checkRd: (7) sampsize.rd:84: Invalid email address: 
checkRd: (7) setTitle.rd:19: Invalid email address: 
checkRd: (7) shapiro.qqnorm.rd:16: Invalid email address: 
checkRd: (7) sortBy.rd:18: Invalid email address: 
checkRd: (7) summ.rd:27: Invalid email address: 
checkRd: (7) tab1.rd:44: Invalid email address: 
checkRd: (7) tableStack.rd:76: Invalid email address: 
checkRd: (7) tabpct.rd:44: Invalid email address: 
checkRd: (7) tally.events.rd:39: Invalid email address: 
checkRd: (7) titleString.rd:32: Invalid email address: 
checkRd: (7) unclassDataframe.rd:15: Invalid email address: 
checkRd: (7) use.rd:18: Invalid email address: 
checkRd: (7) zap.rd:17: Invalid email address: 
* 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 examples ... ERROR
Running examples in 'epicalc-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Outbreak investigation
> ### Title: Dataset from an outbreak of food poisoning on a sportsday,
> ###   Thailand 1990.
> ### Aliases: Outbreak
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Outbreak)
> use(Outbreak)
> 
> # Distribution of reported pieces of eclair taken
> tab1(eclair) 
Error in if (bar.values == "percent") { : the condition has length > 1
Calls: tab1
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  '/magus/work/usr/mports/science/R-cran-epicalc/work/epicalc.Rcheck/00check.log'
for details.

*** Error code 1

Stop.
make: stopped in /usr/mports/science/R-cran-epicalc
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math/R (run)
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