R Development Page

abrem log file (check_x86_64_linux)

Tue Sep  5 02:10:08 2017: Checking package abrem (SVN revision 121) ...
* using log directory ‘/mnt/building/build_2017-09-05-02-05/RF_PKG_CHECK/PKGS/abrem.Rcheck’
* using R version 3.4.1 Patched (2017-09-02 r73195)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘abrem/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘abrem’ version ‘0.1.17.2’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Jacob Ormerod ’

New submission

Strong dependencies not in mainstream repositories:
  pivotals, debias, abremPivotals

Found the following (possibly) invalid URLs:
  URL: http://www.Weibullnews.com/contents.htm
    From: man/abrem-package.Rd
    Status: 404
    Message: Not Found

The Date field is not in ISO 8601 yyyy-mm-dd format.
* checking package namespace information ... NOTE
  Namespaces with empty importFrom:
  ‘abremPivotals’ ‘debias’ ‘pivotals’
* 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 ‘abrem’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
* 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 ... NOTE
Foreign function calls to a different package:
  .Call("MRRw2pXonY", ..., PACKAGE = "pivotals")
  .Call("medianRank", ..., PACKAGE = "pivotals")
  .Call("medianRank1", ..., PACKAGE = "pivotals")
  .Call("pivotalMCw2p", ..., PACKAGE = "pivotals")
  .Call(distri, ..., PACKAGE = "pivotals")
  .Call(ifelse(is_xony, "MRRln2pXonY", "MRRln2pYonX"), ..., PACKAGE = "pivotals")
  .Call(ifelse(is_xony, "MRRw2pXonY", "MRRw2pYonX"), ..., PACKAGE = "pivotals")
  .Call(ifelse(is_xony, "MRRw3pXonY", "MRRw3pYonX"), ..., PACKAGE = "pivotals")
  .Call(ty, ..., PACKAGE = "pivotals")
Registration problems:
  Evaluating ‘ifelse(is_xony, "MRRw2pXonY", "MRRw2pYonX")’ during check gives error
‘object 'is_xony' not found’:
   .Call(ifelse(is_xony, "MRRw2pXonY", "MRRw2pYonX"), x$fit[[i]]$data$time, 
       x$fit[[i]]$data$event, PACKAGE = "pivotals")
  Evaluating ‘ifelse(is_xony, "MRRln2pXonY", "MRRln2pYonX")’ during check gives error
‘object 'is_xony' not found’:
   .Call(ifelse(is_xony, "MRRln2pXonY", "MRRln2pYonX"), x$fit[[i]]$data$time, 
       x$fit[[i]]$data$event, PACKAGE = "pivotals")
  Evaluating ‘ifelse(is_xony, "MRRw3pXonY", "MRRw3pYonX")’ during check gives error
‘object 'is_xony' not found’:
   .Call(ifelse(is_xony, "MRRw3pXonY", "MRRw3pYonX"), x$fit[[i]]$data$time, 
       x$fit[[i]]$data$event, limit = 1e-05, PACKAGE = "pivotals")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [9s/9s] NOTE
Abrem: no visible global function definition for ‘modifyList’
Blifestring : qfun: no visible global function definition for
  ‘qweibull’
Blifestring : qfun: no visible global function definition for ‘qlnorm’
Blifestring : qfun: no visible global function definition for ‘qexp’
Blifestring: no visible binding for global variable ‘Lower’
Blifestring: no visible binding for global variable ‘Upper’
F0inv: no visible global function definition for ‘qweibull’
F0inv: no visible global function definition for ‘qlnorm’
abrem.fit: no visible global function definition for ‘modifyList’
bbb: no visible global function definition for ‘qbeta’
bsll: no visible global function definition for ‘modifyList’
buildSingleDataLegend: no visible global function definition for
  ‘legend’
buildSingleFitLegend: no visible global function definition for
  ‘modifyList’
buildSingleFitLegend: no visible global function definition for
  ‘legend’
calculateSingleConf: no visible global function definition for
  ‘modifyList’
calculateSingleConf : extract: no visible global function definition
  for ‘na.omit’
calculateSingleConf: no visible global function definition for
  ‘approxfun’
calculateSingleConf: no visible global function definition for
  ‘na.omit’
calculateSingleConf : MCfun: no visible global function definition for
  ‘rweibull’
calculateSingleConf: no visible global function definition for
  ‘qweibull’
calculateSingleConf : Tp: no visible global function definition for
  ‘quantile’
calculateSingleFit: no visible global function definition for
  ‘modifyList’
calculateSingleFit : goodness_of_fit: no visible global function
  definition for ‘cor’
calculateSingleFit : goodness_of_fit: no visible global function
  definition for ‘na.omit’
calculateSingleFit : extract: no visible global function definition for
  ‘na.omit’
calculateSingleFit: no visible global function definition for
  ‘qweibull’
calculateSingleFit : rr_weibull2p: no visible global function
  definition for ‘lm’
calculateSingleFit : rr_weibull2p: no visible global function
  definition for ‘coef’
calculateSingleFit: no visible global function definition for ‘qlnorm’
calculateSingleFit : rr_lognormal2p: no visible global function
  definition for ‘lm’
calculateSingleFit : rr_lognormal2p: no visible global function
  definition for ‘coef’
contour.abrem: no visible global function definition for ‘modifyList’
contour.abrem: no visible global function definition for ‘abline’
contour.abrem : plotContours : plotContours2: no visible global
  function definition for ‘modifyList’
contour.abrem : plotContours : plotContours2 : plotContours3: no
  visible global function definition for ‘modifyList’
contour.abrem : plotContours : plotContours2 : plotContours3: no
  visible global function definition for ‘points’
getPlotRangeX: no visible global function definition for ‘par’
getPlotRangeY: no visible global function definition for ‘par’
legendConf: no visible global function definition for ‘modifyList’
legendConf : for.each.blicon: no visible global function definition for
  ‘modifyList’
mrank.data: no visible global function definition for ‘modifyList’
mrank.data: no visible global function definition for ‘qbeta’
options.abrem: no visible binding for '<<-' assignment to
  ‘options_abrem’
options.abrem: no visible binding for global variable ‘options_abrem’
options.abrem: no visible global function definition for ‘modifyList’
params.to.ob: no visible global function definition for ‘modifyList’
params.to.ob: no visible global function definition for ‘qweibull’
params.to.ob: no visible global function definition for ‘qlnorm’
plot.abrem: no visible global function definition for ‘modifyList’
plot.abrem: no visible global function definition for ‘par’
plot.abrem: no visible binding for global variable ‘plot.default’
plot.abrem: no visible global function definition for ‘abline’
plot.abrem: no visible global function definition for ‘axis’
plot.abrem: no visible global function definition for ‘title’
plot.abrem : plotFitsInAbrem: no visible global function definition for
  ‘modifyList’
plot.abrem : plotSingleDataSet: no visible global function definition
  for ‘modifyList’
plot.abrem : plotSingleDataSet: no visible global function definition
  for ‘points’
plot.abrem : plotSingleLegend: no visible global function definition
  for ‘legend’
plotConfsInFit: no visible global function definition for ‘modifyList’
plotSingleConfBound: no visible global function definition for
  ‘modifyList’
plotSingleConfBound: no visible global function definition for ‘lines’
plotSingleFit: no visible global function definition for ‘modifyList’
plotSingleFit: no visible global function definition for ‘curve’
plotSingleFit: no visible global function definition for ‘pweibull’
plotSingleFit: no visible binding for global variable ‘x’
plotSingleFit: no visible global function definition for ‘lines’
plotSingleFit: no visible global function definition for ‘plnorm’
plotSingleFit: no visible global function definition for ‘pexp’
Undefined global functions or variables:
  Lower Upper abline approxfun axis coef cor curve legend lines lm
  modifyList na.omit options_abrem par pexp plnorm plot.default points
  pweibull qbeta qexp qlnorm quantile qweibull rweibull title x
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "par", "plot.default", "points", "title")
  importFrom("stats", "approxfun", "coef", "cor", "lm", "na.omit",
             "pexp", "plnorm", "pweibull", "qbeta", "qexp", "qlnorm",
             "quantile", "qweibull", "rweibull")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: Abrem.Rd:95: Dropping empty section \note
prepare_Rd: abrem-package.Rd:21: Dropping empty section \note
checkRd: (7) options.abrem.Rd:73: Tag \cr is invalid in a \code block
checkRd: (7) options.abrem.Rd:78: Tag \cr is invalid in a \code block
prepare_Rd: params.to.ob.Rd:61: Dropping empty section \seealso
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'S':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'cl':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'conf.blives.sides':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'conf.what':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'dist':
  ‘abrem.fit.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'in.legend':
  ‘abrem.conf.Rd’ ‘abrem.fit.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'method.conf.blives':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'method.fit':
  ‘abrem.fit.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'threshold':
  ‘abrem.fit.Rd’ ‘options.abrem.Rd’
Rd files with duplicated alias 'unrel.n':
  ‘abrem.conf.Rd’ ‘options.abrem.Rd’
* checking Rd line widths ... 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 ... [6s/6s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2017-09-05-02-05/RF_PKG_CHECK/PKGS/abrem.Rcheck/00check.log’
for details.


Run time: 45.75 seconds.