* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ETRep.Rcheck’ * using R Under development (unstable) (2024-10-26 r87273) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * 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 ... [3s/4s] NOTE Maintainer: ‘Mohsen Taheri Shalmani ’ New submission Possibly misspelled words in DESCRIPTION: ETRep (8:669, 8:752) ETReps (3:38, 8:65) Joarn (8:199) Mohsen (8:159, 8:298) Pizer (8:170) RCC (4:30, 8:542) Shalmani (8:312) Taheri (8:151, 8:305) UiS (8:341) * 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 ‘ETRep’ can be installed ... [17s/17s] 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 ‘/srv/hornik/tmp/CRAN_pretest/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 package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R Author: ‘Mohsen Taheri Shalmani ()’ Authors@R: ‘Mohsen Taheri [aut, cre]’ Maintainer field differs from that derived from Authors@R Maintainer: ‘Mohsen Taheri Shalmani ’ Authors@R: ‘Mohsen Taheri ’ * 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 ... [5s/5s] OK * checking whether the package can be loaded with stated dependencies ... [5s/5s] OK * checking whether the package can be unloaded cleanly ... [5s/5s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] 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 ... [25s/25s] 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 ... [0s/0s] 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 ... [0s/0s] 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 ... [47s/31s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed intrinsic_Transformation_Elliptical_Tubes 9.618 2.423 7.219 nonIntrinsic_Transformation_Elliptical_Tubes 8.935 2.636 6.840 simulate_etube 6.689 1.250 4.702 * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 5 NOTEs