Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility, Result: NOTE Maintainer: 'Yuliang Li ' New submission Non-FOSS package license (Johns Hopkins University) Possibly mis-spelled words in DESCRIPTION: BAREB (3:8, 9:220, 9:380) Biclustering (3:36) DPP (9:264) biclustering (9:35) biclusters (9:311) determinantal (9:235) faciliate (9:325) interpretability (9:349) The Title field starts with the package name. Size of tarball: 15969613 bytes Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: package dependencies, Result: NOTE Package in Depends/Imports which should probably only be in LinkingTo: 'RcppArmadillo' Flavor: r-devel-windows-ix86+x86_64 Check: DESCRIPTION meta-information, Result: WARNING Non-standard license specification: Johns Hopkins University Standardizable: FALSE Flavor: r-devel-windows-ix86+x86_64 Check: top-level files, Result: NOTE Non-standard files/directories found at top level: 'BAREB_1.0.pdf' 'gfortran-4.8.2-darwin13.tar.bz2' Flavor: r-devel-windows-ix86+x86_64 Check: S3 generic/method consistency, Result: WARNING update: function(object, ...) update.theta.beta: function(theta, tau, Beta, sig) update: function(object, ...) update.theta.gamma: function(theta, tau, Gamma, S, Ds, sig) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. Found the following apparent S3 methods exported but not registered: update.theta.beta update.theta.gamma See section 'Registering S3 methods' in the 'Writing R Extensions' manual. Flavor: r-devel-windows-ix86+x86_64 Check: R code for possible problems, Result: NOTE update.theta.beta: no visible global function definition for 'rnorm' update.theta.beta: no visible global function definition for 'dnorm' update.theta.beta: no visible global function definition for 'runif' update.theta.gamma: no visible global function definition for 'rnorm' update.theta.gamma: no visible global function definition for 'dnorm' update.theta.gamma: no visible global function definition for 'runif' update_RJ: no visible binding for global variable 'E' update_RJ: no visible binding for global variable 'tau' update_RJ: no visible binding for global variable 'm' update_RJ: no visible binding for global variable 'T0' update_sigma_squre: no visible global function definition for 'na.omit' update_sigma_squre: no visible global function definition for 'rgamma' update_w: no visible global function definition for 'rgamma' update_w_beta: no visible global function definition for 'rgamma' Undefined global functions or variables: E T0 dnorm m na.omit rgamma rnorm runif tau Consider adding importFrom("stats", "dnorm", "na.omit", "rgamma", "rnorm", "runif") to your NAMESPACE file. Flavor: r-devel-windows-ix86+x86_64 Check: Rd line widths, Result: NOTE Rd file 'updateBeta.Rd': \usage lines wider than 90 characters: updateBeta(X, Y, Z, delta, Beta, Gamma, E, R, S, Ds, mustar, mu, sigma, c, C, step, runif, n, m, T0, p, q, D, theta,tau) Rd file 'updateE.Rd': \usage lines wider than 90 characters: updateE( Beta, Gamma,w, X, Y, Z, delta,E, R, S, Ds, mu, mustar, sigma, c, n, m, T0, p, q, D) Rd file 'updateGamma.Rd': \usage lines wider than 90 characters: updateGamma(X, Y, Z, delta, Beta, Gamma, E, R, S, Ds, mu, mustar, sigma, c, step, runif, n, m, T0, p, q, D, theta,tau) Rd file 'updateR.Rd': \usage lines wider than 90 characters: updateR( w ,Gamma,Beta, Y, Z, delta, mu, mu_star, c, S, sigma_square, K, E, X, m,n, q, p, T0) Rd file 'update_w.Rd': \examples lines wider than 100 characters: #Suppose we know the number of patient level cluster is 2, one has 2 site level clusters and one has 3. Rd file 'update_w_beta.Rd': \examples lines wider than 100 characters: #Suppose the current clustering membership indicates 3 patients in cluster 1, 2 patients in cluster 2, 3 patinets in cluster 3, 1 patie ... [TRUNCATED] These lines will be truncated in the PDF manual. Flavor: r-devel-windows-ix86+x86_64 Check: for missing documentation entries, Result: WARNING Undocumented code objects: 'Merge' 'Merge_empty' 'Mergenomiss' 'RJi' 'RJi_empty' 'RJinomiss' 'Split' 'Split_empty' 'Splitnomiss' 'colsome' 'const' 'dmvnrm_arma' 'dmvnrm_arma0' 'getind' 'ind' 'ind1' 'likeli.theta' 'nonnan_ind' 'rmvnorm_row' 'rowsome' 'rtrun_norm' 'sample_int' 'subsome' 'ton' 'updateBetanoDPP' 'updateBetanomiss' 'updateEnomiss' 'updateGammanoDPP' 'updateGammanomiss' 'updateRi' 'updateRinomiss' 'updateRnoDPP' 'updateRnomiss' Undocumented data sets: 'Beta0' 'Gamma0' 'X' 'Y' 'Z' 'delta' 'truth' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. Flavor: r-devel-windows-ix86+x86_64 Check: compilation flags in Makevars, Result: WARNING Variables overriding user/site settings: CFLAGS: -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXXFLAGS: -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion Flavor: r-devel-windows-ix86+x86_64 Check: use of SHLIB_OPENMP_*FLAGS in Makefiles, Result: NOTE src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++ Use of these macros is discussed in sect 1.2.1.1 of 'Writing R Extensions'. The macros for different languages may differ so the matching macro must be used in PKG_CXXFLAGS (etc) and match that used in PKG_LIBS (except for Fortran: see the manual). Flavor: r-devel-windows-ix86+x86_64 Check: compiled code, Result: WARNING File 'BAREB/libs/i386/BAREB.dll': Found '_ZSt4cerr', possibly from 'std::cerr' (C++) Object: 'truncated_normal.o' Found '_ZSt4cout', possibly from 'std::cout' (C++) Object: 'truncated_normal.o' Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Object: 'truncated_normal.o' File 'BAREB/libs/x64/BAREB.dll': Found '_ZSt4cerr', possibly from 'std::cerr' (C++) Object: 'truncated_normal.o' Found '_ZSt4cout', possibly from 'std::cout' (C++) Object: 'truncated_normal.o' Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Object: 'truncated_normal.o' Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. See 'Writing portable packages' in the 'Writing R Extensions' manual. Flavor: r-devel-windows-ix86+x86_64 Check: running examples for arch 'i386', Result: NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed update_RJ 17.5 0.65 18.18 Flavor: r-devel-windows-ix86+x86_64 Check: running examples for arch 'x64', Result: NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed update_RJ 16.12 0.08 16.21 Flavor: r-devel-linux-x86_64-debian-gcc Check: if this is a source package, Result: WARNING Subdirectory 'src' contains: truncated_normal.hpp update8.o-a4f086ec These are unlikely file names for src files. Flavor: r-devel-linux-x86_64-debian-gcc Check: whether package can be installed, Result: ERROR Installation failed. See '/srv/hornik/tmp/CRAN/BAREB.Rcheck/00install.out' for details.