* using log directory 'd:/Rcompile/CRANpkg/local/2.6/JM.Rcheck' * using R version 2.6.2 (2008-02-08) * checking for file 'JM/DESCRIPTION' ... OK * this is package 'JM' version '0.2-0' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'JM' can be installed ... 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 name space can be loaded with stated dependencies ... 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 HessLongPH: no visible binding for global variable 'XtX' HessLongPH: no visible binding for global variable 'sigma' HessLongPH: no visible binding for global variable 'ncx' HessLongPH: no visible binding for global variable 'lambda0.' HessLongPH: no visible binding for global variable 'alpha' HessLongPH: no visible binding for global variable 'indT' HessLongPH: no visible binding for global variable 'p.byt.' HessLongPH: no visible binding for global variable 'wGH' HessSurvPH: no visible binding for global variable 'indT' HessSurvPH: no visible binding for global variable 'ncww' HessSurvPH: no visible binding for global variable 'lambda0.' HessSurvPH: no visible binding for global variable 'p.byt.' HessSurvPH: no visible binding for global variable 'wGH' LogLik.chGH: no visible binding for global variable 'ncx' LogLik.chGH: no visible binding for global variable 'ncww' LogLik.chGH: no visible binding for global variable 'nk' LogLik.chGH: no visible binding for global variable 'diag.D' LogLik.chGH: no visible binding for global variable 'X' LogLik.chGH: no visible binding for global variable 'Xtime' LogLik.chGH: no visible binding for global variable 'WW' LogLik.chGH: no visible binding for global variable 'Ztime.b' LogLik.chGH: no visible binding for global variable 'Ztb' LogLik.chGH: no visible binding for global variable 'y' LogLik.chGH: no visible binding for global variable 'id' LogLik.chGH: no visible binding for global variable 'S' LogLik.chGH: no visible binding for global variable 'd' LogLik.chGH: no visible binding for global variable 'logT' LogLik.chGH: no visible binding for global variable 'ncz' LogLik.chGH: no visible binding for global variable 'b' LogLik.chGH: no visible binding for global variable 'k' LogLik.chGH: no visible binding for global variable 'n' LogLik.chGH: no visible binding for global variable 'wGH' LogLik.chLaplace: no visible binding for global variable 'ncx' LogLik.chLaplace: no visible binding for global variable 'ncww' LogLik.chLaplace: no visible binding for global variable 'nk' LogLik.chLaplace: no visible binding for global variable 'diag.D' LogLik.chLaplace: no visible binding for global variable 'hes.b' LogLik.phGH: no visible binding for global variable 'ncx' LogLik.phGH: no visible binding for global variable 'ncww' LogLik.phGH: no visible binding for global variable 'diag.D' LogLik.phGH: no visible binding for global variable 'X' LogLik.phGH: no visible binding for global variable 'Xtime' LogLik.phGH: no visible binding for global variable 'Xtime2' LogLik.phGH: no visible binding for global variable 'Ztime.b' LogLik.phGH: no visible binding for global variable 'Ztime2.b' LogLik.phGH: no visible binding for global variable 'WW' LogLik.phGH: no visible binding for global variable 'indT' LogLik.phGH: no visible binding for global variable 'd' LogLik.phGH: no visible binding for global variable 'lambda0' LogLik.phGH: no visible binding for global variable 'ind.T0' LogLik.phGH: no visible binding for global variable 'Ztb' LogLik.phGH: no visible binding for global variable 'y' LogLik.phGH: no visible binding for global variable 'id' LogLik.phGH: no visible binding for global variable 'ind0' LogLik.phGH: no visible binding for global variable 'ind.lenN0' LogLik.phGH: no visible binding for global variable 'ind.lambda' LogLik.phGH: no visible binding for global variable 'ncz' LogLik.phGH: no visible binding for global variable 'b' LogLik.phGH: no visible binding for global variable 'k' LogLik.phGH: no visible binding for global variable 'n' LogLik.phGH: no visible binding for global variable 'wGH' LogLik.weibullGH: no visible binding for global variable 'ncx' LogLik.weibullGH: no visible binding for global variable 'ncww' LogLik.weibullGH: no visible binding for global variable 'diag.D' LogLik.weibullGH: no visible binding for global variable 'X' LogLik.weibullGH: no visible binding for global variable 'Xtime' LogLik.weibullGH: no visible binding for global variable 'WW' LogLik.weibullGH: no visible binding for global variable 'Ztime.b' LogLik.weibullGH: no visible binding for global variable 'Ztb' LogLik.weibullGH: no visible binding for global variable 'y' LogLik.weibullGH: no visible binding for global variable 'id' LogLik.weibullGH: no visible binding for global variable 'logT' LogLik.weibullGH: no visible binding for global variable 'd' LogLik.weibullGH: no visible binding for global variable 'ncz' LogLik.weibullGH: no visible binding for global variable 'b' LogLik.weibullGH: no visible binding for global variable 'k' LogLik.weibullGH: no visible binding for global variable 'n' LogLik.weibullGH: no visible binding for global variable 'wGH' MI.fixed.times: no visible binding for global variable 'obs.times' MI.fixed.times: no visible binding for global variable 'id' MI.fixed.times: no visible binding for global variable 'y' MI.fixed.times: no visible binding for global variable 'logT' MI.fixed.times: no visible binding for global variable 'd' MI.fixed.times: no visible binding for global variable 'X' MI.fixed.times: no visible binding for global variable 'Z' MI.fixed.times: no visible binding for global variable 'Xtime' MI.fixed.times: no visible binding for global variable 'Ztime' MI.fixed.times: no visible binding for global variable 'WW' MI.fixed.times: no visible binding for global variable 'object' MI.fixed.times: no visible binding for global variable 'ncz' MI.fixed.times: no visible binding for global variable 'nk' MI.fixed.times: no visible binding for global variable 'type' MI.fixed.times: no visible binding for global variable 'M' MI.fixed.times: no visible binding for global variable 'ncx' MI.fixed.times: no visible binding for global variable 'ncww' MI.fixed.times : : no visible binding for global variable 'ncz' MI.fixed.times : : no visible binding for global variable 'M' MI.fixed.times : : no visible binding for global variable 'object' MI.fixed.times : : no visible binding for global variable 'type' MI.fixed.times : : : no visible binding for global variable 'ncz' MI.fixed.times : : : no visible binding for global variable 'object' MI.fixed.times: no visible binding for global variable 'return.data' MI.random.times: no visible binding for global variable 'obs.times' MI.random.times: no visible binding for global variable 'ni' MI.random.times: no visible binding for global variable 'y' MI.random.times: no visible binding for global variable 'logT' MI.random.times: no visible binding for global variable 'd' MI.random.times: no visible binding for global variable 'X' MI.random.times: no visible binding for global variable 'Z' MI.random.times: no visible binding for global variable 'Xtime' MI.random.times: no visible binding for global variable 'Ztime' MI.random.times: no visible binding for global variable 'WW' MI.random.times: no visible binding for global variable 'id' MI.random.times: no visible binding for global variable 'object' MI.random.times: no visible binding for global variable 'ncz' MI.random.times: no visible binding for global variable 'nk' MI.random.times: no visible binding for global variable 'M' MI.random.times: no visible binding for global variable 'ncx' MI.random.times: no visible binding for global variable 'ncww' MI.random.times: no visible binding for global variable 'n' MI.random.times: no visible binding for global variable 'type' MI.random.times : : no visible binding for global variable 'ncz' MI.random.times : : no visible binding for global variable 'object' MI.random.times : : no visible binding for global variable 'n' SclongCH: no visible binding for global variable 'X' SclongCH: no visible binding for global variable 'Xtime' SclongCH: no visible binding for global variable 'y' SclongCH: no visible binding for global variable 'Zb' SclongCH: no visible binding for global variable 'sigma' SclongCH: no visible binding for global variable 'Ztime' SclongCH: no visible binding for global variable 'b' SclongCH: no visible binding for global variable 'eta.tw' SclongCH: no visible binding for global variable 'alpha' SclongCH: no visible binding for global variable 'trc.t1' SclongCH: no visible binding for global variable 'd' Score.chGH: no visible binding for global variable 'ncx' Score.chGH: no visible binding for global variable 'ncww' Score.chGH: no visible binding for global variable 'nk' Score.chGH: no visible binding for global variable 'diag.D' Score.chGH: no visible binding for global variable 'X' Score.chGH: no visible binding for global variable 'Xtime' Score.chGH: no visible binding for global variable 'WW' Score.chGH: no visible binding for global variable 'Ztime.b' Score.chGH: no visible binding for global variable 'Ztb' Score.chGH: no visible binding for global variable 'y' Score.chGH: no visible binding for global variable 'id' Score.chGH: no visible binding for global variable 'S' Score.chGH: no visible binding for global variable 'd' Score.chGH: no visible binding for global variable 'logT' Score.chGH: no visible binding for global variable 'ncz' Score.chGH: no visible binding for global variable 'b' Score.chGH: no visible binding for global variable 'k' Score.chGH: no visible binding for global variable 'n' Score.chGH: no visible binding for global variable 'wGH' Score.chGH: no visible binding for global variable 'b2' Score.chGH: no visible binding for global variable 'Z' Score.chGH: no visible binding for global variable 'ZtZ' Score.chGH: no visible binding for global variable 'SS' Score.chGH: no visible binding for global variable 'N' Score.chLaplace: no visible binding for global variable 'ncx' Score.chLaplace: no visible binding for global variable 'ncww' Score.chLaplace: no visible binding for global variable 'nk' Score.chLaplace: no visible binding for global variable 'diag.D' Score.chLaplace: no visible binding for global variable 'n' Score.chLaplace: no visible binding for global variable 'ncz' Score.chLaplace: no visible binding for global variable 'X' Score.chLaplace: no visible binding for global variable 'Xtime' Score.chLaplace: no visible binding for global variable 'WW' Score.chLaplace: no visible binding for global variable 'S' Score.chLaplace: no visible binding for global variable 'Ztime' Score.chLaplace: no visible binding for global variable 'outer.Ztime' Score.chLaplace: no visible binding for global variable 'Z' Score.chLaplace: no visible binding for global variable 'id' Score.chLaplace: no visible binding for global variable 'ZtZ' Score.chLaplace: no visible binding for global variable 'y' Score.chLaplace: no visible binding for global variable 'd' Score.chLaplace: no visible binding for global variable 'SS' Score.chLaplace: no visible binding for global variable 'N' Score.phGH: no visible binding for global variable 'ncx' Score.phGH: no visible binding for global variable 'ncww' Score.phGH: no visible binding for global variable 'diag.D' Score.phGH: no visible binding for global variable 'X' Score.phGH: no visible binding for global variable 'Xtime' Score.phGH: no visible binding for global variable 'Xtime2' Score.phGH: no visible binding for global variable 'Ztime.b' Score.phGH: no visible binding for global variable 'Ztime2.b' Score.phGH: no visible binding for global variable 'WW' Score.phGH: no visible binding for global variable 'indT' Score.phGH: no visible binding for global variable 'd' Score.phGH: no visible binding for global variable 'lambda0' Score.phGH: no visible binding for global variable 'ind.T0' Score.phGH: no visible binding for global variable 'Ztb' Score.phGH: no visible binding for global variable 'y' Score.phGH: no visible binding for global variable 'id' Score.phGH: no visible binding for global variable 'ind0' Score.phGH: no visible binding for global variable 'ind.lenN0' Score.phGH: no visible binding for global variable 'ind.lambda' Score.phGH: no visible binding for global variable 'ncz' Score.phGH: no visible binding for global variable 'b' Score.phGH: no visible binding for global variable 'k' Score.phGH: no visible binding for global variable 'n' Score.phGH: no visible binding for global variable 'wGH' Score.phGH: no visible binding for global variable 'b2' Score.phGH: no visible binding for global variable 'Z' Score.phGH: no visible binding for global variable 'ZtZ' Score.phGH: no visible binding for global variable 'N' Score.weibullGH: no visible binding for global variable 'ncx' Score.weibullGH: no visible binding for global variable 'ncww' Score.weibullGH: no visible binding for global variable 'diag.D' Score.weibullGH: no visible binding for global variable 'X' Score.weibullGH: no visible binding for global variable 'Xtime' Score.weibullGH: no visible binding for global variable 'WW' Score.weibullGH: no visible binding for global variable 'Ztime.b' Score.weibullGH: no visible binding for global variable 'Ztb' Score.weibullGH: no visible binding for global variable 'y' Score.weibullGH: no visible binding for global variable 'id' Score.weibullGH: no visible binding for global variable 'logT' Score.weibullGH: no visible binding for global variable 'd' Score.weibullGH: no visible binding for global variable 'ncz' Score.weibullGH: no visible binding for global variable 'b' Score.weibullGH: no visible binding for global variable 'k' Score.weibullGH: no visible binding for global variable 'n' Score.weibullGH: no visible binding for global variable 'wGH' Score.weibullGH: no visible binding for global variable 'b2' Score.weibullGH: no visible binding for global variable 'Z' Score.weibullGH: no visible binding for global variable 'ZtZ' Score.weibullGH: no visible binding for global variable 'N' ScsurvCH: no visible binding for global variable 'ncww' ScsurvCH: no visible binding for global variable 'nk' ScsurvCH: no visible binding for global variable 'eta.yxT' ScsurvCH: no visible binding for global variable 'Ztime' ScsurvCH: no visible binding for global variable 'b' ScsurvCH: no visible binding for global variable 'WW' ScsurvCH: no visible binding for global variable 'S' ScsurvCH: no visible binding for global variable 'trc.t1' ScsurvCH: no visible binding for global variable 'trc.t2' ScsurvCH: no visible binding for global variable 'd' ScsurvCH: no visible binding for global variable 'SS' fn.b: no visible binding for global variable 'eta.yxi' fn.b: no visible binding for global variable 'Z.ind.i' fn.b: no visible binding for global variable 'ni' fn.b: no visible binding for global variable 'i' fn.b: no visible binding for global variable 'yi' fn.b: no visible binding for global variable 'sigma' fn.b: no visible binding for global variable 'eta.twi' fn.b: no visible binding for global variable 'alpha' fn.b: no visible binding for global variable 'eta.yxT' fn.b: no visible binding for global variable 'Ztime.i' fn.b: no visible binding for global variable 'd' fn.b: no visible binding for global variable 'sc' fn.b: no visible binding for global variable 'logT' fn.b: no visible binding for global variable 'diag.D' gr.b: no visible binding for global variable 'Z.ind.i' gr.b: no visible binding for global variable 'yi.eta.yxi' gr.b: no visible binding for global variable 'sigma' gr.b: no visible binding for global variable 'eta.twi' gr.b: no visible binding for global variable 'alpha' gr.b: no visible binding for global variable 'eta.yxT' gr.b: no visible binding for global variable 'i' gr.b: no visible binding for global variable 'Ztime.i' gr.b: no visible binding for global variable 'd' gr.b: no visible binding for global variable 'diag.D' gr.longCH: no visible binding for global variable 'X' gr.longCH: no visible binding for global variable 'Xtime' gr.longCH: no visible binding for global variable 'Ztime.b' gr.longCH: no visible binding for global variable 'eta.tw' gr.longCH: no visible binding for global variable 'alpha' gr.longCH: no visible binding for global variable 'y' gr.longCH: no visible binding for global variable 'Zb' gr.longCH: no visible binding for global variable 'sigma' gr.longCH: no visible binding for global variable 'd' gr.longCH: no visible binding for global variable 'p.byt' gr.longCH: no visible binding for global variable 'wGH' gr.longPH: no visible binding for global variable 'y' gr.longPH: no visible binding for global variable 'eta.yx' gr.longPH: no visible binding for global variable 'Zb' gr.longPH: no visible binding for global variable 'sigma' gr.longPH: no visible binding for global variable 'lambda0.' gr.longPH: no visible binding for global variable 'alpha' gr.longPH: no visible binding for global variable 'indT' gr.longPH: no visible binding for global variable 'p.byt.' gr.longPH: no visible binding for global variable 'wGH' gr.longPH: no visible binding for global variable 'd' gr.longWB: no visible binding for global variable 'X' gr.longWB: no visible binding for global variable 'Xtime' gr.longWB: no visible binding for global variable 'Ztime.b' gr.longWB: no visible binding for global variable 'WW' gr.longWB: no visible binding for global variable 'gammas' gr.longWB: no visible binding for global variable 'alpha' gr.longWB: no visible binding for global variable 'y' gr.longWB: no visible binding for global variable 'Zb' gr.longWB: no visible binding for global variable 'sigma' gr.longWB: no visible binding for global variable 'logT' gr.longWB: no visible binding for global variable 'sigma.t' gr.longWB: no visible binding for global variable 'd' gr.longWB: no visible binding for global variable 'p.byt' gr.longWB: no visible binding for global variable 'wGH' gr.survCH: no visible binding for global variable 'ncww' gr.survCH: no visible binding for global variable 'nk' gr.survCH: no visible binding for global variable 'WW' gr.survCH: no visible binding for global variable 'Y' gr.survCH: no visible binding for global variable 'S' gr.survCH: no visible binding for global variable 'Ztime.b' gr.survCH: no visible binding for global variable 'd' gr.survCH: no visible binding for global variable 'p.byt' gr.survCH: no visible binding for global variable 'wGH' gr.survCH: no visible binding for global variable 'SS' gr.survCH: no visible binding for global variable 'eta.yxT' gr.survPH: no visible binding for global variable 'lambda0.' gr.survPH: no visible binding for global variable 'indT' gr.survPH: no visible binding for global variable 'p.byt.' gr.survPH: no visible binding for global variable 'wGH' gr.survPH: no visible binding for global variable 'd' gr.survPH: no visible binding for global variable 'p.byt' gr.survWB: no visible binding for global variable 'ncww' gr.survWB: no visible binding for global variable 'WW' gr.survWB: no visible binding for global variable 'Y' gr.survWB: no visible binding for global variable 'logT' gr.survWB: no visible binding for global variable 'd' gr.survWB: no visible binding for global variable 'p.byt' gr.survWB: no visible binding for global variable 'wGH' logsurvCH: no visible binding for global variable 'eta.twi' logsurvCH: no visible binding for global variable 'eta.yxT' logsurvCH: no visible binding for global variable 'i' logsurvCH: no visible binding for global variable 'Ztime.i' logsurvCH: no visible binding for global variable 'd' logsurvCH: no visible binding for global variable 'sc' logsurvCH: no visible binding for global variable 'logT' opt.longWB: no visible binding for global variable 'X' opt.longWB: no visible binding for global variable 'Xtime' opt.longWB: no visible binding for global variable 'Ztime.b' opt.longWB: no visible binding for global variable 'eta.tw' opt.longWB: no visible binding for global variable 'alpha' opt.longWB: no visible binding for global variable 'Ztb' opt.longWB: no visible binding for global variable 'y' opt.longWB: no visible binding for global variable 'sigma' opt.longWB: no visible binding for global variable 'id' opt.longWB: no visible binding for global variable 'logT' opt.longWB: no visible binding for global variable 'sigma.t' opt.longWB: no visible binding for global variable 'd' opt.longWB: no visible binding for global variable 'p.byt' opt.longWB: no visible binding for global variable 'wGH' opt.survCH: no visible binding for global variable 'ncww' opt.survCH: no visible binding for global variable 'nk' opt.survCH: no visible binding for global variable 'WW' opt.survCH: no visible binding for global variable 'Y' opt.survCH: no visible binding for global variable 'S' opt.survCH: no visible binding for global variable 'd' opt.survCH: no visible binding for global variable 'logT' opt.survCH: no visible binding for global variable 'p.byt' opt.survCH: no visible binding for global variable 'wGH' opt.survPH: no visible binding for global variable 'WW' opt.survPH: no visible binding for global variable 'Y' opt.survPH: no visible binding for global variable 'Y2' opt.survPH: no visible binding for global variable 'indT' opt.survPH: no visible binding for global variable 'd' opt.survPH: no visible binding for global variable 'lambda0T' opt.survPH: no visible binding for global variable 'ind0' opt.survPH: no visible binding for global variable 'ind.lenN0' opt.survPH: no visible binding for global variable 'lambda0' opt.survPH: no visible binding for global variable 'ind.lambda' opt.survPH: no visible binding for global variable 'p.byt' opt.survPH: no visible binding for global variable 'wGH' opt.survWB: no visible binding for global variable 'ncww' opt.survWB: no visible binding for global variable 'WW' opt.survWB: no visible binding for global variable 'Y' opt.survWB: no visible binding for global variable 'logT' opt.survWB: no visible binding for global variable 'd' opt.survWB: no visible binding for global variable 'p.byt' opt.survWB: no visible binding for global variable 'wGH' posterior.b: no visible binding for global variable 'eta.yxT' posterior.b: no visible binding for global variable 'Ztime.missO' posterior.b: no visible binding for global variable 'eta.tw' posterior.b: no visible binding for global variable 'alpha.new' posterior.b: no visible binding for global variable 'eta.yx' posterior.b: no visible binding for global variable 'Z.missO' posterior.b: no visible binding for global variable 'id3.miss' posterior.b: no visible binding for global variable 'y.missO' posterior.b: no visible binding for global variable 'sigma.new' posterior.b: no visible binding for global variable 'id.miss' posterior.b: no visible binding for global variable 'method' posterior.b: no visible binding for global variable 'object' posterior.b: no visible binding for global variable 'logT' posterior.b: no visible binding for global variable 'd' posterior.b: no visible binding for global variable 'Xtime2' posterior.b: no visible binding for global variable 'betas.new' posterior.b: no visible binding for global variable 'Ztime2' posterior.b: no visible binding for global variable 'id4.miss' posterior.b: no visible binding for global variable 'WW' posterior.b: no visible binding for global variable 'WW.missO' posterior.b: no visible binding for global variable 'gammas.new' posterior.b: no visible binding for global variable 'd.missO' posterior.b: no visible binding for global variable 'ind0' posterior.b: no visible binding for global variable 'logT.missO' posterior.b: no visible binding for global variable 'sigma.t.new' posterior.b: no visible binding for global variable 'nk' posterior.b: no visible binding for global variable 'ncz' posterior.b: no visible binding for global variable 'D.new' posterior.b: no visible binding for global variable 'diag.D' posterior.b: no visible binding for global variable 'k' update.bCH: no visible binding for global variable 'n' update.bCH: no visible binding for global variable 'X' update.bCH: no visible binding for global variable 'Xtime' update.bCH: no visible binding for global variable 'ncww' update.bCH: no visible binding for global variable 'nk' update.bCH: no visible binding for global variable 'WW' update.bCH: no visible binding for global variable 'S' update.bCH: no visible binding for global variable 'id' update.bCH: no visible binding for global variable 'y' update.bCH: no visible binding for global variable 'logT' update.bCH: no visible binding for global variable 'Z' update.bCH: no visible binding for global variable 'Ztime' update.bCH: no visible binding for global variable 'ncz' update.bCH: no visible binding for global variable 'ni' update.bCH: no visible binding for global variable 'diag.D' update.bCH: no visible binding for global variable 'cons.logLik' * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * creating JM-Ex.R ... OK * checking examples ... OK * creating JM-manual.tex ... OK * checking JM-manual.tex ... OK