* using log directory 'd:/Rcompile/CRANpkg/local/2.14/RAFM.Rcheck' * using R version 2.14.2 (2012-02-29) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'RAFM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RAFM' version '1.0' * 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 whether package 'RAFM' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level 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 for unstated 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 AFM: no visible binding for '<<-' assignment to 'epsilon' AFM: no visible binding for '<<-' assignment to 'nloci' AFM: no visible binding for '<<-' assignment to 'npop' AFM: no visible binding for '<<-' assignment to 'pAnc' AFM: no visible binding for '<<-' assignment to 'z' AFM: no visible binding for global variable 'npop' AFM: no visible binding for global variable 'nloci' AFM: no visible binding for '<<-' assignment to 'nal' AFM: no visible binding for global variable 'pAnc' AFM: no visible binding for global variable 'nal' AFM: no visible binding for global variable 'epsilon' AFM: no visible binding for global variable 'z' AFM: no visible binding for '<<-' assignment to 'kap' AFM: no visible binding for global variable 'kap' AFM: no visible binding for '<<-' assignment to 'propAnc' AFM: no visible binding for '<<-' assignment to 'propz' AFM: no visible binding for '<<-' assignment to 'propkap' AFM: no visible binding for '<<-' assignment to 'propalpha' AFM: no visible binding for '<<-' assignment to 'iterno' AFM: no visible binding for '<<-' assignment to 'prioralpha' AFM: no visible binding for '<<-' assignment to 'priorkap' AFM: no visible binding for global variable 'priorkap' AFM: no visible binding for '<<-' assignment to 'priorAnc' AFM: no visible binding for global variable 'priorAnc' AFM: no visible binding for '<<-' assignment to 'clike1' AFM: no visible binding for '<<-' assignment to 'clike2' AFM: no visible binding for '<<-' assignment to 'clike3' AFM: no visible binding for '<<-' assignment to 'clike4' AFM: no visible binding for '<<-' assignment to 'clike5' AFM: no visible binding for global variable 'clike1' AFM: no visible binding for global variable 'clike2' AFM: no visible binding for global variable 'clike5' AFM: no visible binding for global variable 'clike3' AFM: no visible binding for global variable 'prioralpha' AFM: no visible binding for global variable 'clike4' AFM: no visible binding for '<<-' assignment to 'acAnc' AFM: no visible binding for '<<-' assignment to 'acz' AFM: no visible binding for '<<-' assignment to 'ackap' AFM: no visible binding for '<<-' assignment to 'acalpha' AFM: no visible binding for global variable 'iterno' adjust.prop: no visible binding for '<<-' assignment to 'iterno' adjust.prop: no visible binding for global variable 'iterno' adjust.prop: no visible binding for '<<-' assignment to 'ackap' adjust.prop: no visible binding for global variable 'ackap' adjust.prop: no visible binding for '<<-' assignment to 'acAnc' adjust.prop: no visible binding for global variable 'acAnc' adjust.prop: no visible binding for '<<-' assignment to 'acz' adjust.prop: no visible binding for global variable 'acz' adjust.prop: no visible binding for '<<-' assignment to 'acalpha' adjust.prop: no visible binding for global variable 'acalpha' adjust.prop: no visible binding for '<<-' assignment to 'propkap' adjust.prop: no visible binding for global variable 'propkap' adjust.prop: no visible binding for '<<-' assignment to 'propAnc' adjust.prop: no visible binding for global variable 'propAnc' adjust.prop: no visible binding for '<<-' assignment to 'propz' adjust.prop: no visible binding for global variable 'propz' adjust.prop: no visible binding for '<<-' assignment to 'propalpha' adjust.prop: no visible binding for global variable 'propalpha' updatealpha: no visible binding for global variable 'npop' updatealpha: no visible binding for global variable 'logalpha' updatealpha: no visible binding for global variable 'propalpha' updatealpha: no visible binding for global variable 'clike3' updatealpha: no visible binding for global variable 'clike2' updatealpha: no visible binding for global variable 'prioralpha' updatealpha: no visible binding for global variable 'nloci' updatealpha: no visible binding for global variable 'z' updatealpha: no visible binding for global variable 'pAnc' updatealpha: no visible binding for global variable 'epsilon' updatealpha: no visible binding for '<<-' assignment to 'logalpha' updatealpha: no visible binding for '<<-' assignment to 'clike2' updatealpha: no visible binding for '<<-' assignment to 'clike3' updatealpha: no visible binding for '<<-' assignment to 'acalpha' updatealpha: no visible binding for global variable 'acalpha' updateanc: no visible binding for global variable 'nloci' updateanc: no visible binding for global variable 'clike1' updateanc: no visible binding for global variable 'clike2' updateanc: no visible binding for global variable 'pAnc' updateanc: no visible binding for global variable 'propAnc' updateanc: no visible binding for global variable 'epsilon' updateanc: no visible binding for global variable 'priorAnc' updateanc: no visible binding for global variable 'npop' updateanc: no visible binding for global variable 'z' updateanc: no visible binding for global variable 'logalpha' updateanc: no visible binding for '<<-' assignment to 'pAnc' updateanc: no visible binding for '<<-' assignment to 'clike1' updateanc: no visible binding for '<<-' assignment to 'clike2' updateanc: no visible binding for '<<-' assignment to 'acAnc' updateanc: no visible binding for global variable 'acAnc' updatekap: no visible binding for global variable 'npop' updatekap: no visible binding for global variable 'kap' updatekap: no visible binding for global variable 'propkap' updatekap: no visible binding for global variable 'epsilon' updatekap: no visible binding for global variable 'clike4' updatekap: no visible binding for global variable 'clike5' updatekap: no visible binding for global variable 'priorkap' updatekap: no visible binding for global variable 'nloci' updatekap: no visible binding for global variable 'z' updatekap: no visible binding for '<<-' assignment to 'kap' updatekap: no visible binding for '<<-' assignment to 'clike4' updatekap: no visible binding for '<<-' assignment to 'clike5' updatekap: no visible binding for '<<-' assignment to 'ackap' updatekap: no visible binding for global variable 'ackap' updatez: no visible binding for global variable 'nloci' updatez: no visible binding for global variable 'npop' updatez: no visible binding for global variable 'clike2' updatez: no visible binding for global variable 'clike5' updatez: no visible binding for global variable 'z' updatez: no visible binding for global variable 'propz' updatez: no visible binding for global variable 'epsilon' updatez: no visible binding for global variable 'logalpha' updatez: no visible binding for global variable 'pAnc' updatez: no visible binding for global variable 'kap' updatez: no visible binding for '<<-' assignment to 'z' updatez: no visible binding for '<<-' assignment to 'clike2' updatez: no visible binding for '<<-' assignment to 'clike5' updatez: no visible binding for '<<-' assignment to 'acz' updatez: no visible binding for global variable 'acz' * checking Rd files ... OK * checking Rd metadata ... 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 ... OK * checking PDF version of manual ... OK