R Development Page

eatRep log file (check_x86_64_linux)

Wed Feb 20 11:11:34 2019: Checking package eatRep (SVN revision 769) ...
* using log directory ‘/srv/rf/building/build_2019-02-20-11-09/RF_PKG_CHECK/PKGS/eatRep.Rcheck’
* using R version 3.5.2 Patched (2019-02-19 r76133)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘eatRep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eatRep’ version ‘0.9.5’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Sebastian Weirich ’

New submission

No package encoding and non-ASCII characters in the following R files:
  R/jk2.R
    808:                   suppressWarnings(eval(parse(text=do)))                        ### Warning erklaert in Word-Doc, wird unterdrueckt da irrelevant fr Paket
    816:                   namen   <- uu[1, allNam[["group"]], drop=FALSE]               ### Warning erklaert in Word-Doc, wird unterdrueckt da irrelevant fr Paket

The Date field is over a month old.
* 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 serialization versions ... OK
* checking whether package ‘eatRep’ can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [20s/20s] NOTE
addSig : : no visible global function definition for ‘pnorm’
compareParameters : : no visible global function definition
  for ‘pnorm’
computeTrend: no visible global function definition for ‘as.formula’
computeTrend: no visible global function definition for ‘pnorm’
conv.mean : : no visible global function definition for
  ‘na.omit’
conv.mean :  : : no visible global function
  definition for ‘flush.console’
conv.quantile : : no visible binding for global variable
  ‘sd’
conv.table : : no visible global function definition for
  ‘chisq.test’
dG : : no visible global function definition for ‘pt’
desk : : no visible global function definition for ‘var’
desk : : no visible global function definition for ‘na.omit’
desk : : no visible global function definition for ‘sd’
desk : : no visible global function definition for ‘t.test’
desk : : no visible global function definition for ‘median’
eatRep: no visible global function definition for ‘flush.console’
eatRep : : no visible global function definition for
  ‘na.omit’
eatRep : : no visible global function definition for
  ‘flush.console’
eatRep :  : : no visible global function
  definition for ‘flush.console’
eatRep :  :  :  : : no
  visible global function definition for ‘flush.console’
eatRep :  :  :  :  :
  : no visible global function definition for ‘var’
getOutputIfSingular: no visible global function definition for
  ‘na.omit’
getOutputIfSingular: no visible global function definition for ‘coef’
getOutputIfSingular: no visible global function definition for ‘var’
getOutputIfSingularT1: no visible global function definition for
  ‘na.omit’
getOutputIfSingularT1: no visible global function definition for ‘coef’
getOutputIfSingularT1: no visible global function definition for ‘sd’
getOutputIfSingularT1: no visible global function definition for ‘var’
jackknife.glm : : no visible global function definition for
  ‘glm’
jackknife.glm : : no visible binding for global variable
  ‘glm.family’
jackknife.glm : : no visible global function definition for
  ‘var’
jackknife.glm : : no visible global function definition for
  ‘capture.output’
jackknife.glm : : no visible global function definition for
  ‘flush.console’
jackknife.mean : : no visible binding for global variable
  ‘res’
jackknife.mean : : no visible global function definition for
  ‘as.formula’
jackknife.mean : : no visible global function definition for
  ‘coef’
jackknife.mean : : no visible global function definition for
  ‘vcov’
jackknife.mean :  : : no visible global function
  definition for ‘flush.console’
jackknife.quantile: no visible global function definition for
  ‘as.formula’
jackknife.table: no visible global function definition for ‘as.formula’
jackknife.table : : no visible global function definition
  for ‘as.formula’
jk2.glm: no visible binding for global variable ‘gaussian’
jk2.table: no visible global function definition for ‘as.formula’
jk2.table: no visible global function definition for ‘model.matrix’
pool.corr: no visible global function definition for ‘pnorm’
pool.corr: no visible global function definition for ‘qnorm’
report: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula capture.output chisq.test coef flush.console gaussian glm
  glm.family median model.matrix na.omit pnorm pt qnorm res sd t.test
  var vcov
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "coef", "gaussian",
             "glm", "median", "model.matrix", "na.omit", "pnorm", "pt",
             "qnorm", "sd", "t.test", "var", "vcov")
  importFrom("utils", "capture.output", "flush.console")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: existsBackgroundVariables.Rd:21-23: Dropping empty section \details
prepare_Rd: existsBackgroundVariables.Rd:32-34: Dropping empty section \references
prepare_Rd: facToChar.Rd:24-26: Dropping empty section \details
prepare_Rd: facToChar.Rd:41-43: Dropping empty section \note
prepare_Rd: facToChar.Rd:35-37: Dropping empty section \references
prepare_Rd: facToChar.Rd:47-49: Dropping empty section \seealso
prepare_Rd: jk2.glm.Rd:146-148: Dropping empty section \references
prepare_Rd: jk2.glm.Rd:152-154: Dropping empty section \seealso
prepare_Rd: jk2.mean.Rd:134-136: Dropping empty section \references
prepare_Rd: jk2.quantile.Rd:149-151: Dropping empty section \references
prepare_Rd: removeNonNumeric.Rd:15-17: Dropping empty section \details
prepare_Rd: removeNonNumeric.Rd:32-34: Dropping empty section \note
prepare_Rd: removeNonNumeric.Rd:26-28: Dropping empty section \references
prepare_Rd: removeNonNumeric.Rd:38-40: Dropping empty section \seealso
prepare_Rd: removeNumeric.Rd:15-17: Dropping empty section \details
prepare_Rd: removeNumeric.Rd:32-34: Dropping empty section \note
prepare_Rd: removeNumeric.Rd:26-28: Dropping empty section \references
prepare_Rd: removeNumeric.Rd:38-40: Dropping empty section \seealso
prepare_Rd: removePattern.Rd:19-21: Dropping empty section \details
prepare_Rd: removePattern.Rd:36-38: Dropping empty section \note
prepare_Rd: removePattern.Rd:30-32: Dropping empty section \references
prepare_Rd: removePattern.Rd:42-44: Dropping empty section \seealso
prepare_Rd: eatRep-package.rd:113-114: Dropping empty section \seealso
prepare_Rd: eatRep-package.rd:115-116: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'asNumericIfPossible.Rd':
  \usage lines wider than 90 characters:
     asNumericIfPossible(dataFrame, set.numeric=TRUE, transform.factors=FALSE, maintain.factor.scores = TRUE,

Rd file 'jk2.mean.Rd':
  \usage lines wider than 90 characters:
               repWgt = NULL, nest=NULL, imp=NULL, groups = NULL, group.splits = length(groups),
  \examples lines wider than 100 characters:
     means1 <- jk2.mean(datL = rdN1y10, ID="idstud", wgt="wgt", type = "JK2", PSU = "jkzone", repInd = "jkrep",
     means1a<- jk2.mean(datL = rdN1y10, ID="idstud", wgt="wgt", type = "JK2", PSU = "jkzone", repInd = "jkrep",
     print(res1a[intersect(grep("wholeGroup.vs.", res1a[,"group"]), which(res1a[,"parameter"] == "mean")), ], digits = 3)
               imp="imp", nest="nest", groups = c("country", "sex"), group.splits = 0:2, group.differences.by="sex",
                      imp="imp", nest="nest", groups = c("country", "sex"), group.splits = 0:2, group.differences.by="sex",
                      cross.differences = list(c(0,1), c(0,2)), dependent = "score", na.rm=FALSE, doCheck=TRUE,

Rd file 'jk2.quantile.Rd':
  \usage lines wider than 90 characters:
     jk2.quantile(datL, ID, wgt = NULL, type = c("JK1", "JK2", "BRR"), PSU = NULL, repInd = NULL, 
                 repWgt = NULL, nest=NULL, imp=NULL, groups = NULL, group.splits = length(groups),
                 cross.differences = FALSE, group.delimiter = "_", trend = NULL, linkErr = NULL, dependent,

Rd file 'jk2.table.Rd':
  \usage lines wider than 90 characters:
               repWgt = NULL, nest=NULL, imp=NULL, groups = NULL, group.splits = length(groups), 
               group.differences.by = NULL, cross.differences = FALSE, chiSquare = FALSE, correct = TRUE, group.delimiter = "_",
               trend = NULL, linkErr = NULL, dependent, separate.missing.indicator = FALSE, na.rm=FALSE, 

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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [437s/437s] NOTE
Examples with CPU or elapsed time > 5s
                user system elapsed
jk2.table    238.863  0.504 239.372
jk2.mean     161.161  1.135 162.300
jk2.glm       16.941  0.152  17.109
jk2.quantile  13.972  0.156  14.128
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [56s/56s] OK
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/srv/rf/building/build_2019-02-20-11-09/RF_PKG_CHECK/PKGS/eatRep.Rcheck/00check.log’
for details.


Run time: 617.57 seconds.