R Development Page

retistruct log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2016-08-30-17-23/RF_PKG_CHECK/PKGS/retistruct.Rcheck'
* using R version 3.3.1 Patched (2016-08-27 r71160)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'retistruct/DESCRIPTION' ... OK
* this is package 'retistruct' version '0.5.11'
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: 'David C. Sterratt '
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'retistruct' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
ReconstructedOutline: no visible global function definition for
  'dev.set'
TriangulatedOutline: no visible global function definition for
  'na.omit'
compute.kernel.estimate: no visible global function definition for
  'contourLines'
compute.kernel.estimate: no visible global function definition for
  'aggregate'
computeTearRelationships: no visible global function definition for
  'na.omit'
csv.read.dataset: no visible global function definition for 'read.csv'
flatplot.dataset: no visible global function definition for 'text'
flatplot.reconstructedOutline: no visible global function definition
  for 'palette'
flatplot.reconstructedOutline: no visible global function definition
  for 'rainbow'
flatplot.reconstructedOutline: no visible global function definition
  for 'segments'
idt.connect.segments: no visible global function definition for 'dist'
idt.plot.box: no visible global function definition for 'lines'
idt.plot.map: no visible global function definition for 'par'
idt.plot.map: no visible global function definition for 'plot'
idt.plot.map: no visible global function definition for 'rainbow'
idt.plot.map: no visible global function definition for 'text'
idt.plot.map: no visible global function definition for 'lines'
idt.points.sys: no visible global function definition for 'points'
idt.read.dataset: no visible global function definition for 'na.omit'
idt.read.dataset: no visible binding for global variable 'sd'
idt.read.dataset: no visible global function definition for 'points'
idt.read.map: no visible global function definition for 'read.csv'
karcher.mean.sphere: no visible global function definition for
  'na.omit'
karcher.mean.sphere: no visible global function definition for 'optim'
kde.compute.concentration: no visible global function definition for
  'optimise'
kr.compute.concentration: no visible global function definition for
  'optimise'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'palette'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'rainbow'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'plot'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'par'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'abline'
lvsLplot.reconstructedOutline: no visible global function definition
  for 'text'
optimiseMapping: no visible global function definition for 'optim'
optimiseMapping: no visible global function definition for 'dev.set'
panlabel: no visible global function definition for 'mtext'
panlabel: no visible global function definition for 'par'
polartext: no visible global function definition for 'mtext'
projection.default: no visible global function definition for
  'plot.new'
projection.reconstructedDataset: no visible global function definition
  for 'points'
projection.reconstructedDataset: no visible global function definition
  for 'text'
projection.reconstructedDataset: no visible global function definition
  for 'lines'
projection.reconstructedOutline: no visible global function definition
  for 'na.omit'
projection.reconstructedOutline: no visible global function definition
  for 'plot'
projection.reconstructedOutline: no visible global function definition
  for 'polygon'
projection.reconstructedOutline: no visible global function definition
  for 'lines'
projection.reconstructedOutline: no visible global function definition
  for 'points'
projection.reconstructedOutline: no visible global function definition
  for 'optimise'
projection.reconstructedOutline: no visible global function definition
  for 'text'
read.datapoints: no visible global function definition for 'read.csv'
read.datapoints: no visible global function definition for 'na.omit'
read.image: no visible global function definition for 'as.raster'
read.scale: no visible global function definition for 'read.csv'
retistruct : require.package: no visible global function definition for
  'install.packages'
retistruct : h.add: no visible global function definition for 'dev.set'
retistruct : h.remove: no visible global function definition for
  'dev.set'
retistruct : h.move: no visible global function definition for
  'dev.set'
retistruct : h.mark.n: no visible global function definition for
  'dev.set'
retistruct : h.mark.d: no visible global function definition for
  'dev.set'
retistruct : h.mark.od: no visible global function definition for
  'dev.set'
retistruct : h.mark.od: no visible global function definition for
  'identify'
retistruct : print.bitmap: no visible binding for global variable 'png'
retistruct : print.bitmap: no visible binding for global variable
  'jpeg'
retistruct : print.bitmap: no visible binding for global variable
  'tiff'
retistruct : print.bitmap: no visible global function definition for
  'dev.set'
retistruct : print.bitmap: no visible global function definition for
  'dev.print'
retistruct : print.pdf: no visible global function definition for
  'dev.set'
retistruct : print.pdf: no visible global function definition for
  'dev.print'
retistruct : print.pdf: no visible binding for global variable 'pdf'
retistruct : do.plot: no visible global function definition for
  'dev.set'
retistruct : do.plot: no visible global function definition for 'par'
retistruct : version.string: no visible global function definition for
  'packageDescription'
retistruct: no visible global function definition for 'dev.cur'
retistruct.batch: no visible global function definition for 'write.csv'
retistruct.batch.analyse.summary: no visible global function definition
  for 'read.csv'
retistruct.batch.analyse.summary: no visible global function definition
  for 'na.omit'
retistruct.batch.analyse.summary: no visible global function definition
  for 'sd'
retistruct.batch.analyse.summary: no visible global function definition
  for 'dev.new'
retistruct.batch.analyse.summary: no visible global function definition
  for 'par'
retistruct.batch.analyse.summary: no visible global function definition
  for 'hist'
retistruct.batch.analyse.summary: no visible global function definition
  for 'axis'
retistruct.batch.analyse.summary: no visible global function definition
  for 'mtext'
retistruct.batch.analyse.summary: no visible global function definition
  for 'dev.print'
retistruct.batch.analyse.summary: no visible binding for global
  variable 'svg'
retistruct.batch.analyse.summary: no visible global function definition
  for 'lm'
retistruct.batch.analyse.summary: no visible global function definition
  for 'abline'
retistruct.batch.analyse.summary: no visible global function definition
  for 'boxplot'
retistruct.batch.analyse.summary: no visible global function definition
  for 'dev.copy2pdf'
retistruct.batch.plot.ods: no visible global function definition for
  'na.omit'
retistruct.batch.plot.titrations: no visible global function definition
  for 'par'
retistruct.batch.plot.titrations: no visible global function definition
  for 'plot'
retistruct.batch.plot.titrations: no visible global function definition
  for 'lines'
retistruct.batch.plot.titrations: no visible global function definition
  for 'mtext'
retistruct.batch.plot.titrations: no visible global function definition
  for 'dev.copy2pdf'
retistruct.batch.plot.titrations: no visible global function definition
  for 'svg'
retistruct.batch.plot.titrations: no visible global function definition
  for 'abline'
retistruct.batch.plot.titrations: no visible global function definition
  for 'dev.off'
retistruct.cli.figure: no visible binding for global variable 'pdf'
retistruct.cli.figure: no visible binding for global variable 'png'
retistruct.cli.figure: no visible binding for global variable 'jpeg'
retistruct.cli.figure: no visible binding for global variable 'tiff'
retistruct.cli.figure: no visible global function definition for 'par'
retistruct.cli.figure: no visible global function definition for
  'title'
retistruct.cli.figure: no visible global function definition for
  'dev.off'
retistruct.export.matlab: no visible global function definition for
  'na.omit'
retistruct.read.markup: no visible global function definition for
  'read.csv'
simplify.outline: no visible global function definition for 'segments'
simplify.outline: no visible global function definition for 'points'
solveMappingCart: no visible global function definition for 'dev.set'
strain.colours: no visible global function definition for 'palette'
strain.colours: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  abline aggregate as.raster axis boxplot contourLines dev.copy2pdf
  dev.cur dev.new dev.off dev.print dev.set dist hist identify
  install.packages jpeg lines lm mtext na.omit optim optimise
  packageDescription palette par pdf plot plot.new png points polygon
  rainbow read.csv sd segments svg text tiff title write.csv
Consider adding
  importFrom("grDevices", "as.raster", "contourLines", "dev.copy2pdf",
             "dev.cur", "dev.new", "dev.off", "dev.print", "dev.set",
             "jpeg", "palette", "pdf", "png", "rainbow", "svg", "tiff")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "identify",
             "lines", "mtext", "par", "plot", "plot.new", "points",
             "polygon", "segments", "text", "title")
  importFrom("stats", "aggregate", "dist", "lm", "na.omit", "optim",
             "optimise", "sd")
  importFrom("utils", "install.packages", "packageDescription",
             "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'getFuns.R'
  Comparing 'getFuns.Rout' to 'getFuns.Rout.save' ... OK
  Running 'ijroi-format.R'
  Comparing 'ijroi-format.Rout' to 'ijroi-format.Rout.save' ... OK
  Running 'reconstruct.R'
Warning message:
running command '"R:/lib/R/R-PATC~1/bin/i386/R" CMD BATCH --vanilla  "reconstruct.R" "reconstruct.Rout"' had status 1 
 ERROR
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
        k =   34 ; sb/Sb = 0 ; sb = 0
        k =  414 ; sb/Sb = 0.60237132329825 ; sb = 387.816744112795
        Creating new point: f = 0.830052794117553
  Triangulating...
  Internal error in finddirection():  Unable to find a
    triangle leading from (-195.467775468, 4725.74636175) to  (192.266112266, 4832.37318087).
    Please report this bug to jrs@cs.berkeley.edu
    Include the message above, your input data set, and the exact
      command line you used to run Triangle.
  Error in RTriangle::triangulate(RTriangle::pslg(P = out$P, S = out$S[out$SB ==  : 
    Triangle exit, code $i
  Calls: retistruct.reconstruct ... ReconstructedOutline -> TriangulatedOutline ->  -> .Call
  Execution halted
** running tests for arch 'x64' ...
  Running 'getFuns.R'
  Comparing 'getFuns.Rout' to 'getFuns.Rout.save' ... OK
  Running 'ijroi-format.R'
  Comparing 'ijroi-format.Rout' to 'ijroi-format.Rout.save' ... OK
  Running 'reconstruct.R' [30s]
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'R:/run/building/build_2016-08-30-17-23/RF_PKG_CHECK/PKGS/retistruct.Rcheck/00check.log'
for details.

Run time: 117.9 seconds.