* using log directory 'd:/RCompile/CRANincoming/R-devel/ETRep.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ETRep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ETRep' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Mohsen Taheri Shalmani <MohsenTaheriShalmani@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  ETRep (8:573, 8:656)
  ETReps (3:38, 8:65)
  Mohsen (8:159)
  Pizer (8:170)
  RCC (4:30, 8:446)
  Taheri (8:151)
  rn (8:202)

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Reference'

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mohsen", "Taheri"),
                    family = "Shalmani",
                    role = c("aut", "cre"),
                    email = "mohsentaherishalmani@gmail.com")
as necessary.
* 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 'ETRep' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Warning: replacing previous import 'shapes::tr' by 'matlib::tr' when loading 'ETRep'
  Warning: replacing previous import 'rgl::GramSchmidt' by 'matlib::GramSchmidt' when loading 'ETRep'
  Warning: replacing previous import 'rgl::mtext3d' by 'plotrix::mtext3d' when loading 'ETRep'
  Warning: replacing previous import 'matlib::getYmult' by 'plotrix::getYmult' when loading 'ETRep'
  Warning: replacing previous import 'matlib::vec' by 'Directional::vec' when loading 'ETRep'
  Warning: replacing previous import 'plotrix::color.scale' by 'fields::color.scale' when loading 'ETRep'
  Warning: replacing previous import 'matlib::inv' by 'pracma::inv' when loading 'ETRep'
  Warning: replacing previous import 'shapes::repmat' by 'pracma::repmat' when loading 'ETRep'
  Warning: replacing previous import 'Matrix::expm' by 'pracma::expm' when loading 'ETRep'
  Warning: replacing previous import 'matlib::angle' by 'pracma::angle' when loading 'ETRep'
  Warning: replacing previous import 'shapes::mod' by 'pracma::mod' when loading 'ETRep'
  Warning: replacing previous import 'Matrix::lu' by 'pracma::lu' when loading 'ETRep'
  Warning: replacing previous import 'Matrix::tril' by 'pracma::tril' when loading 'ETRep'
  Warning: replacing previous import 'Matrix::triu' by 'pracma::triu' when loading 'ETRep'
  Warning: replacing previous import 'doBy::taylor' by 'pracma::taylor' when loading 'ETRep'
  Warning: replacing previous import 'shapes::select' by 'dplyr::select' when loading 'ETRep'
  Warning: replacing previous import 'doBy::order_by' by 'dplyr::order_by' when loading 'ETRep'
See 'd:/RCompile/CRANincoming/R-devel/ETRep.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  'cran-comments.md'
* 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 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 ... [32s] NOTE
HotellingT2: no visible global function definition for 'cov'
HotellingT2: no visible global function definition for 'pf'
MahalanobisDistance: no visible global function definition for 'cov'
MahalanobisDistance_1D: no visible global function definition for 'var'
curvatureOf3Points: no visible global function definition for 'pip2d'
fisher.method: no visible global function definition for 'pchisq'
intersectionPointsBetween2Ellipses_In3D: no visible global function
  definition for 'rayTriangleIntersection'
meanDifferenceTest1D: no visible global function definition for
  't.test'
plot_Elliptical_Tube: no visible global function definition for
  'pvalue_to_color'
randS2: no visible global function definition for 'rnorm'
randVonMises: no visible global function definition for 'runif'
randomPointOnTriangle: no visible global function definition for
  'runif'
simulate_etube: no visible global function definition for 'runif'
simulate_etube: no visible global function definition for
  'colorRampPalette'
splineFitWithEquidistancePoints: no visible global function definition
  for 'lm'
splineFitWithEquidistancePoints: no visible global function definition
  for 'predict'
splineFitWithEquidistancePoints : distanceBetween2PointsOnCurve: no
  visible global function definition for 'integrate'
splineFitWithEquidistancePoints: no visible global function definition
  for 'integrate'
tubeCrossSetionsIndicesWith_NonLocal_SelfIntersections: no visible
  global function definition for 'txtProgressBar'
tubeCrossSetionsIndicesWith_NonLocal_SelfIntersections: no visible
  global function definition for 'setTxtProgressBar'
verticesNormals_mesh2D: no visible global function definition for
  'pip2d'
Undefined global functions or variables:
  colorRampPalette cov integrate lm pchisq pf pip2d predict
  pvalue_to_color rayTriangleIntersection rnorm runif setTxtProgressBar
  t.test txtProgressBar var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "cov", "integrate", "lm", "pchisq", "pf",
             "predict", "rnorm", "runif", "t.test", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'create_Elliptical_Tube.Rd':
  \examples lines wider than 100 characters:
      plot_Elliptical_Tube(e_tube = tube,plot_frames = FALSE,plot_skeletal_sheet = TRUE,plot_r_project = FALSE,plot_r_max = FALSE,add = FALS ... [TRUNCATED]

Rd file 'intrinsic_Transformation_Elliptical_Tubes.Rd':
  \examples lines wider than 100 characters:
     transformation_Tubes<-nonIntrinsic_Transformation_Elliptical_Tubes(tube1 = tube_A, tube2 = tube_B, numberOfSteps = numberOfSteps , plot ... [TRUNCATED]
       plot_Elliptical_Tube(e_tube = transformation_Tubes[[i]],plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r ... [TRUNCATED]

Rd file 'intrinsic_mean_tube.Rd':
  \examples lines wider than 100 characters:
     plot_Elliptical_Tube(e_tube = intrinsic_mean,plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r_max = FALSE, ... [TRUNCATED]
     plot_Elliptical_Tube(e_tube = intrinsic_mean,plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r_max = FALSE, ... [TRUNCATED]

Rd file 'nonIntrinsic_Transformation_Elliptical_Tubes.Rd':
  \examples lines wider than 100 characters:
     transformation_Tubes<-intrinsic_Transformation_Elliptical_Tubes(tube1 = tube_A, tube2 = tube_B, numberOfSteps = numberOfSteps , plottin ... [TRUNCATED]
       plot_Elliptical_Tube(e_tube = transformation_Tubes[[i]],plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r ... [TRUNCATED]

Rd file 'nonIntrinsic_mean_tube.Rd':
  \examples lines wider than 100 characters:
     plot_Elliptical_Tube(e_tube = nonIntrinsic_mean,plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r_max = FAL ... [TRUNCATED]
     plot_Elliptical_Tube(e_tube = nonIntrinsic_mean,plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r_max = FAL ... [TRUNCATED]

Rd file 'simulate_etube.Rd':
  \examples lines wider than 100 characters:
     random_Tubes<-simulate_etube(referenceTube = colon3D, numberOfSimulation = numberOfSimulation, sd_v = sd_v, sd_psi = sd_psi, sd_x = sd_ ... [TRUNCATED]
       plot_Elliptical_Tube(e_tube = random_Tubes[[i]],plot_frames = FALSE,plot_skeletal_sheet = FALSE,plot_r_project = FALSE,plot_r_max = F ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HotellingT2' 'MahalanobisDistance' 'MahalanobisDistance_1D'
  'PyramidGenerator' 'allAdjacentVertices2D' 'cartesian_to_spherical'
  'clockwiseAngle' 'convertMatrixIn6DHyperbola2Tube'
  'convertVec2unitVec' 'convertVec2unitVec2'
  'convert_v_to_TangentVector' 'curvatureOf3Points'
  'discretePathBetween2PointsIn_6D_Hyperbola'
  'distanceOfaPoint2aLine_2D' 'drawCircleOnUnitSphere' 'drawCircleS2'
  'ellipse_Radius_InPolarCoordinate' 'ellipsoidGenerator_2D'
  'ellipsoidGenerator_2D_2' 'fisher.method'
  'fitRadialVectorsModelBasedOnParallelSlicing' 'frechetMean'
  'frenetFrame3Dcurve' 'generatePointsBetween2Points'
  'generatePointsBetween2Points2' 'generatePointsBetween3Points'
  'generateSpheresBetween2Points_2D' 'geodesic2D_of2Vertices'
  'geodesicDistance' 'geodesicPathOnUnitSphere'
  'intersectionOfALineWithAPlane'
  'intersectionPointsBetween2Ellipses_In3D'
  'intrinsic_Distance_Between2tubes' 'isOnLineSegment'
  'linesegmentsIntersection' 'makeSphereMesh'
  'map6DcylinderTo6Dhyperbola' 'map6DhyperbolaTo6Dcylinder'
  'meanDifferenceTest1D' 'meanDifferenceTestMultivariate'
  'myCrossProduct' 'myNorm' 'nonIntrinsic_Distance_Between2tubes'
  'nonIntrinsic_Transformation_Elliptical_Tubes_Without_SelfIntersection'
  'normalOfaVertex' 'normalOfaVertex2' 'permutation1D'
  'permutationMultivariate' 'plotProcTube' 'randS2' 'randVonMises'
  'randomPointOnTriangle' 'rotateFrameToMainAxesAndRotateBack_standard'
  'rotateFrameToMainAxes_standard' 'rotationAboutXYZaxis'
  'rotationAbout_uAxis_byThetaAngle' 'sortIndices' 'sphereGenerator_2D'
  'spherical_to_cartesian' 'splineFitWithEquidistancePoints'
  'starConvexSetGenerator_2D' 'sumOfSquaredDistances' 'triangleArea'
  'triangleGenerator' 'tube2vectorsIn6DCylinder'
  'tube2vectorsIn6DHyperbola'
  'tubeCrossSetionsIndicesWith_NonLocal_SelfIntersections'
  'unitNormalOfTriangle' 'urchinInterpolation_2D'
  'verticesNormals_mesh2D'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ETRepSize.Rd'
  'tube'

Undocumented arguments in Rd file 'calculate_r_project_Length.Rd'
  'a' 'b' 'theta'

Undocumented arguments in Rd file 'calculate_theta.Rd'
  'materialFrameBasedOnParent' 'tolerance'

Undocumented arguments in Rd file 'create_Elliptical_Tube.Rd'
  'initialFrame' 'initialPoint' 'add'

Undocumented arguments in Rd file 'intrinsic_Transformation_Elliptical_Tubes.Rd'
  'type' 'colorBoundary'

Undocumented arguments in Rd file 'nonIntrinsic_Transformation_Elliptical_Tubes.Rd'
  'tube1' 'tube2' 'type' 'numberOfSteps' 'plotting' 'colorBoundary'
  'add'

Undocumented arguments in Rd file 'plot_Elliptical_Tube.Rd'
  'e_tube' 'plot_spine' 'plot_normal_vec' 'plot_skeletal_sheet'
  'decorate' 'colSkeletalSheet' 'colorBoundary'
  'userMatrix4plotOrientation' 'plotSignificantFeatures' 'p_values_v'
  'p_values_psi' 'p_values_x' 'p_values_a' 'p_values_b'
  'lwdSignificant' 'add' 'mainTitle'
Documented arguments not in \usage in Rd file 'plot_Elliptical_Tube.Rd':
  'tube'

Undocumented arguments in Rd file 'scaleETRepToHaveTheSizeAsOne.Rd'
  'tube' 'plotting'

Undocumented arguments in Rd file 'simulate_etube.Rd'
  'sd_psi' 'sd_x' 'sd_a' 'sd_b'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                      old_size new_size compress
  colon3D.rda            174Kb    152Kb       xz
  simulatedColons.rda    1.2Mb    759Kb       xz
  tube_A.rda             160Kb     94Kb       xz
  tube_B.rda             200Kb    128Kb       xz
* checking examples ... [27s] OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 WARNINGs, 4 NOTEs