* using log directory 'd:/Rcompile/CRANpkg/local/3.0/FTICRMS.Rcheck' * using R version 3.0.3 (2014-03-06) * using platform: i386-w64-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'FTICRMS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FTICRMS' version '0.8' * 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 'FTICRMS' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'Matrix' 'splines' Please remove these calls from your code. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .alignment: warning in lm(Y ~ X, dat = fr): partial argument match of 'dat' to 'data' .alignment: warning in lm(as.formula(form), dat = fr): partial argument match of 'dat' to 'data' display.tests: no visible binding for global variable 'parameter.list' display.tests: no visible binding for global variable 'sigs' display.tests: no visible binding for global variable 'clust.mat' display.tests : : no visible binding for global variable 'clust.mat' display.tests : : no visible binding for global variable 'parameter.list' run.analysis: no visible binding for global variable 'centers' run.cluster.matrix: no visible binding for global variable 'amps' run.cluster.matrix: no visible binding for global variable 'clust.constant' run.cluster.matrix: no visible binding for global variable 'spect.base' run.lrg.peaks: no visible binding for global variable 'spect.base' * checking Rd files ... NOTE prepare_Rd: baseline.Rd:123: Dropping empty section \examples prepare_Rd: display.tests.Rd:43: Dropping empty section \references prepare_Rd: display.tests.Rd:57: Dropping empty section \examples prepare_Rd: extract.pars.Rd:114: Dropping empty section \examples prepare_Rd: locate.peaks.Rd:72: Dropping empty section \examples prepare_Rd: make.par.file.Rd:117: Dropping empty section \examples prepare_Rd: run.all.Rd:76: Dropping empty section \examples prepare_Rd: run.analysis.Rd:153: Dropping empty section \examples prepare_Rd: run.baselines.Rd:91: Dropping empty section \examples prepare_Rd: run.cluster.matrix.Rd:171: Dropping empty section \examples prepare_Rd: run.lrg.peaks.Rd:95: Dropping empty section \examples prepare_Rd: run.peaks.Rd:99: Dropping empty section \examples prepare_Rd: run.strong.peaks.Rd:115: Dropping empty section \examples * 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 examples ... NONE * checking PDF version of manual ... OK NOTE: There were 3 notes.