* using log directory 'd:/Rcompile/CRANpkg/local/3.3/OligoSpecificitySystem.Rcheck' * using R version 3.3.2 (2016-10-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'OligoSpecificitySystem/DESCRIPTION' ... OK * this is package 'OligoSpecificitySystem' version '1.3' * 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 'OligoSpecificitySystem' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 * 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 calc2: warning in matrix(nr = 1, nc = 3): partial argument match of 'nr' to 'nrow' calc2: warning in matrix(nr = 1, nc = 3): partial argument match of 'nc' to 'ncol' calc3: warning in matrix(nr = 1, nc = 7): partial argument match of 'nr' to 'nrow' calc3: warning in matrix(nr = 1, nc = 7): partial argument match of 'nc' to 'ncol' OSS: no visible binding for '<<-' assignment to 'ONDB1name' OSS: no visible binding for '<<-' assignment to 'ONDB2name' OSS: no visible binding for '<<-' assignment to 'ONDB3name' OSS: no visible binding for '<<-' assignment to 'ONDB4name' OSS : .write: no visible binding for global variable 'ONDB1name' OSS : .write: no visible binding for global variable 'ONDB2name' OSS : .write: no visible binding for global variable 'ONDB3name' OSS : .write: no visible binding for global variable 'ONDB4name' OSS : run: no visible binding for global variable 'txt' OSS : example1: no visible binding for '<<-' assignment to 'ONDB1name' OSS : example1: no visible binding for global variable 'fil' OSS : example1: no visible binding for global variable 'separator' OSS : example2: no visible binding for '<<-' assignment to 'ONDB2name' OSS : example2: no visible binding for global variable 'fil' OSS : example2: no visible binding for global variable 'separator' OSS : example3: no visible binding for '<<-' assignment to 'ONDB3name' OSS : example3: no visible binding for global variable 'fil' OSS : example3: no visible binding for global variable 'separator' OSS : reset1: no visible binding for '<<-' assignment to 'ONDB1name' OSS : reset2: no visible binding for '<<-' assignment to 'ONDB2name' OSS : reset3: no visible binding for '<<-' assignment to 'ONDB3name' OSS : reset4: no visible binding for '<<-' assignment to 'ONDB4name' OSS : OnOk: no visible binding for global variable 'Name' OSS : OnOk: no visible binding for global variable 'Namenbseq' OSS : calc: no visible binding for global variable 'txt4' OSS : calc: no visible binding for global variable 'txt3' OSS : dprim: no visible binding for global variable 'txt4' OSS : dprim: no visible binding for global variable 'txt3' OSS : effic: no visible binding for global variable 'txt4' OSS : effic: no visible binding for global variable 'txt3' OSS : impr: no visible binding for global variable 'txt4' OSS : impr: no visible binding for global variable 'txt3' OSS: no visible binding for '<<-' assignment to 'Name' OSS: no visible binding for global variable 'Name' OSS: no visible binding for '<<-' assignment to 'Namenbseq' OSS: no visible binding for global variable 'Namenbseq' OnOk: no visible binding for global variable 'Name' OnOk: no visible binding for global variable 'Namenbseq' calc2: no visible binding for global variable 'txt1' calc2: no visible binding for global variable 'txt2' calc3: no visible binding for global variable 'txt1' calc3: no visible binding for global variable 'txt2' calc3: no visible binding for global variable 'txt3' concatenate: no visible binding for global variable 'txt3' concatenate: no visible binding for global variable 'txt4' concatenate: no visible binding for global variable 'txt1' concatenate: no visible binding for global variable 'txt2' concatenate : calc: no visible binding for '<<-' assignment to 'txt1' concatenate : calc: no visible binding for '<<-' assignment to 'txt2' concatenate : calc: no visible binding for '<<-' assignment to 'txt3' concatenate : calc: no visible binding for '<<-' assignment to 'ONDB1name' concatenate : calc: no visible binding for '<<-' assignment to 'ONDB2name' concatenate : calc: no visible binding for '<<-' assignment to 'ONDB3name' dbb1: no visible global function definition for 'choose.files' dbb1: no visible binding for global variable 'Filters' dbb1: no visible binding for '<<-' assignment to 'ONDB1name' dbb1: no visible binding for global variable 'separator' dbb1: no visible global function definition for 'dev.off' dbb2: no visible global function definition for 'choose.files' dbb2: no visible binding for global variable 'Filters' dbb2: no visible binding for '<<-' assignment to 'ONDB2name' dbb2: no visible binding for global variable 'separator' dbb2: no visible global function definition for 'dev.off' dbb3: no visible global function definition for 'choose.files' dbb3: no visible binding for global variable 'Filters' dbb3: no visible binding for '<<-' assignment to 'ONDB3name' dbb3: no visible binding for global variable 'separator' dbb3: no visible global function definition for 'dev.off' dbb4: no visible global function definition for 'choose.dir' dbb4: no visible binding for global variable 'separator' dbb4: no visible global function definition for 'dev.off' dbb4: no visible binding for global variable 'txt1' dbb4: no visible binding for global variable 'txt2' dbb4: no visible binding for global variable 'txt3' dbb4: no visible binding for '<<-' assignment to 'ONDB4name' degencal2 : temp: no visible global function definition for 'symbols' degencal2 : temp: no visible global function definition for 'text' degencal2 : temp: no visible binding for global variable 'nbsequence' degencal2 : temp: no visible binding for global variable 'zz1' degencal3 : temp: no visible global function definition for 'symbols' degencal3 : temp: no visible global function definition for 'text' degencal3 : temp: no visible binding for global variable 'nbsequence' degencal3 : temp: no visible binding for global variable 'zz1' degencal4: no visible binding for global variable 'txt1' degencal4: no visible binding for global variable 'txt2' degencal4: no visible binding for global variable 'txt3' degencal4: no visible binding for global variable 'txt4' degencal4: no visible binding for global variable 'nbsequence' exportglobal: no visible binding for global variable 'txt1' exportglobal: no visible binding for global variable 'txt2' exportglobal: no visible binding for global variable 'txt3' exportglobal: no visible binding for global variable 'newdb' glob2d : temp: no visible global function definition for 'symbols' glob2d : temp: no visible global function definition for 'text' glob2d : temp : normal_prct: no visible global function definition for 'text' glob2d : temp : normal_prct: no visible binding for global variable 'zz1' glob2d : temp : normal_prct: no visible binding for global variable 'nbsequence' glob2d : temp : normal: no visible global function definition for 'text' glob2d : temp : normal: no visible binding for global variable 'zz1' glob2d : temp: no visible binding for global variable 'nbsequence' glob3d : temp: no visible global function definition for 'symbols' glob3d : temp: no visible global function definition for 'text' glob3d : temp : normal: no visible global function definition for 'text' glob3d : temp : normal: no visible binding for global variable 'zz1' glob3d : temp : normal_prct: no visible global function definition for 'text' glob3d : temp : normal_prct: no visible binding for global variable 'zz1' glob3d : temp : normal_prct: no visible binding for global variable 'nbsequence' glob3d : temp: no visible binding for global variable 'nbsequence' impr2d : temp: no visible global function definition for 'symbols' impr2d : temp: no visible global function definition for 'text' impr2d : temp: no visible binding for global variable 'nbsequence' impr2d : temp: no visible binding for global variable 'zz1' impr3d : temp: no visible global function definition for 'symbols' impr3d : temp: no visible global function definition for 'text' impr3d : temp: no visible binding for global variable 'nbsequence' impr3d : temp: no visible binding for global variable 'zz1' optxt: no visible binding for '<<-' assignment to 'fil' optxt: no visible binding for global variable 'bg' pcrcal2 : temp: no visible binding for global variable 'zz1' pcrcal2 : temp: no visible global function definition for 'symbols' pcrcal2 : temp: no visible global function definition for 'text' pcrcal2 : temp : normal: no visible global function definition for 'text' pcrcal2 : temp : normal_prct: no visible global function definition for 'text' pcrcal2 : temp : normal_prct: no visible binding for global variable 'nbsequence' pcrcal2 : temp: no visible binding for global variable 'nbsequence' pcrcal3 : temp: no visible global function definition for 'symbols' pcrcal3 : temp: no visible global function definition for 'text' pcrcal3 : temp: no visible binding for global variable 'nbsequence' pcrcal3 : temp: no visible binding for global variable 'zz1' pcrcal4: no visible binding for global variable 'myfiles' pcrcal4: no visible binding for global variable 'txt1' pcrcal4: no visible binding for global variable 'txt2' pcrcal4: no visible binding for global variable 'txt3' pcrcal4: no visible binding for global variable 'txt4' pcrcal4: no visible binding for global variable 'nbsequence' security: no visible binding for global variable 'txt4' security: no visible binding for global variable 'txt1' security: no visible binding for global variable 'txt2' security: no visible binding for global variable 'txt3' waitGUI : temp: no visible global function definition for 'plot' waitGUI : temp: no visible global function definition for 'segments' waitGUI : temp: no visible global function definition for 'text' waitGUI: no visible binding for '<<-' assignment to 'z' waitGUI: no visible binding for global variable 'z' Undefined global functions or variables: Filters Name Namenbseq ONDB1name ONDB2name ONDB3name ONDB4name bg choose.dir choose.files dev.off fil myfiles nbsequence newdb plot segments separator symbols text txt txt1 txt2 txt3 txt4 z zz1 Consider adding importFrom("grDevices", "dev.off") importFrom("graphics", "plot", "segments", "symbols", "text") importFrom("utils", "Filters", "choose.dir", "choose.files") to your NAMESPACE file. * 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking examples ... [0s] OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs