Check results for 'texmex'

using R version 2.14.2 RC (2012-02-23 r58468)
using platform: i686-pc-linux-gnu (32-bit)
using session charset: UTF-8
checking for file ‘texmex/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘texmex’ version ‘1.2’
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
checking for executable files ... OK
checking whether package ‘texmex’ can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... 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 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
.ismev.gpd.fit: multiple local function definitions for ‘gpd.lik’ with
different formal arguments
bgpdSetSeed: possible error in assign(".Random.seed", x$seed, where =
1): unused argument(s) (where = 1)
gpd : proposal: possible error in rmvnorm(1, mean, cov = sigma): unused
argument(s) (cov = sigma)
mexDependence : qfun: warning in filled.contour(a.grid, b.grid,
-NegProfLik, main = paste("Profile likelihood", PlotLikTitle), color
= terrain.colors, xlab = "a", ylab = "b", plot.axes = {: partial
argument match of 'color' to 'color.palette'
mexDependence : qfun: warning in axis(1): partial argument match of
'color' to 'color.palette'
mexDependence : qfun: warning in axis(2): partial argument match of
'color' to 'color.palette'
mexDependence : qfun: warning in points(o$par[1], o$par[2]): partial
argument match of 'color' to 'color.palette'
mexDependence : qfun: warning in }): partial argument match of 'color'
to 'color.palette'
plot.bgpd: no visible global function definition for ‘bandwidth.hb’
test.bootgpd: warning in checkEqualsNumeric(cse[1], bse[1], tol = tol,
msg = "bootgpd: rain se(sigma) matches Coles"): partial argument
match of 'tol' to 'tolerance'
test.bootgpd: warning in checkEqualsNumeric(cse[2], bse[2], tol = tol,
msg = "bootgpd: rain se(xi) matches Coles"): partial argument match
of 'tol' to 'tolerance'
test.bootgpd: warning in checkEqualsNumeric(cest[1], best[1], tol =
tol, msg = "bootgpd: rain median of sigma matches point estimate"):
partial argument match of 'tol' to 'tolerance'
test.bootgpd: warning in checkEqualsNumeric(cest[2], best[2], tol =
tol, msg = "bootgpd: rain medians of xi matches point estimate"):
partial argument match of 'tol' to 'tolerance'
test.bootgpd: no visible binding for global variable ‘ALT.M’
test.bootgpd: no visible binding for global variable ‘ALT.B’
test.bootmex: warning in migpd(wavesurge, mq = 0.7): partial argument
match of 'mq' to 'mqu'
test.dgpd : <anonymous>: warning in rgpd(nsim, sig = p[i, 1], xi = p[i,
2], u = thresh[i]): partial argument match of 'sig' to 'sigma'
test.gpd: no visible binding for global variable ‘rainfall’
test.gpd: no visible binding for global variable ‘ALT.M’
test.gpd: no visible binding for global variable ‘ALT.B’
test.gpd: no visible binding for global variable ‘y’
test.gpd: warning in require(MASS, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
test.gpd: no visible binding for global variable ‘resids’
test.info.gpd: no visible binding for global variable ‘ALT.M’
test.info.gpd: no visible binding for global variable ‘y’
test.mexDependence: warning in checkEqualsNumeric(jhWdepO3,
myWdepO3$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Winter O3"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhWdepNO2,
myWdepNO2$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Winter NO2"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhWdepNO,
myWdepNO$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Winter NO"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhWdepSO2,
myWdepSO2$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Winter SO2"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhWdepPM10,
myWdepPM10$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Winter PM10"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhSdepO3,
mySdepO3$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Summer O3"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhSdepNO2,
mySdepNO2$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Summer NO2"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhSdepNO,
mySdepNO$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Summer NO"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhSdepSO2,
mySdepSO2$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Summer SO2"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in checkEqualsNumeric(jhSdepPM10,
mySdepPM10$dependence$coefficients[1:4, ], tol = tol, msg =
"mexDependence: Summer PM10"): partial argument match of 'tol' to
'tolerance'
test.mexDependence: warning in migpd(wavesurge, mq = 0.7): partial
argument match of 'mq' to 'mqu'
test.mexDependence: warning in
checkEqualsNumeric(summer.mex1$dependence$coefficients,
summer.mex2$dependence$coefficients, tol = tol, msg = "mexDependence:
summer starting values: class(start)='mex'"): partial argument match
of 'tol' to 'tolerance'
test.mexDependence: warning in
checkEqualsNumeric(summer.mex1$dependence$coefficients,
summer.mex3$dependence$coefficients, tol = tol, msg = "mexDependence:
summer starting values: start= matrix "): partial argument match of
'tol' to 'tolerance'
test.mexDependence: warning in
checkEqualsNumeric(summer.mex1$dependence$coefficients,
summer.mex4$dependence$coefficients, tol = tol, msg = "mexDependence:
summer starting values: start= vector"): partial argument match of
'tol' to 'tolerance'
test.mexDependence: warning in checkEqualsNumeric(KTPest, HTSest, tol =
tol, mesg = paste("mexDependence: constrained estimation threshold",
i)): partial argument match of 'tol' to 'tolerance'
test.mexRangeFit: warning in migpd(wavesurge, mq = 0.7): partial
argument match of 'mq' to 'mqu'
test.migpd: warning in checkEqualsNumeric(htsummer[i, ], summer.gpd[i,
], tol = tol[i], msg = paste("migpd: Table 4 summer", i)): partial
argument match of 'tol' to 'tolerance'
test.migpd: warning in checkEqualsNumeric(htwinter[i, ], winter.gpd[i,
], tol = tol[i], msg = paste("migpd: Table 4 winter", i)): partial
argument match of 'tol' to 'tolerance'
test.migpd: warning in migpd(wavesurge, mq = 0.7): partial argument
match of 'mq' to 'mqu'
test.migpd: warning in
checkEqualsNumeric(wavesurge.fit$models$wave$loglik,
gpd(wavesurge$wave, qu = 0.7)$loglik, tol = 0.001, msg = "migpd: 2-d
data gpd fit wave"): partial argument match of 'tol' to 'tolerance'
test.migpdCoefs: warning in require(MASS, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
test.migpdCoefs: no visible binding for global variable ‘alt’
test.migpdCoefs: no visible binding for global variable ‘ast’
test.migpdCoefs: warning in migpdCoefs(Dmod, which = c("alt", "ast"),
coef = list(altco, astco)): partial argument match of 'coef' to
'coefs'
test.pgpd : <anonymous>: warning in rgpd(nsim, sig = p[i, 1], xi = p[i,
2], u = thresh[i]): partial argument match of 'sig' to 'sigma'
test.plot.predict.mex: warning in mex(winter, mqu = 0.7, penalty =
"none", wh = "NO", dqu = 0.7, margins = "gumbel", constrain = FALSE):
partial argument match of 'wh' to 'which'
test.plot.predict.mex: warning in mex(wavesurge, mq = 0.7, which = 1,
margins = "laplace"): partial argument match of 'mq' to 'mqu'
test.predict.mex: warning in checkEqualsNumeric(Table5summer,
resSummer, tol = tol, msg = "predict.mex: Table 5 summer data"):
partial argument match of 'tol' to 'tolerance'
test.predict.mex: warning in checkEqualsNumeric(Table5winter,
resWinter, tol = tol, msg = "predict.mex: Table 5 winter data"):
partial argument match of 'tol' to 'tolerance'
test.predict.mex: warning in checkEqualsNumeric(pointEstSummer,
resSummer[1, ], tol = tol, msg = "predict.mex: point est vs boot,
summer data"): partial argument match of 'tol' to 'tolerance'
test.predict.mex: warning in checkEqualsNumeric(pointEstWinter,
resWinter[1, ], tol = tol, msg = "predict.mex: point est vs boot,
winter data"): partial argument match of 'tol' to 'tolerance'
test.predict.mex: warning in mex(wavesurge, mq = 0.7, dqu = 0.7,
margins = "laplace", which = 1): partial argument match of 'mq' to
'mqu'
test.predict.mex: warning in checkEqualsNumeric(lap.ans, gum.ans, tol =
tol, msg = paste("predict.mex Laplace predictions equal to Gumbel,
test replicate", i)): partial argument match of 'tol' to 'tolerance'
test.revTransform: warning in checkEqualsNumeric(x.l.e, x, tol = 1e-04,
msg = "revTransform: empirical transformation, laplace target"):
partial argument match of 'tol' to 'tolerance'
test.revTransform: warning in checkEqualsNumeric(x.l.m, x, tol = 1e-04,
msg = "revTransform: mixture transformation, laplace target"):
partial argument match of 'tol' to 'tolerance'
test.revTransform: warning in checkEqualsNumeric(x.g.e, x, tol = 1e-04,
msg = "revTransform: empirical transformation, gumbel target"):
partial argument match of 'tol' to 'tolerance'
test.revTransform: warning in checkEqualsNumeric(x.g.m, x, tol = 1e-04,
msg = "revTransform: mixture transformation, gumbel target"): partial
argument match of 'tol' to 'tolerance'
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